Publications

Publications

2020

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Integrated cross-study datasets of genetic dependencies in cancer
Pacini C, Dempster JM, Gonçalves E, Najgebauer H, Karakoc E, van der Meer D, Barthorpe A, Lightfoot H, Jaaks P, McFarland JM, Garnett MJ, Tsherniak A, Iorio F. Preprint DOI: 10.1101/2020.05.22.110247
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The Polygenic Score Catalog: an open database for reproducibility and systematic evaluation
Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JA, Inouye M. Preprint DOI: 10.1101/2020.05.20.20108217
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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Jerber J, Seaton D, Cuomo A, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder M, Mountjoy E, Ghoussaini M, Lancaster M, Marioni J, Merkle F, Stegle O, Gaffney D, HipSci Consortium. Preprint DOI: 10.1101/2020.05.21.103820
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Controlling for off-target genetic effects using polygenic scores improves the power of genome-wide association studies
Bennett D, Morris D, Seoighe C. Preprint DOI: 10.1101/2020.05.21.097691
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Ten simple rules for making training materials FAIR.
Garcia L, Batut B, Burke ML, Kuzak M, Psomopoulos F, Arcila R, Attwood TK, Beard N, Carvalho-Silva D, Dimopoulos AC, Del Angel VD, Dumontier M, Gurwitz KT, Krause R, McQuilton P, Le Pera L, Morgan SL, Rauste P, Via A, Kahlem P, Rustici G, van Gelder CWG, Palagi PM. PLoS computational biology Volume 16 (2020) p.e1007854 DOI: 10.1371/journal.pcbi.1007854
Putative cell type discovery from single-cell gene expression data.
Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A, Teichmann SA. Nature methods (2020) DOI: 10.1038/s41592-020-0825-9
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Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium.
Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH, Sood RK, Gerstung M, Martincorena I, Hall BA, Jones PH. Nature genetics (2020) DOI: 10.1038/s41588-020-0624-3
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Connecting data, tools and people across Europe: ELIXIR's response to the COVID-19 pandemic.
Blomberg N, Lauer KB. European journal of human genetics : EJHG (2020) DOI: 10.1038/s41431-020-0637-5
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OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data
Haselimashhadi H, Mason JC, Mallon A, Smedley D, Meehan TF, Parkinson H. Preprint DOI: 10.1101/2020.05.13.091157
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Stimulation strength controls the rate of initiation but not the molecular organization of TCR-induced signalling.
Ma CY, Marioni JC, Griffiths GM, Richard AC. eLife Volume 9 (2020) DOI: 10.7554/elife.53948
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Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.
Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC. Journal of Alzheimer's disease : JAD (2020) DOI: 10.3233/jad-200207
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Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.
Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium. Nature genetics (2020) DOI: 10.1038/s41588-020-0634-1
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin M, UniProt Consortium. Bioinformatics (Oxford, England) (2020) DOI: 10.1093/bioinformatics/btaa485
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CEN-tools: An integrative platform to identify the ‘contexts’ of essential genes
Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E. Preprint DOI: 10.1101/2020.05.10.087668
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Explainable multi-view framework for dissecting inter-cellular signaling from highly multiplexed spatial data
Tanevski J, Gabor A, Flores ROR, Schapiro D, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.05.08.084145
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Improving reporting standards for polygenic scores in risk prediction studies
Wand H, Lambert SA, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis KR, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJ, Goddard KA, Kraft P, MacArthur JA, Inouye M, Wojcik GL. Preprint DOI: 10.1101/2020.04.23.20077099
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Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy.
Grants JM, Wegrzyn-Woltosz J, Hui T, O'Neill K, Shadbolt M, Knapp DJHF, Parker JD, Deng D, Gopal A, Docking TR, Fuller M, Li J, Boldin M, Eaves CJ, Hirst M, Karsan A. Blood (2020) DOI: 10.1182/blood.2019003105
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COSS: A fast and user-friendly tool for spectral library searching.
Shiferaw GA, Vandermarliere E, Hulstaert N, Gabriels R, Martens L, Volders PJ. Journal of proteome research (2020) DOI: 10.1021/acs.jproteome.9b00743
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Exploring the conformational space of a receptor for drug design: an ERα case study
Schneider M, Pons J, Labesse G. Preprint DOI: 10.1101/2020.05.06.081000
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Ten simple rules to run a successful BioHackathon.
Garcia L, Antezana E, Garcia A, Bolton E, Jimenez R, Prins P, Banda JM, Katayama T. PLoS computational biology Volume 16 (2020) p.e1007808 DOI: 10.1371/journal.pcbi.1007808
The omics discovery REST interface.
Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning BA, Hermjakob H, Perez-Riverol Y. Nucleic acids research (2020) DOI: 10.1093/nar/gkaa326
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Chromosomal arrangement of synthetic lethal gene pairs: repulsion or attraction?
Hosseini S, Wadie B, Petsalaki E. Preprint DOI: 10.1101/2020.05.05.078626
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. RNA (New York, N.Y.) (2020) DOI: 10.1261/rna.075341.120
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COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Scientific data Volume 7 (2020) p.136 DOI: 10.1038/s41597-020-0477-8
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A statistical framework for assessing pharmacological response and biomarkers with confidence
Wang D, Hensman J, Kutkaite G, Toh TS, Dry JR, Saez-Rodriguez J, Garnett MJ, Menden MP, Dondelinger F, GDSC Screening Team. Preprint DOI: 10.1101/2020.05.01.072983
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Longevity, clonal relationship and transcriptional program of celiac disease-specific plasma cells
Lindeman I, Zhou C, Eggesbø LM, Miao Z, Polak J, Lundin KEA, Jahnsen J, Qiao S, Iversen R, Sollid LM. Preprint DOI: 10.1101/2020.04.30.058560
Mutational signatures are jointly shaped by DNA damage and repair.
Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Vöhringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. Nature communications Volume 11 (2020) p.2169 DOI: 10.1038/s41467-020-15912-7
CELLector: Genomics-Guided Selection of Cancer In Vitro Models.
Najgebauer H, Yang M, Francies HE, Pacini C, Stronach EA, Garnett MJ, Saez-Rodriguez J, Iorio F. Cell systems Volume 10 (2020) p.424-432.e6 DOI: 10.1016/j.cels.2020.04.007
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Prenatal development of human immunity.
Park JE, Jardine L, Gottgens B, Teichmann SA, Haniffa M. Science (New York, N.Y.) Volume 368 (2020) p.600-603 DOI: 10.1126/science.aaz9330
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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. Nature (2020) DOI: 10.1038/s41586-020-2286-9
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Utility of Animal Models to Understand Human Alzheimer's Disease, Using the Mastermind Research Approach to Avoid Unnecessary Further Sacrifices of Animals.
Qin T, Prins S, Groeneveld GJ, Van Westen G, de Vries HE, Wong YC, Bischoff LJM, de Lange ECM. International journal of molecular sciences Volume 21 (2020) DOI: 10.3390/ijms21093158
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Data Forensic Determination of the Accuracy of International COVID-19 Reporting: Using Zipf's Law for Pandemic Investigation
Iorliam A, Ho AT, Tirunagari S, Windridge D. Preprint DOI: 10.20944/preprints202004.0531.v1
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Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation.
King HW, Orban N, Riches JC, Clear AJ, Warnes G, Teichmann SA, James LK. Preprint DOI: 10.1101/2020.04.28.054775
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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AWC, Heaton MP, Phillippy AM, Hiendleder S, Smith TPL, Williams JL. Nature communications Volume 11 (2020) p.2071 DOI: 10.1038/s41467-020-15848-y
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Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate.
Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, NIHR BioResource, Carss KJ, Thornton J, Raymond FL. Molecular genetics & genomic medicine (2020) p.e1106 DOI: 10.1002/mgg3.1106
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Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors.
Burggraaff L, Lenselink EB, Jespers W, van Engelen J, Bongers BJ, González MG, Liu R, Hoos HH, van Vlijmen HWT, IJzerman AP, van Westen GJP. Journal of chemical information and modeling (2020) DOI: 10.1021/acs.jcim.9b01204
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The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)
Touré V, Vercruysse S, Acencio ML, Lovering R, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Licata L, Lægreid A, Mungall C, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Thieffry D, Thomas P, Türei D, Saez-Rodriguez J, Kuiper M. Preprint DOI: 10.20944/preprints202004.0480.v1
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Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses
Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Emdal KB, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.04.23.057893
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scHLAcount: Allele-specific HLA expression from single-cell gene expression data.
Darby CA, Stubbington MJT, Marks PJ, Barrio ÁM, Fiddes IT. Bioinformatics (Oxford, England) (2020) DOI: 10.1093/bioinformatics/btaa264
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Sex chromosome evolution in parasitic nematodes of humans.
Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N, Korlach J, Li Y, Libro S, Lustigman S, Michalski ML, Paulini M, Rogers MB, Teigen L, Twaddle A, Welch L, Berriman M, Dunning Hotopp JC, Ghedin E. Nature communications Volume 11 (2020) p.1964 DOI: 10.1038/s41467-020-15654-6
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GlyGen data model and processing workflow.
Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman B, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Castro LJG, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R. Bioinformatics (Oxford, England) (2020) DOI: 10.1093/bioinformatics/btaa238
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A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AM, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. Preprint DOI: 10.12688/f1000research.20559.1
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Fr-PPIChem: An Academic Compound Library Dedicated to Protein-Protein Interactions.
Bosc N, Muller C, Hoffer L, Lagorce D, Bourg S, Derviaux C, Gourdel ME, Rain JC, Miller TW, Villoutreix BO, Miteva MA, Bonnet P, Morelli X, Sperandio O, Roche P. ACS chemical biology (2020) DOI: 10.1021/acschembio.0c00179
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Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, Soliman S, Chaouiya C, Helikar T, Calzone L. Briefings in bioinformatics (2020) DOI: 10.1093/bib/bbaa046
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ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. Preprint DOI: 10.1101/2020.04.16.044958
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RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia.
Fuller GG, Han T, Freeberg MA, Moresco JJ, Ghanbari Niaki A, Roach NP, Yates JR, Myong S, Kim JK. eLife Volume 9 (2020) DOI: 10.7554/elife.48480
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Autotransporters drive biofilm formation and auto-aggregation in the diderm Firmicute Veillonella parvula
Béchon N, Jiménez-Fernández A, Witwinowski J, Bierque E, Taib N, Cokelaer T, Ma L, Ghigo J, Gribaldo S, Beloin C. Preprint DOI: 10.1101/2020.04.15.042101
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Identification of male heterogametic sex-determining regions on the Atlantic herring Clupea harengus genome.
Í Kongsstovu S, Dahl HA, Gislason H, Homrum E, Jacobsen JA, Flicek P, Mikalsen SO. Journal of fish biology (2020) DOI: 10.1111/jfb.14349
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A unified nomenclature for vertebrate olfactory receptors.
Olender T, Jones TEM, Bruford E, Lancet D. BMC evolutionary biology Volume 20 (2020) p.42 DOI: 10.1186/s12862-020-01607-6
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Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times.
Bouwmeester R, Martens L, Degroeve S. Analytical chemistry Volume 92 (2020) p.6571-6578 DOI: 10.1021/acs.analchem.0c00233
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BlobToolKit - Interactive Quality Assessment of Genome Assemblies.
Challis R, Richards E, Rajan J, Cochrane G, Blaxter M. G3 (Bethesda, Md.) Volume 10 (2020) p.1361-1374 DOI: 10.1534/g3.119.400908
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User-friendly, scalable tools and workflows for single-cell analysis
Moreno P, Huang N, Manning J, Mohammed S, Solovyev A, Polanski K, Chazarra R, Talavera-Lopez C, Doyle M, Marnier G, Grüning B, Rasche H, Bacon W, Perez-Riverol Y, Haeussler M, Meyer K, Teichmann S, Papatheodorou I. Preprint DOI: 10.1101/2020.04.08.032698
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Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences.
Matamoros S, Hendriksen RS, Pataki BÁ, Pakseresht N, Rossello M, Silvester N, Amid C, Aarestrup FM, Koopmans M, Cochrane G, Csabai I, Lund O, Schultsz C, The Compare Ml-Amr Group. Microbial genomics (2020) DOI: 10.1099/mgen.0.000342
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KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species
Hassani-Pak K, Singh A, Brandizi M, Hearnshaw J, Amberkar S, Phillips AL, Doonan JH, Rawlings C. Preprint DOI: 10.1101/2020.04.02.017004
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Precursor intensity-based label-free quantification software tools for proteomic and multiomic analysis within the Galaxy Platform
Mehta S, Easterly C, Sajulga R, Millikin RJ, Argentini A, Eguinoa I, Martens L, Shortreed MR, Smith LM, McGowan T, Kumar P, Johnson JE, Griffin TJ, Jagtap P. Preprint DOI: 10.1101/2020.04.01.003988
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Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs.
Miller DT, Cortés-Ciriano I, Pillay N, Hirbe AC, Snuderl M, Bui MM, Piculell K, Al-Ibraheemi A, Dickson BC, Hart J, Jones K, Jordan JT, Kim RH, Lindsay D, Nishida Y, Ullrich NJ, Wang X, Park PJ, Flanagan AM. Genes Volume 11 (2020) DOI: 10.3390/genes11040387
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SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts.
Martínez-García E, Goñi-Moreno A, Bartley B, McLaughlin J, Sánchez-Sampedro L, Del Pozo HP, Hernández CP, Marletta AS, De Lucrezia D, Sánchez-Fernández G, Fraile S, de Lorenzo V. Nucleic acids research Volume 48 (2020) p.3395 DOI: 10.1093/nar/gkaa114
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Determination of the melanocortin-4 receptor structure identifies Ca2+ as a cofactor for ligand binding.
Yu J, Gimenez LE, Hernandez CC, Wu Y, Wein AH, Han GW, McClary K, Mittal SR, Burdsall K, Stauch B, Wu L, Stevens SN, Peisley A, Williams SY, Chen V, Millhauser GL, Zhao S, Cone RD, Stevens RC. Science (New York, N.Y.) Volume 368 (2020) p.428-433 DOI: 10.1126/science.aaz8995
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Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity.
Kosol S, Contreras-Martos S, Piai A, Varadi M, Lazar T, Bekesi A, Lebrun P, Felli IC, Pierattelli R, Tompa P. Scientific reports Volume 10 (2020) p.5753 DOI: 10.1038/s41598-020-62069-w
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Publisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Garcia HD, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Nature genetics Volume 52 (2020) p.464 DOI: 10.1038/s41588-020-0598-1
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Cell Atlas technologies and insights into tissue architecture.
Wilbrey-Clark A, Roberts K, Teichmann SA. The Biochemical journal Volume 477 (2020) p.1427-1442 DOI: 10.1042/bcj20190341
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amplimap: a versatile tool to process and analyze targeted NGS data.
Koelling N, Bernkopf M, Calpena E, Maher GJ, Miller KA, Ralph HK, Goriely A, Wilkie AOM. Bioinformatics (Oxford, England) Volume 36 (2020) p.2643 DOI: 10.1093/bioinformatics/btz905
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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. Nature biotechnology Volume 38 (2020) p.504 DOI: 10.1038/s41587-020-0477-4
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CD8+ T-cell transcription and DNA methylation show age specific differences and lack correlation with clinical outcome in pediatric Inflammatory Bowel Disease
Gasparetto M, Payne F, Nayak K, Kraiczy J, Glemas C, Philip-McKenzie Y, Ross A, Edgar R, Zerbino D, Salvestrini C, Torrente F, Sarkies P, Heuschkel R, Zilbauer M. Preprint DOI: 10.1101/2020.03.30.015446
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MSqRob Takes the Missing Hurdle: Uniting Intensity- and Count-Based Proteomics.
Goeminne LJE, Sticker A, Martens L, Gevaert K, Clement L. Analytical chemistry Volume 92 (2020) p.6278-6287 DOI: 10.1021/acs.analchem.9b04375
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Minimal phenotyping yields genome-wide association signals of low specificity for major depression.
Cai N, Revez JA, Adams MJ, Andlauer TFM, Breen G, Byrne EM, Clarke TK, Forstner AJ, Grabe HJ, Hamilton SP, Levinson DF, Lewis CM, Lewis G, Martin NG, Milaneschi Y, Mors O, Müller-Myhsok B, Penninx BWJH, Perlis RH, Pistis G, Potash JB, Preisig M, Shi J, Smoller JW, Streit F, Tiemeier H, Uher R, Van der Auwera S, Viktorin A, Weissman MM, MDD Working Group of the Psychiatric Genomics Consortium, Kendler KS, Flint J. Nature genetics Volume 52 (2020) p.437-447 DOI: 10.1038/s41588-020-0594-5
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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Preprint DOI: 10.1101/2020.03.29.014159
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Single molecule real-time DNA sequencing of the full HLA-E gene for 212 reference cell lines.
Lucas JAM, Hayhurst JD, Turner TR, Gymer AW, Leen G, Robinson J, Marsh SGE, Mayor NP. HLA Volume 95 (2020) p.561-572 DOI: 10.1111/tan.13882
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Bouwmeester R, Gabriels R, Hulstaert N, Martens L, Degroeve S. Preprint DOI: 10.1101/2020.03.28.013003
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DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases.
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Ensembl 2020.
Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Davidson C, Dodiya K, Fatima R, Gall A, Giron CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Maurel T, McDowall M, McMahon A, Mohanan S, Moore B, Nuhn M, Oheh DN, Parker A, Parton A, Patricio M, Sakthivel MP, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sycheva M, Szuba M, Taylor K, Thormann A, Threadgold G, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Hunt SE, IIsley G, Kostadima M, Langridge N, Loveland JE, Martin FJ, Morales J, Mudge JM, Muffato M, Perry E, Ruffier M, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR, Flicek P. Nucleic acids research Volume 48 (2020) p.D682-D688 DOI: 10.1093/nar/gkz966
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CancerGeneNet: linking driver genes to cancer hallmarks.
Iannuccelli M, Micarelli E, Surdo PL, Palma A, Perfetto L, Rozzo I, Castagnoli L, Licata L, Cesareni G. Nucleic acids research Volume 48 (2020) p.D416-D421 DOI: 10.1093/nar/gkz871
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Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Sillitoe I, Andreeva A, Blundell TL, Buchan DWA, Finn RD, Gough J, Jones D, Kelley LA, Paysan-Lafosse T, Lam SD, Murzin AG, Pandurangan AP, Salazar GA, Skwark MJ, Sternberg MJE, Velankar S, Orengo C. Nucleic acids research Volume 48 (2020) p.D314-D319 DOI: 10.1093/nar/gkz967
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GlyGen: Computational and Informatics Resources for Glycoscience.
York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W. Glycobiology Volume 30 (2020) p.72-73 DOI: 10.1093/glycob/cwz080
Expression Atlas update: from tissues to single cells.
Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A. Nucleic acids research Volume 48 (2020) p.D77-D83 DOI: 10.1093/nar/gkz947
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Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity.
Schneider M, Pons JL, Bourguet W, Labesse G. Bioinformatics (Oxford, England) Volume 36 (2020) p.160-168 DOI: 10.1093/bioinformatics/btz538
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences.
Cook CE, Stroe O, Cochrane G, Birney E, Apweiler R. Nucleic acids research Volume 48 (2020) p.D17-D23 DOI: 10.1093/nar/gkz1033
The European Nucleotide Archive in 2019.
Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G. Nucleic acids research Volume 48 (2020) p.D70-D76 DOI: 10.1093/nar/gkz1063
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Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing.
Lloret-Llinares M, Jensen TH. Methods in molecular biology (Clifton, N.J.) Volume 2062 (2020) p.127-145 DOI: 10.1007/978-1-4939-9822-7_7
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Computational methods for single-cell omics across modalities.
Efremova M, Teichmann SA. Nature methods Volume 17 (2020) p.14-17 DOI: 10.1038/s41592-019-0692-4
Ensembl Genomes 2020-enabling non-vertebrate genomic research.
Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P. Nucleic acids research Volume 48 (2020) p.D689-D695 DOI: 10.1093/nar/gkz890
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PHI-base: the pathogen-host interactions database.
Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, De Silva N, Martinez MC, Pedro H, Yates AD, Hassani-Pak K, Hammond-Kosack KE. Nucleic acids research Volume 48 (2020) p.D613-D620 DOI: 10.1093/nar/gkz904
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SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update.
Licata L, Lo Surdo P, Iannuccelli M, Palma A, Micarelli E, Perfetto L, Peluso D, Calderone A, Castagnoli L, Cesareni G. Nucleic acids research Volume 48 (2020) p.D504-D510 DOI: 10.1093/nar/gkz949
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Pervasive and non-random recombination in near full-length HIV genomes from Uganda.
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Virus Evolution Volume 6 (2020) p.veaa004 DOI: 10.1093/ve/veaa004
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Plant Reactome: a knowledgebase and resource for comparative pathway analysis.
Naithani S, Gupta P, Preece J, D'Eustachio P, Elser JL, Garg P, Dikeman DA, Kiff J, Cook J, Olson A, Wei S, Tello-Ruiz MK, Mundo AF, Munoz-Pomer A, Mohammed S, Cheng T, Bolton E, Papatheodorou I, Stein L, Ware D, Jaiswal P. Nucleic acids research Volume 48 (2020) p.D1093-D1103 DOI: 10.1093/nar/gkz996
MetaboLights: a resource evolving in response to the needs of its scientific community.
Haug K, Cochrane K, Nainala VC, Williams M, Chang J, Jayaseelan KV, O'Donovan C. Nucleic acids research Volume 48 (2020) p.D440-D444 DOI: 10.1093/nar/gkz1019
The International Genome Sample Resource (IGSR) collection of open human genomic variation resources.
Fairley S, Lowy-Gallego E, Perry E, Flicek P. Nucleic acids research Volume 48 (2020) p.D941-D947 DOI: 10.1093/nar/gkz836
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Alliance of Genome Resources Portal: unified model organism research platform.
Alliance of Genome Resources Consortium. Nucleic acids research Volume 48 (2020) p.D650-D658 DOI: 10.1093/nar/gkz813
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Transcriptome visualization and data availability at the Saccharomyces Genome Database.
Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM. Nucleic acids research Volume 48 (2020) p.D743-D748 DOI: 10.1093/nar/gkz892
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Personalized signaling models for personalized treatments.
Saez-Rodriguez J, Blüthgen N. Molecular systems biology Volume 16 (2020) p.e9042 DOI: 10.15252/msb.20199042
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The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Nucleic acids research Volume 48 (2020) p.D1145-D1152 DOI: 10.1093/nar/gkz984
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IPD-IMGT/HLA Database.
Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. Nucleic acids research Volume 48 (2020) p.D948-D955 DOI: 10.1093/nar/gkz950
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PhaSepDB: a database of liquid-liquid phase separation related proteins.
You K, Huang Q, Yu C, Shen B, Sevilla C, Shi M, Hermjakob H, Chen Y, Li T. Nucleic acids research Volume 48 (2020) p.D354-D359 DOI: 10.1093/nar/gkz847
Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics.
Walzer M, Vizcaíno JA. Methods in molecular biology (Clifton, N.J.) Volume 2051 (2020) p.345-371 DOI: 10.1007/978-1-4939-9744-2_15
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PDBe-KB: a community-driven resource for structural and functional annotations.
PDBe-KB consortium. Nucleic acids research Volume 48 (2020) p.D344-D353 DOI: 10.1093/nar/gkz853
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The reactome pathway knowledgebase.
Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 48 (2020) p.D498-D503 DOI: 10.1093/nar/gkz1031
BioModels-15 years of sharing computational models in life science.
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H. Nucleic acids research Volume 48 (2020) p.D407-D415 DOI: 10.1093/nar/gkz1055
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The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. Nucleic acids research Volume 48 (2020) p.D704-D715 DOI: 10.1093/nar/gkz997
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A draft genome sequence of the elusive giant squid, Architeuthis dux.
da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP. GigaScience Volume 9 (2020) DOI: 10.1093/gigascience/giz152
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WormBase: a modern Model Organism Information Resource.
Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Cho J, Davis P, Gao S, Grove CA, Kishore R, Lee RYN, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers FH, Russell M, Schindelman G, Auken KV, Wang Q, Williams G, Wright AJ, Yook K, Howe KL, Schedl T, Stein L, Sternberg PW. Nucleic acids research Volume 48 (2020) p.D762-D767 DOI: 10.1093/nar/gkz920
PDBe: improved findability of macromolecular structure data in the PDB.
Armstrong DR, Berrisford JM, Conroy MJ, Gutmanas A, Anyango S, Choudhary P, Clark AR, Dana JM, Deshpande M, Dunlop R, Gane P, Gáborová R, Gupta D, Haslam P, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Paysan-Lafosse T, Pravda L, Sehnal D, Salih O, Smart O, Tolchard J, Varadi M, Svobodova-Vařeková R, Zaki H, Kleywegt GJ, Velankar S. Nucleic acids research Volume 48 (2020) p.D335-D343 DOI: 10.1093/nar/gkz990

2019

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scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, Harding P, Polanski K, Huang N, Nowicki-Osuch K, Fitzgerald RC, Loudon KW, Ferdinand JR, Clatworthy MR, Tsingene A, van Dongen S, Dabrowska M, Patel M, Stubbington MJT, Teichmann SA, Stegle O, Meyer KB. Genome biology Volume 21 (2019) p.1 DOI: 10.1186/s13059-019-1906-x
Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project.
Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P, 1000 Genomes Project Consortium. Wellcome Open Research Volume 4 (2019) p.50 DOI: 10.12688/wellcomeopenres.15126.2
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Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition.
Lensink MF, Nadzirin N, Velankar S, Wodak SJ. Proteins (2019) DOI: 10.1002/prot.25870
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Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project
Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P, The 1000 Genomes Project Consortium. Preprint DOI: 10.12688/wellcomeopenres.15126.2
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Bringing data from curated pathway resources to Cytoscape with OmniPath.
Ceccarelli F, Turei D, Gabor A, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 36 (2020) p.2632-2633 DOI: 10.1093/bioinformatics/btz968
The neurocognitive gains of diagnostic reasoning training using simulated interactive veterinary cases.
Nassar M. Scientific reports Volume 9 (2019) p.19878 DOI: 10.1038/s41598-019-56404-z
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Publisher Correction: In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.
Memon D, Bi J, Miller CJ. Scientific reports Volume 9 (2019) p.20211 DOI: 10.1038/s41598-019-55753-z
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Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles.
Malas TB, Leonhard WN, Bange H, Granchi Z, Hettne KM, Van Westen GJP, Price LS, 't Hoen PAC, Peters DJM. EBioMedicine Volume 51 (2020) p.102585 DOI: 10.1016/j.ebiom.2019.11.046
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A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum.
Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen'ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. PloS one Volume 14 (2019) p.e0226485 DOI: 10.1371/journal.pone.0226485
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Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.
Dempster JM, Pacini C, Pantel S, Behan FM, Green T, Krill-Burger J, Beaver CM, Younger ST, Zhivich V, Najgebauer H, Allen F, Gonçalves E, Shepherd R, Doench JG, Yusa K, Vazquez F, Parts L, Boehm JS, Golub TR, Hahn WC, Root DE, Garnett MJ, Tsherniak A, Iorio F. Nature communications Volume 10 (2019) p.5817 DOI: 10.1038/s41467-019-13805-y
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Estimating the quality of eukaryotic genomes recovered from metagenomic analysis
Saary P, Mitchell AL, Finn RD. Preprint DOI: 10.1101/2019.12.19.882753
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A map of transcriptional heterogeneity and regulatory variation in human microglia
Young AM, Kumasaka N, Calvert F, Hammond TR, Knights A, Panousis N, Schwartzentruber J, Liu J, Kundu K, Segel M, Murphy N, McMurran CE, Bulstrode H, Correia J, Budohoski KP, Joannides A, Guilfoyle MR, Trivedi R, Kirollos R, Morris R, Garnett MR, Fernandes H, Timofeev I, Jalloh I, Holland K, Mannion R, Mair R, Watts C, Price SJ, Kirkpatrick PJ, Santarius T, Soranzo N, Stevens B, Hutchinson PJ, Franklin RJ, Gaffney DJ. Preprint DOI: 10.1101/2019.12.20.874099
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Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid.
Roberts LW, Catchpoole E, Jennison AV, Bergh H, Hume A, Heney C, George N, Paterson DL, Schembri MA, Beatson SA, Harris PNA. Microbial genomics Volume 6 (2020) DOI: 10.1099/mgen.0.000321
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Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases
Ritchie SC, Liu Y, Lambert SA, Teo SM, Scepanovic P, Marten J, Zahid S, Chaffin M, Abraham G, Ouwehand WH, Roberts DJ, Watkins NA, Di Angelantonio E, Soranzo N, Burgess S, Drew BG, Kathiresan S, Calkin AC, Khera AV, Danesh J, Butterworth AS, Inouye M. Preprint DOI: 10.1101/2019.12.14.876474
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Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks.
Maruyama SR, Carvalho B, González-Porta M, Rung J, Brazma A, Gustavo Gardinassi L, Ferreira BR, Banin TM, Veríssimo CJ, Katiki LM, de Miranda-Santos IKF. NPJ vaccines Volume 4 (2019) p.53 DOI: 10.1038/s41541-019-0145-1
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A roadmap for gene functional characterisation in wheat
Adamski NM, Borrill P, Brinton J, Harrington S, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BB, Uauy C. Preprint DOI: 10.7287/peerj.preprints.26877v2
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Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system.
Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR. eLife Volume 8 (2019) DOI: 10.7554/elife.45833
A guide to UniProt for students
Bye-A-Jee H, Pundir S. DOI: 10.6019/tol.uniprotguide-w.2019.00001.1
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High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation.
Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak AO, Duque-Correa MA, White JK, Ramirez-Solis R, Saran N, Bull KR, Morón B, Iwasaki J, Barton PR, Caetano S, Hng KI, Cambridge E, Forman S, Crockford TL, Griffiths M, Kane L, Harcourt K, Brandt C, Notley G, Babalola KO, Warren J, Mason JC, Meeniga A, Karp NA, Melvin D, Cawthorne E, Weinrick B, Rahim A, Drissler S, Meskas J, Yue A, Lux M, Song-Zhao GX, Chan A, Ballesteros Reviriego C, Abeler J, Wilson H, Przemska-Kosicka A, Edmans M, Strevens N, Pasztorek M, Meehan TF, Powrie F, Brinkman R, Dougan G, Jacobs W, Lloyd CM, Cornall RJ, Maloy KJ, Grencis RK, Griffiths GM, Adams DJ, Hayday AC. Nature immunology Volume 21 (2020) p.86-100 DOI: 10.1038/s41590-019-0549-0
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Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Nature genetics Volume 52 (2020) p.29-34 DOI: 10.1038/s41588-019-0547-z
Genome3D annotations in InterPro
Paysan-Lafosse T. DOI: 10.6019/tol.genome3dinterpro-w.2019.00001.1
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Cancer Risks Associated With Germline PALB2 Pathogenic Variants: An International Study of 524 Families.
Yang X, Leslie G, Doroszuk A, Schneider S, Allen J, Decker B, Dunning AM, Redman J, Scarth J, Plaskocinska I, Luccarini C, Shah M, Pooley K, Dorling L, Lee A, Adank MA, Adlard J, Aittomäki K, Andrulis IL, Ang P, Barwell J, Bernstein JL, Bobolis K, Borg Å, Blomqvist C, Claes KBM, Concannon P, Cuggia A, Culver JO, Damiola F, de Pauw A, Diez O, Dolinsky JS, Domchek SM, Engel C, Evans DG, Fostira F, Garber J, Golmard L, Goode EL, Gruber SB, Hahnen E, Hake C, Heikkinen T, Hurley JE, Janavicius R, Kleibl Z, Kleiblova P, Konstantopoulou I, Kvist A, Laduca H, Lee ASG, Lesueur F, Maher ER, Mannermaa A, Manoukian S, McFarland R, McKinnon W, Meindl A, Metcalfe K, Mohd Taib NA, Moilanen J, Nathanson KL, Neuhausen S, Ng PS, Nguyen-Dumont T, Nielsen SM, Obermair F, Offit K, Olopade OI, Ottini L, Penkert J, Pylkäs K, Radice P, Ramus SJ, Rudaitis V, Side L, Silva-Smith R, Silvestri V, Skytte AB, Slavin T, Soukupova J, Tondini C, Trainer AH, Unzeitig G, Usha L, van Overeem Hansen T, Whitworth J, Wood M, Yip CH, Yoon SY, Yussuf A, Zogopoulos G, Goldgar D, Hopper JL, Chenevix-Trench G, Pharoah P, George SHL, Balmaña J, Houdayer C, James P, El-Haffaf Z, Ehrencrona H, Janatova M, Peterlongo P, Nevanlinna H, Schmutzler R, Teo SH, Robson M, Pal T, Couch F, Weitzel JN, Elliott A, Southey M, Winqvist R, Easton DF, Foulkes WD, Antoniou AC, Tischkowitz M. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Volume 38 (2020) p.674-685 DOI: 10.1200/jco.19.01907
ChEMBL: Quick tour
Hersey A. DOI: 10.6019/tol.chembl-qt.2019.00001.1
Ensembl gene annotation for clinical genomics
Perry E, Morales J. DOI: 10.6019/tol.ensembl_clingen-w.2019.00001.1
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Induced aneuploidy disrupts MCF10A acini formation and CCND1 expression
Waschow M, Wang Q, Saary P, Klein C, Aschenbrenner S, Jechow K, Maier L, Tirier S, Schoell B, Chudoba I, Dietz C, Dreidax D, Jauch A, Sprick M, Herrmann C, Eils R, Conrad C. Preprint DOI: 10.1101/2019.12.15.876763
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Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
Huang Y, McCarthy DJ, Stegle O. Genome biology Volume 20 (2019) p.273 DOI: 10.1186/s13059-019-1865-2
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BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.
Xavier BB, Mysara M, Bolzan M, Ribeiro-Gonçalves B, Alako BTF, Harrison P, Lammens C, Kumar-Singh S, Goossens H, Carriço JA, Cochrane G, Malhotra-Kumar S. iScience Volume 23 (2020) p.100769 DOI: 10.1016/j.isci.2019.100769
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Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells.
Barrio-Hernandez I, Jafari A, Rigbolt KTG, Hallenborg P, Sanchez-Quiles V, Skovrind I, Akimov V, Kratchmarova I, Dengjel J, Kassem M, Blagoev B. Genome research Volume 30 (2020) p.127-137 DOI: 10.1101/gr.248286.119
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Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells.
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Interoperable and scalable data analysis with microservices: applications in metabolomics.
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Bioinformatics (Oxford, England) Volume 35 (2019) p.3752-3760 DOI: 10.1093/bioinformatics/btz160
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Advances and Applications in the Quest for Orthologs.
Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Molecular biology and evolution Volume 36 (2019) p.2157-2164 DOI: 10.1093/molbev/msz150
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Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index.
Hassing GJ, van der Wall HEC, van Westen GJP, Kemme MJB, Adiyaman A, Elvan A, Burggraaf J, Gal P. Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation Volume 27 (2019) p.506-512 DOI: 10.1007/s12471-019-1282-x
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. Cell reports Volume 29 (2019) p.202-211.e6 DOI: 10.1016/j.celrep.2019.08.077
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CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.
Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L. Bioinformatics (Oxford, England) Volume 35 (2019) p.3779-3785 DOI: 10.1093/bioinformatics/btz132
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Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.
Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. Nature genetics Volume 51 (2019) p.1429-1433 DOI: 10.1038/s41588-019-0500-1
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Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.
Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA. Cell systems Volume 9 (2019) p.401-413 DOI: 10.1016/j.cels.2019.08.003
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A five-level classification system for proteoform identifications.
Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolić L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, Kelleher NL. Nature methods Volume 16 (2019) p.939-940 DOI: 10.1038/s41592-019-0573-x
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A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes.
Mostajo NF, Lataretu M, Krautwurst S, Mock F, Desirò D, Lamkiewicz K, Collatz M, Schoen A, Weber F, Marz M, Hölzer M. NAR genomics and bioinformatics Volume 2 (2020) p.lqz006 DOI: 10.1093/nargab/lqz006
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Systematic assessment of regulatory effects of human disease variants in pluripotent cells
Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D’Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Horta D, Smith EN, Frazer KA, Montgomery SB, Stegle O, HipSci Consortium, iPSCORE Consortium, GENESiPS Consortium, PhLiPS Consortium. Preprint DOI: 10.1101/784967
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The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid.
Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD. PLoS pathogens Volume 15 (2019) p.e1007948 DOI: 10.1371/journal.ppat.1007948
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Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration.
Palma A, Cerquone Perpetuini A, Ferrentino F, Fuoco C, Gargioli C, Giuliani G, Iannuccelli M, Licata L, Micarelli E, Paoluzi S, Perfetto L, Petrilli LL, Reggio A, Rosina M, Sacco F, Vumbaca S, Zuccotti A, Castagnoli L, Cesareni G. Frontiers in physiology Volume 10 (2019) p.1216 DOI: 10.3389/fphys.2019.01216
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COPO: a metadata platform for brokering FAIR data in the life sciences
Etuk A, Shaw F, Gonzalez-Beltran A, Johnson D, Laporte M, Rocca-Serra P, Arnaud E, Devare M, Kersey PJ, Sansone S, Davey RP. Preprint DOI: 10.1101/782771
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MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics
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Detection of Cell Surface Ligands for Human Synovial γδ T Cells.
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Thrombospondin module 1 domain (TSP1) of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers
Xu E, Lafita A, Bateman A, Hyvönen M. Preprint DOI: 10.1101/779553
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BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
Katayama T, Kawashima S, Micklem G, Kawano S, Kim J, Kocbek S, Okamoto S, Wang Y, Wu H, Yamaguchi A, Yamamoto Y, Antezana E, Aoki-Kinoshita KF, Arakawa K, Banno M, Baran J, Bolleman JT, Bonnal RJ, Bono H, Fernández-Breis JT, Buels R, Campbell MP, Chiba H, Cock PJA, Cohen KB, Dumontier M, Fujisawa T, Fujiwara T, Garcia L, Gaudet P, Hattori E, Hoehndorf R, Itaya K, Ito M, Jamieson D, Jupp S, Juty N, Kalderimis A, Kato F, Kawaji H, Kawashima T, Kinjo AR, Komiyama Y, Kotera M, Kushida T, Malone J, Matsubara M, Mizuno S, Mizutani S, Mori H, Moriya Y, Murakami K, Nakazato T, Nishide H, Nishimura Y, Ogishima S, Ohta T, Okuda S, Ono H, Perez-Riverol Y, Shinmachi D, Splendiani A, Strozzi F, Suzuki S, Takehara J, Thompson M, Tokimatsu T, Uchiyama I, Verspoor K, Wilkinson MD, Wimalaratne S, Yamada I, Yamamoto N, Yarimizu M, Kawamoto S, Takagi T. Preprint DOI: 10.12688/f1000research.18238.1
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Smad7 Binds Differently to Individual and Tandem WW3 and WW4 Domains of WWP2 Ubiquitin Ligase Isoforms.
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FAIR adoption, assessment and challenges at UniProt.
Garcia L, Bolleman J, Gehant S, Redaschi N, Martin M, UniProt Consortium. Scientific data Volume 6 (2019) p.175 DOI: 10.1038/s41597-019-0180-9
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, Frankish A, Kellis M. Genome research Volume 29 (2019) p.2073-2087 DOI: 10.1101/gr.246462.118
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Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons
Barnes IHA, Ibarra-Soria X, Fitzgerald S, Gonzalez JM, Davidson C, Hardy MP, Manthravadi D, Van Gerven L, Jorissen M, Zeng Z, Khan M, Mombaerts P, Harrow J, Logan DW, Frankish A. Preprint DOI: 10.1101/774612
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A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD. Preprint DOI: 10.1101/762682
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Ontology based mining of pathogen-disease associations from literature.
Kafkas Ş, Hoehndorf R. Journal of biomedical semantics Volume 10 (2019) p.15 DOI: 10.1186/s13326-019-0208-2
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DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules.
Foscato M, Venkatraman V, Jensen VR. Journal of chemical information and modeling Volume 59 (2019) p.4077-4082 DOI: 10.1021/acs.jcim.9b00516
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Sequencing-based microsatellite instability testing using as few as six markers for high-throughput clinical diagnostics.
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The mutational landscape of a prion-like domain.
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Understanding life sciences data curation practices via user research
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Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas
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Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.
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Integrated evolutionary and structural analysis reveals xenobiotics and pathogens as the major drivers of mammalian adaptation
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An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.
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Similarities and differences in patterns of germline mutation between mice and humans.
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DCAF8, a novel MuRF1 interaction partner, promotes muscle atrophy.
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p13CMFA: Parsimonious 13C metabolic flux analysis.
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Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host.
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Geleophysic dysplasia: novel missense variants and insights into ADAMTSL2 intracellular trafficking.
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Non-coding RNA regulatory networks.
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Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants.
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Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers.
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Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.
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A new reference genome sequence for Caenorhabditis elegans?
Howe KL. Lab animal Volume 48 (2019) p.267-268 DOI: 10.1038/s41684-019-0371-1
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Detection of Epidemic Scarlet Fever Group A Streptococcus in Australia.
Walker MJ, Brouwer S, Forde BM, Worthing KA, McIntyre L, Sundac L, Maloney S, Roberts LW, Barnett TC, Richter J, Cork AJ, Irwin AD, You Y, Zhang J, Dougan G, Yuen KY, Nizet V, Beatson SA, Grimwood K, Davies MR. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Volume 69 (2019) p.1232-1234 DOI: 10.1093/cid/ciz099
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Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
Rifaioglu AS, Atas H, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. Briefings in bioinformatics Volume 20 (2019) p.1878-1912 DOI: 10.1093/bib/bby061
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Spatiotemporal immune zonation of the human kidney.
Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Vieira Braga FA, Botting RA, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Del Castillo Velasco-Herrera M, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Behjati S, Clatworthy MR. Science (New York, N.Y.) Volume 365 (2019) p.1461-1466 DOI: 10.1126/science.aat5031
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Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account.
Drakakis G, Cortés-Ciriano I, Alexander-Dann B, Bender A. Current protocols in chemical biology Volume 11 (2019) p.e73 DOI: 10.1002/cpch.73
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Mechanisms of Progression of Myeloid Preleukemia to Transformed Myeloid Leukemia in Children with Down Syndrome.
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Finding enzyme cofactors in Protein Data Bank.
Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S. Bioinformatics (Oxford, England) Volume 35 (2019) p.3510-3511 DOI: 10.1093/bioinformatics/btz115
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A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. Cell Volume 178 (2019) p.1465-1477.e17 DOI: 10.1016/j.cell.2019.08.018
Know Thy PDX Model.
Meehan TF. Cancer research Volume 79 (2019) p.4324-4325 DOI: 10.1158/0008-5472.can-19-2023
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Correction to: The official unified nomenclature adopted by the HGNC calls for the use of the acronyms, CCN1-6, and discontinuation in the use of CYR61, CTGF, NOV and WISP 1-3 respectively.
Perbal B, Tweedie S, Bruford E. Journal of cell communication and signaling Volume 13 (2019) p.435 DOI: 10.1007/s12079-019-00532-8
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Reduced stomatal density in bread wheat leads to increased water-use efficiency.
Dunn J, Hunt L, Afsharinafar M, Meselmani MA, Mitchell A, Howells R, Wallington E, Fleming AJ, Gray JE. Journal of experimental botany Volume 70 (2019) p.4737-4748 DOI: 10.1093/jxb/erz248
Author Correction: Challenges in measuring and understanding biological noise.
Eling N, Morgan MD, Marioni JC. Nature reviews. Genetics Volume 20 (2019) p.562 DOI: 10.1038/s41576-019-0142-2
Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Molecular biology and evolution Volume 36 (2019) p.2086-2103 DOI: 10.1093/molbev/msz122
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Robustness and applicability of functional genomics tools on scRNA-seq data
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Challenges in measuring and understanding biological noise.
Eling N, Morgan MD, Marioni JC. Nature reviews. Genetics Volume 20 (2019) p.536-548 DOI: 10.1038/s41576-019-0130-6
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Gene networks in cancer are biased by aneuploidies and sample impurities
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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
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Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors.
Janssen APA, van Hengst JMA, Béquignon OJM, Deng H, van Westen GJP, van der Stelt M. Journal of medicinal chemistry Volume 62 (2019) p.7910-7922 DOI: 10.1021/acs.jmedchem.9b00686
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Assessment of network module identification across complex diseases.
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One Thousand and One Software for Proteomics: Tales of the Toolmakers of Science.
Tsiamis V, Ienasescu HI, Gabrielaitis D, Palmblad M, Schwämmle V, Ison J. Journal of proteome research Volume 18 (2019) p.3580-3585 DOI: 10.1021/acs.jproteome.9b00219
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scHLAcount: Allele-specific HLA expression from single-cell gene expression data
Darby CA, Stubbington MJT, Marks PJ, Barrio ÁM, Fiddes IT. Preprint DOI: 10.1101/750612
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Population Structure, Stratification and Introgression of Human Structural Variation
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Development of Ubiquitin-Based Probe for Metalloprotease Deubiquitinases.
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Leveraging European infrastructures to access 1 million human genomes by 2022.
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Assessment of protein assembly prediction in CASP13.
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Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.
Bruno L, Ramlall V, Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG, Siggers T, Beltrao P, Merkenschlager M. Nature immunology Volume 20 (2019) p.1372-1380 DOI: 10.1038/s41590-019-0471-5
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iTRAQ-Based Global Phosphoproteomics Reveals Novel Molecular Differences Between Toxoplasma gondii Strains of Different Genotypes.
Wang ZX, Zhou CX, Calderón-Mantilla G, Petsalaki E, He JJ, Song HY, Elsheikha HM, Zhu XQ. Frontiers in cellular and infection microbiology Volume 9 (2019) p.307 DOI: 10.3389/fcimb.2019.00307
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Genomic landscape and chronological reconstruction of driver events in multiple myeloma.
Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Abascal F, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JMC, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, Campbell PJ. Nature communications Volume 10 (2019) p.3835 DOI: 10.1038/s41467-019-11680-1
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12 Grand Challenges in Single-Cell Data Science
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Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B.
Vögtle T, Sharma S, Mori J, Nagy Z, Semeniak D, Scandola C, Geer MJ, Smith CW, Lane J, Pollack S, Lassila R, Jouppila A, Barr AJ, Ogg DJ, Howard TD, McMiken HJ, Warwicker J, Geh C, Rowlinson R, Abbott WM, Eckly A, Schulze H, Wright GJ, Mazharian A, Fütterer K, Rajesh S, Douglas MR, Senis YA. eLife Volume 8 (2019) DOI: 10.7554/elife.46840
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Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.
Viehweger A, Krautwurst S, Lamkiewicz K, Madhugiri R, Ziebuhr J, Hölzer M, Marz M. Genome research Volume 29 (2019) p.1545-1554 DOI: 10.1101/gr.247064.118
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A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity.
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Comparison of Associations with Different Macular Inner Retinal Thickness Parameters in a Large Cohort: The UK Biobank.
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Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
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Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Frontiers in genetics Volume 10 (2019) p.709 DOI: 10.3389/fgene.2019.00709
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Distinct Molecular Trajectories Converge to Induce Naive Pluripotency.
Stuart HT, Stirparo GG, Lohoff T, Bates LE, Kinoshita M, Lim CY, Sousa EJ, Maskalenka K, Radzisheuskaya A, Malcolm AA, Alves MRP, Lloyd RL, Nestorowa S, Humphreys P, Mansfield W, Reik W, Bertone P, Nichols J, Göttgens B, Silva JCR. Cell stem cell Volume 25 (2019) p.388-406.e8 DOI: 10.1016/j.stem.2019.07.009
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HENA, heterogeneous network-based data set for Alzheimer's disease.
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Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.
Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM. Genome biology Volume 20 (2019) p.146 DOI: 10.1186/s13059-019-1753-9
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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii.
Hölzer M, Schoen A, Wulle J, Müller MA, Drosten C, Marz M, Weber F. iScience Volume 19 (2019) p.647-661 DOI: 10.1016/j.isci.2019.08.016
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NaPLeS: a natural products likeness scorer-web application and database.
Sorokina M, Steinbeck C. Journal of cheminformatics Volume 11 (2019) p.55 DOI: 10.1186/s13321-019-0378-z
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Assembly of B4GALT1/ST6GAL1 heteromers in the Golgi membranes involves lateral interactions via highly charged surface domains.
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Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer.
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A Report from a Workshop of the International Stem Cell Banking Initiative, Held in Collaboration of Global Alliance for iPSC Therapies and the Harvard Stem Cell Institute, Boston, 2017.
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Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus.
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Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach.
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The impact of chemo- and radiotherapy treatments on selfish de novo FGFR2 mutations in sperm of cancer survivors.
Maher GJ, Bernkopf M, Koelling N, Wilkie AOM, Meistrich ML, Goriely A. Human reproduction (Oxford, England) Volume 34 (2019) p.1404-1415 DOI: 10.1093/humrep/dez090
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Contrasting gene expression patterns in grain of high and low asparagine wheat genotypes in response to sulphur supply.
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The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.
Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN. Science (New York, N.Y.) Volume 365 (2019) DOI: 10.1126/science.aaw2619
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Somatic evolution and global expansion of an ancient transmissible cancer lineage.
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PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.
Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M. GigaScience Volume 8 (2019) DOI: 10.1093/gigascience/giz088
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Correction: IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients.
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Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data.
Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M. Molecular systems biology Volume 15 (2019) p.e8828 DOI: 10.15252/msb.20198828
Origins of peptidases.
Rawlings ND, Bateman A. Biochimie Volume 166 (2019) p.4-18 DOI: 10.1016/j.biochi.2019.07.026
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Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function.
Moore BA, Flenniken AM, Clary D, Moshiri AS, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, McKerlie C, International Mouse Phenotyping Consortium, Thomasy SM, Lloyd KCK, Murphy CJ, Moshiri A. Scientific reports Volume 9 (2019) p.11211 DOI: 10.1038/s41598-019-47286-2
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The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1.
Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. Genes & development Volume 33 (2019) p.1221-1235 DOI: 10.1101/gad.328492.119
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Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AW, Heaton MP, Phillippy AM, Hiendleder S, Smith TP, Williams JL. Preprint DOI: 10.1101/720797
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MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment.
Burgin J, Molitor C, Mohareb F. Bioinformatics (Oxford, England) Volume 35 (2019) p.2671-2673 DOI: 10.1093/bioinformatics/bty1013
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Very low-depth whole-genome sequencing in complex trait association studies.
Gilly A, Southam L, Suveges D, Kuchenbaecker K, Moore R, Melloni GEM, Hatzikotoulas K, Farmaki AE, Ritchie G, Schwartzentruber J, Danecek P, Kilian B, Pollard MO, Ge X, Tsafantakis E, Dedoussis G, Zeggini E. Bioinformatics (Oxford, England) Volume 35 (2019) p.2555-2561 DOI: 10.1093/bioinformatics/bty1032
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A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.
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Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2.
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Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors.
Segal JM, Kent D, Wesche DJ, Ng SS, Serra M, Oulès B, Kar G, Emerton G, Blackford SJI, Darmanis S, Miquel R, Luong TV, Yamamoto R, Bonham A, Jassem W, Heaton N, Vigilante A, King A, Sancho R, Teichmann S, Quake SR, Nakauchi H, Rashid ST. Nature communications Volume 10 (2019) p.3350 DOI: 10.1038/s41467-019-11266-x
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Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans
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Epstein-Barr virus reprograms human B lymphocytes immediately in the prelatent phase of infection.
Mrozek-Gorska P, Buschle A, Pich D, Schwarzmayr T, Fechtner R, Scialdone A, Hammerschmidt W. Proceedings of the National Academy of Sciences of the United States of America Volume 116 (2019) p.16046-16055 DOI: 10.1073/pnas.1901314116
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Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits.
Porcu E, Rüeger S, Lepik K, eQTLGen Consortium, BIOS Consortium, Santoni FA, Reymond A, Kutalik Z. Nature communications Volume 10 (2019) p.3300 DOI: 10.1038/s41467-019-10936-0
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Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
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Benchmark and integration of resources for the estimation of human transcription factor activities.
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Genome research Volume 29 (2019) p.1363-1375 DOI: 10.1101/gr.240663.118
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Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
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Transcriptome sequencing, molecular markers, and transcription factor discovery of Platanus acerifolia in the presence of Corythucha ciliata.
Li F, Wu C, Gao M, Jiao M, Qu C, Gonzalez-Uriarte A, Luo C. Scientific data Volume 6 (2019) p.128 DOI: 10.1038/s41597-019-0111-9
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Roraregulates activated T helper cells during inflammation
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When Three Isn't a Crowd: A Digyny Concept for Treatment-Resistant, Near-Triploid Human Cancers.
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A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
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Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status.
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NFDI4Chem: Shaping a Digital and Cultural Change in Chemistry.
Herres-Pawlis S, Koepler O, Steinbeck C. Angewandte Chemie (International ed. in English) Volume 58 (2019) p.10766-10768 DOI: 10.1002/anie.201907260
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Proteome-wide inference of protein kinase regulatory circuits
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A simple approach for accurate peptide quantification in MS-based proteomics
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RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets.
de Lima Nichio BT, de Oliveira AMR, de Pierri CR, Santos LGC, Lejambre AQ, Vialle RA, da Rocha Coimbra NA, Guizelini D, Marchaukoski JN, de Oliveira Pedrosa F, Raittz RT. BMC bioinformatics Volume 20 (2019) p.392 DOI: 10.1186/s12859-019-2973-4
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Automated structure prediction of trans-acyltransferase polyketide synthase products.
Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Nature chemical biology Volume 15 (2019) p.813-821 DOI: 10.1038/s41589-019-0313-7
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Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.
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Detection of simple and complex de novo mutations without, with, or with multiple reference sequences
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Mechanisms of Progression of Myeloid Preleukemia to Transformed Myeloid Leukemia in Children with Down Syndrome.
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Genetic interactions of G-quadruplexes in humans.
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Gene-based analysis in HRC imputed genome wide association data identifies three novel genes for Alzheimer's disease.
Baker E, Sims R, Leonenko G, Frizzati A, Harwood JC, Grozeva D, GERAD/PERADES, CHARGE, ADGC, EADI, IGAP consortia, Morgan K, Passmore P, Holmes C, Powell J, Brayne C, Gill M, Mead S, Bossù P, Spalletta G, Goate AM, Cruchaga C, Maier W, Heun R, Jessen F, Peters O, Dichgans M, FröLich L, Ramirez A, Jones L, Hardy J, Ivanov D, Hill M, Holmans P, Allen ND, Morgan BP, Seshadri S, Schellenberg GD, Amouyel P, Williams J, Escott-Price V. PloS one Volume 14 (2019) p.e0218111 DOI: 10.1371/journal.pone.0218111
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Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer.
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T. NPJ systems biology and applications Volume 5 (2019) p.20 DOI: 10.1038/s41540-019-0098-z
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IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.
Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M. EMBO reports Volume 20 (2019) p.e47379 DOI: 10.15252/embr.201847379
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CYRI/FAM49B negatively regulates RAC1-driven cytoskeletal remodelling and protects against bacterial infection.
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Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula.
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Systems Genetics of Hepatic Metabolome Reveals Octopamine as a Target for Non-Alcoholic Fatty Liver Disease Treatment.
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A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.
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Genomic analysis reveals a functional role for myocardial trabeculae in adults
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Single-cell immune profiling reveals new insights into colorectal cancer.
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A single-cell molecular map of mouse gastrulation and early organogenesis.
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Update on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an "evolutionary bloom".
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Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.
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Comprehensive and Empirical Evaluation of Machine Learning Algorithms for Small Molecule LC Retention Time Prediction.
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Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools.
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Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dys-regulation of Epithelial-Mesenchymal Transition and subcellular re-localization of Beta-Catenin
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A new genomic blueprint of the human gut microbiota.
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Efficient exact associative structure for sequencing data
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Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1
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Unveiling the Kinomes of Leishmania infantum and L. braziliensis Empowers the Discovery of New Kinase Targets and Antileishmanial Compounds.
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Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Gabriels R, Martens L, Degroeve S. Preprint DOI: 10.1101/544965
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Comparison of Human and Murine Enteroendocrine Cells by Transcriptomic and Peptidomic Profiling.
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Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
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Addiction Theories and Constructs: a new series.
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Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis
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The functional landscape of the human phosphoproteome
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From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL
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Ultrafast search of all deposited bacterial and viral genomic data.
Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z. Nature biotechnology Volume 37 (2019) p.152-159 DOI: 10.1038/s41587-018-0010-1
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A human gut bacterial genome and culture collection for improved metagenomic analyses.
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Tang H, Finn RD, Thomas PD. Bioinformatics (Oxford, England) Volume 35 (2019) p.518-520 DOI: 10.1093/bioinformatics/bty625
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Sharma S, Petsalaki E. Current opinion in genetics & development Volume 54 (2019) p.118-124 DOI: 10.1016/j.gde.2019.05.001
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Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
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SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.
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LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics.
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Supported Ru olefin metathesis catalysts via a thiolate tether.
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Correction to: The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation
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Endorsing and extending the repertory of nutraceutical and antioxidant sources in mangoes during postharvest shelf life.
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Minocycline and the risk of acute psychiatric events in adolescence: A self-controlled case series.
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Disentangling the complexity of low complexity proteins.
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The comparative genomics and complex population history of Papio baboons.
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An integrated transcriptional analysis of the developing human retina.
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Transfer of regulatory knowledge from human to mouse for functional genomic analysis
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GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals.
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The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes
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Modelling structural constraints on protein evolution via side-chain conformational states
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Preprint DOI: 10.1101/530634
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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
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The variability of expression of many genes and most functional pathways is observed to increase with age in brain transcriptome data
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Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI.
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Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords
GUR T. Preprint DOI: 10.1101/520841
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Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes
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Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors.
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Targeted Resequencing of the Coding Sequence of 38 Genes Near Breast Cancer GWAS Loci in a Large Case-Control Study.
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Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification: Supplementary Figures
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Bosc N, Atkinson F, Felix E, Gaulton A, Hersey A, Leach AR. Journal of cheminformatics Volume 11 (2019) p.4 DOI: 10.1186/s13321-018-0325-4
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Using the drug-protein interactome to identify anti-ageing compounds for humans.
Fuentealba M, Dönertaş HM, Williams R, Labbadia J, Thornton JM, Partridge L. PLoS computational biology Volume 15 (2019) p.e1006639 DOI: 10.1371/journal.pcbi.1006639
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iProteinDB: An Integrative Database of Drosophila Post-translational Modifications.
Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N. G3 (Bethesda, Md.) Volume 9 (2019) p.1-11 DOI: 10.1534/g3.118.200637
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Copy number aberrations drive kinase re-wiring leading to genetic vulnerabilities in cancer
Memon D, Gill MG, Papachristou E, Ochoa D, D'Santos C, Miller ML, Beltrao P. Preprint DOI: 10.1101/515932
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PROREPAIR-B: A Prospective Cohort Study of the Impact of Germline DNA Repair Mutations on the Outcomes of Patients With Metastatic Castration-Resistant Prostate Cancer.
Castro E, Romero-Laorden N, Del Pozo A, Lozano R, Medina A, Puente J, Piulats JM, Lorente D, Saez MI, Morales-Barrera R, Gonzalez-Billalabeitia E, Cendón Y, García-Carbonero I, Borrega P, Mendez Vidal MJ, Montesa A, Nombela P, Fernández-Parra E, Gonzalez Del Alba A, Villa-Guzmán JC, Ibáñez K, Rodriguez-Vida A, Magraner-Pardo L, Perez-Valderrama B, Vallespín E, Gallardo E, Vazquez S, Pritchard CC, Lapunzina P, Olmos D. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Volume 37 (2019) p.490-503 DOI: 10.1200/jco.18.00358
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Wnt3a disrupts GR-TEAD4-PPARγ2 positive circuits and cytoskeletal rearrangement in a β-catenin-dependent manner during early adipogenesis.
Park B, Chang S, Lee GJ, Kang B, Kim JK, Park H. Cell death & disease Volume 10 (2019) p.16 DOI: 10.1038/s41419-018-1249-7
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Matching the genetics of released and local Aedes aegypti populations is critical to assure Wolbachia invasion.
Garcia GA, Sylvestre G, Aguiar R, da Costa GB, Martins AJ, Lima JBP, Petersen MT, Lourenço-de-Oliveira R, Shadbolt MF, Rašić G, Hoffmann AA, Villela DAM, Dias FBS, Dong Y, O'Neill SL, Moreira LA, Maciel-de-Freitas R. PLoS neglected tropical diseases Volume 13 (2019) p.e0007023 DOI: 10.1371/journal.pntd.0007023
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ELECTOR: Evaluator for long reads correction methods
Marchet C, Morisse P, Lecompte L, Lefebvre A, Lecroq T, Peterlongo P, Limasset A. Preprint DOI: 10.1101/512889
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A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis.
Morgan M, Kabayama Y, Much C, Ivanova I, Di Giacomo M, Auchynnikava T, Monahan JM, Vitsios DM, Vasiliauskaitė L, Comazzetto S, Rappsilber J, Allshire RC, Porse BT, Enright AJ, O'Carroll D. Cell research Volume 29 (2019) p.221-232 DOI: 10.1038/s41422-018-0128-1
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Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.
Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB. PeerJ Volume 7 (2019) p.e6160 DOI: 10.7717/peerj.6160
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Towards quality assurance and quality control in untargeted metabolomics studies.
Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O'Donovan C, Playdon M, Raftery D, Shaughnessy D, Souza A, Spaeder T, Spalholz B, Tayyari F, Ubhi B, Verma M, Walk T, Wilson I, Witkin K, Bearden DW, Zanetti KA. Metabolomics : Official journal of the Metabolomic Society Volume 15 (2019) p.4 DOI: 10.1007/s11306-018-1460-7
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What Makes a Kinase Promiscuous for Inhibitors?
Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA. Cell chemical biology Volume 26 (2019) p.390-399.e5 DOI: 10.1016/j.chembiol.2018.11.005
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Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.
IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Hermjakob H, Orchard S, Porras P. Nature communications Volume 10 (2019) p.10 DOI: 10.1038/s41467-018-07709-6
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Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes.
Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo ML, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA. Cell reports Volume 26 (2019) p.1059-1069.e6 DOI: 10.1016/j.celrep.2018.12.098
The COMPARE Data Hubs.
Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, Dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz136
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. Nucleic acids research Volume 47 (2019) p.D1005-D1012 DOI: 10.1093/nar/gky1120
Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Methods in molecular biology (Clifton, N.J.) Volume 1851 (2019) p.263-275 DOI: 10.1007/978-1-4939-8736-8_14
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Literature-Based Enrichment Insights into Redox Control of Vascular Biology
Essack M, Salhi A, Stanimirovic J, Tifratene F, Raies A, Hungler A, Uludag M, Neste CV, Trpkovic A, Bajic VP, Bajic VB, Isenovic ER. Oxidative medicine and cellular longevity Volume 2019 (2019) DOI: 10.1155/2019/1769437
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CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, Tolulope A, Scholes HM, Senatorov I, Bujan A, Ceballos Rodriguez-Conde F, Dowling B, Thornton J, Orengo CA. Nucleic acids research Volume 47 (2019) p.D280-D284 DOI: 10.1093/nar/gky1097
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Single-Stranded DNA Virus Sequencing (SSV-Seq) for Characterization of Residual DNA and AAV Vector Genomes.
Lecomte E, Leger A, Penaud-Budloo M, Ayuso E. Methods in molecular biology (Clifton, N.J.) Volume 1950 (2019) p.85-106 DOI: 10.1007/978-1-4939-9139-6_5
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. Nucleic acids research Volume 47 (2019) p.D351-D360 DOI: 10.1093/nar/gky1100
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Annotation of gene product function from high-throughput studies using the Gene Ontology.
Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S, Gene Ontology Consortium. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz007
Open Targets Platform: new developments and updates two years on.
Carvalho-Silva D, Pierleoni A, Pignatelli M, Ong C, Fumis L, Karamanis N, Carmona M, Faulconbridge A, Hercules A, McAuley E, Miranda A, Peat G, Spitzer M, Barrett J, Hulcoop DG, Papa E, Koscielny G, Dunham I. Nucleic acids research Volume 47 (2019) p.D1056-D1065 DOI: 10.1093/nar/gky1133
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S. Nucleic acids research Volume 47 (2019) p.D482-D489 DOI: 10.1093/nar/gky1114
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Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D.
Yang M, Zhang W, Yao G, Zhang H, Li W. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz092
BioSamples database: an updated sample metadata hub.
Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T. Nucleic acids research Volume 47 (2019) p.D1172-D1178 DOI: 10.1093/nar/gky1061
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 47 (2019) p.D221-D229 DOI: 10.1093/nar/gky1034
PDX Finder: A portal for patient-derived tumor xenograft model discovery.
Conte N, Mason JC, Halmagyi C, Neuhauser S, Mosaku A, Yordanova G, Chatzipli A, Begley DA, Krupke DM, Parkinson H, Meehan TF, Bult CC. Nucleic acids research Volume 47 (2019) p.D1073-D1079 DOI: 10.1093/nar/gky984
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The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.
Pandurangan AP, Stahlhacke J, Oates ME, Smithers B, Gough J. Nucleic acids research Volume 47 (2019) p.D490-D494 DOI: 10.1093/nar/gky1130
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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Nucleic acids research Volume 47 (2019) p.D1018-D1027 DOI: 10.1093/nar/gky1105
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Sharing Programming Resources Between Bio* Projects.
Bonnal RJP, Yates A, Goto N, Gautier L, Willis S, Fields C, Katayama T, Prins P. Methods in molecular biology (Clifton, N.J.) Volume 1910 (2019) p.747-766 DOI: 10.1007/978-1-4939-9074-0_25
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Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.
Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H, Lun ATL, Marioni JC, Reik W. Cell reports Volume 26 (2019) p.815-824.e4 DOI: 10.1016/j.celrep.2018.12.099
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HmtVar: a new resource for human mitochondrial variations and pathogenicity data.
Preste R, Vitale O, Clima R, Gasparre G, Attimonelli M. Nucleic acids research Volume 47 (2019) p.D1202-D1210 DOI: 10.1093/nar/gky1024
The European Nucleotide Archive in 2018.
Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G. Nucleic acids research Volume 47 (2019) p.D84-D88 DOI: 10.1093/nar/gky1078
Genenames.org: the HGNC and VGNC resources in 2019.
Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, Yates B, Bruford E. Nucleic acids research Volume 47 (2019) p.D786-D792 DOI: 10.1093/nar/gky930
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COSMIC: the Catalogue Of Somatic Mutations In Cancer.
Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, Fish P, Harsha B, Hathaway C, Jupe SC, Kok CY, Noble K, Ponting L, Ramshaw CC, Rye CE, Speedy HE, Stefancsik R, Thompson SL, Wang S, Ward S, Campbell PJ, Forbes SA. Nucleic acids research Volume 47 (2019) p.D941-D947 DOI: 10.1093/nar/gky1015
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htsget: a protocol for securely streaming genomic data.
Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A, Marshall J, Nowak A, Senf A, Tovar-Corona JM, Vikhorev A, Keane TM, GA4GH Streaming Task Team. Bioinformatics (Oxford, England) Volume 35 (2019) p.119-121 DOI: 10.1093/bioinformatics/bty492
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.
Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S. Nucleic acids research Volume 47 (2019) p.D550-D558 DOI: 10.1093/nar/gky1001
Using BRIE to Detect and Analyze Splicing Isoforms in scRNA-Seq Data.
Huang Y, Sanguinetti G. Methods in molecular biology (Clifton, N.J.) Volume 1935 (2019) p.175-185 DOI: 10.1007/978-1-4939-9057-3_12
GENCODE reference annotation for the human and mouse genomes.
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. Nucleic acids research Volume 47 (2019) p.D766-D773 DOI: 10.1093/nar/gky955
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Root colonizing and soil borne communities of arbuscular mycorrhizal fungi differ among soybean fields with contrasting historical land use
Faggioli VS, Fernanda Covacevich, Gabriel Grilli, Maarja Öpik, Marta Noemí Cabello, Martti Vasar. Agriculture, Ecosystems & Environment Volume 269 (2019) p.174-182 DOI: 10.1016/j.agee.2018.10.002
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iProX: an integrated proteome resource.
Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y. Nucleic acids research Volume 47 (2019) p.D1211-D1217 DOI: 10.1093/nar/gky869
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3DPatch: fast 3D structure visualization with residue conservation.
Jakubec D, Vondrášek J, Finn RD. Bioinformatics (Oxford, England) Volume 35 (2019) p.332-334 DOI: 10.1093/bioinformatics/bty464
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Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.
Gourdine JF, Brush MH, Vasilevsky NA, Shefchek K, Köhler S, Matentzoglu N, Munoz-Torres MC, McMurry JA, Zhang XA, Robinson PN, Haendel MA. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz114
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LNCipedia 5: towards a reference set of human long non-coding RNAs.
Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. Nucleic acids research Volume 47 (2019) p.D135-D139 DOI: 10.1093/nar/gky1031
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Integrating Genomics into Healthcare: A Global Responsibility.
Stark Z, Dolman L, Manolio TA, Ozenberger B, Hill SL, Caulfied MJ, Levy Y, Glazer D, Wilson J, Lawler M, Boughtwood T, Braithwaite J, Goodhand P, Birney E, North KN. American journal of human genetics Volume 104 (2019) p.13-20 DOI: 10.1016/j.ajhg.2018.11.014
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Toward unrestricted use of public genomic data.
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Science (New York, N.Y.) Volume 363 (2019) p.350-352 DOI: 10.1126/science.aaw1280
Reactome and ORCID-fine-grained credit attribution for community curation.
Viteri G, Matthews L, Varusai T, Gillespie M, Milacic M, Cook J, Weiser J, Shorser S, Sidiropoulos K, Fabregat A, Haw R, Wu G, Stein L, D'Eustachio P, Hermjakob H. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz123
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Updates in Rhea: SPARQLing biochemical reaction data.
Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A. Nucleic acids research Volume 47 (2019) p.D596-D600 DOI: 10.1093/nar/gky876
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Computational approaches for discovery of mutational signatures in cancer.
Baez-Ortega A, Gori K. Briefings in bioinformatics Volume 20 (2019) p.77-88 DOI: 10.1093/bib/bbx082
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MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins.
Ribeiro DM, Briere G, Bely B, Spinelli L, Brun C. Nucleic acids research Volume 47 (2019) p.D398-D402 DOI: 10.1093/nar/gky1039
ArrayExpress update - from bulk to single-cell expression data.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. Nucleic acids research Volume 47 (2019) p.D711-D715 DOI: 10.1093/nar/gky964
ChEMBL: towards direct deposition of bioassay data.
Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, Gordillo-Marañón M, Hunter F, Junco L, Mugumbate G, Rodriguez-Lopez M, Atkinson F, Bosc N, Radoux CJ, Segura-Cabrera A, Hersey A, Leach AR. Nucleic acids research Volume 47 (2019) p.D930-D940 DOI: 10.1093/nar/gky1075
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PopTargs: a database for studying population evolutionary genetics of human microRNA target sites.
Hatlen A, Helmy M, Marco A. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz102
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Protein Data Bank: the single global archive for 3D macromolecular structure data.
wwPDB consortium. Nucleic acids research Volume 47 (2019) p.D520-D528 DOI: 10.1093/nar/gky949
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Nucleic acids research Volume 47 (2019) p.D442-D450 DOI: 10.1093/nar/gky1106
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Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine?
Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Genome biology and evolution Volume 11 (2019) p.220-231 DOI: 10.1093/gbe/evy262
Ensembl 2019.
Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P. Nucleic acids research Volume 47 (2019) p.D745-D751 DOI: 10.1093/nar/gky1113
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Integration of macromolecular complex data into the Saccharomyces Genome Database.
Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, SGD Project. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz008
The European Bioinformatics Institute in 2018: tools, infrastructure and training.
Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. Nucleic acids research Volume 47 (2019) p.D15-D22 DOI: 10.1093/nar/gky1124
The Pfam protein families database in 2019.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD. Nucleic acids research Volume 47 (2019) p.D427-D432 DOI: 10.1093/nar/gky995
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.
Richardson LJ, Rawlings ND, Salazar GA, Almeida A, Haft DR, Ducq G, Sutton GG, Finn RD. Nucleic acids research Volume 47 (2019) p.D564-D572 DOI: 10.1093/nar/gky1013
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De novo clustering of long reads by gene from transcriptomics data.
Marchet C, Lecompte L, Silva CD, Cruaud C, Aury JM, Nicolas J, Peterlongo P. Nucleic acids research Volume 47 (2019) p.e2 DOI: 10.1093/nar/gky834
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Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.
Korlević P, Meyer M. Methods in molecular biology (Clifton, N.J.) Volume 1963 (2019) p.15-19 DOI: 10.1007/978-1-4939-9176-1_2
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Interspecific variation of olfactory preferences in flies, mice, and humans.
Manoel D, Makhlouf M, Scialdone A, Saraiva LR. Chemical senses Volume 44 (2019) p.7-9 DOI: 10.1093/chemse/bjy074
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 47 (2019) p.D1250-D1251 DOI: 10.1093/nar/gky1206
Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities.
Jarnuczak AF, Ternent T, Vizcaíno JA. Methods in molecular biology (Clifton, N.J.) Volume 1977 (2019) p.217-235 DOI: 10.1007/978-1-4939-9232-4_14

2018

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Rapid identification of novel protein families using similarity searches
Jeffryes M, Bateman A. Preprint DOI: 10.12688/f1000research.17315.1
Rapid identification of novel protein families using similarity searches.
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The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury.
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Identification of new allosteric sites and modulators of AChE through computational and experimental tools.
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Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.
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Strategies and opportunities for promoting bioinformatics in Zimbabwe.
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Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach.
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Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.
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Antigen Specificity and Clinical Significance of IgG and IgA Autoantibodies Produced in situ by Tumor-Infiltrating B Cells in Breast Cancer.
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Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury.
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Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes.
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Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks.
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FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.
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Expanding the Use of Spectral Libraries in Proteomics.
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Using the drug-protein interactome to identify anti-ageing compounds for humans
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From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge.
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Haplosaurus computes protein haplotypes for use in precision drug design.
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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
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Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma.
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
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Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.
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Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands.
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Transform-MinER: transforming molecules in enzyme reactions.
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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
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DNA G-quadruplex structures mold the DNA methylome.
Mao SQ, Ghanbarian AT, Spiegel J, Martínez Cuesta S, Beraldi D, Di Antonio M, Marsico G, Hänsel-Hertsch R, Tannahill D, Balasubramanian S. Nature structural & molecular biology Volume 25 (2018) p.951-957 DOI: 10.1038/s41594-018-0131-8
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A synthesis approach of mouse studies to identify genes and proteins in arterial thrombosis and bleeding.
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Classification and Personalized Prognosis in Myeloproliferative Neoplasms.
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Minimum Information for Reusable Arthropod Abundance Data (MIReAAD)
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Human genes: Time to follow the roads less traveled?
Dunham I. PLoS biology Volume 16 (2018) p.e3000034 DOI: 10.1371/journal.pbio.3000034
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Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.
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Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. The New England journal of medicine Volume 379 (2018) p.1403-1415 DOI: 10.1056/nejmoa1800474
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Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate.
Tischler J, Gruhn WH, Reid J, Allgeyer E, Buettner F, Marr C, Theis F, Simons BD, Wernisch L, Surani MA. The EMBO journal Volume 38 (2019) DOI: 10.15252/embj.201899518
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Akdemir KC, Le VT, Killcoyne S, King DA, Li Y, Tian Y, Inoue A, Amin S, Robinson FS, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O’Brien J, Li L, Verhaak RG, Campbell P, Fitzgerald R, Morrison AJ, Dixon JR, Andrew Futreal P. Preprint DOI: 10.1101/426080
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Romero JP, Ortiz-Estévez M, Muniategui A, Carrancio S, de Miguel FJ, Carazo F, Montuenga LM, Loos R, Pío R, Trotter MWB, Rubio A. BMC genomics Volume 19 (2018) p.703 DOI: 10.1186/s12864-018-5082-2
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Dawn and photoperiod sensing by phytochrome A.
Seaton DD, Toledo-Ortiz G, Ganpudi A, Kubota A, Imaizumi T, Halliday KJ. Proceedings of the National Academy of Sciences of the United States of America Volume 115 (2018) p.10523-10528 DOI: 10.1073/pnas.1803398115
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Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.
Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J, LifeLines cohort study, BIOS consortium. Nature genetics Volume 50 (2018) p.1524-1532 DOI: 10.1038/s41588-018-0224-7
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Functional characterization of TBR1 variants in neurodevelopmental disorder.
den Hoed J, Sollis E, Venselaar H, Estruch SB, Deriziotis P, Fisher SE. Scientific reports Volume 8 (2018) p.14279 DOI: 10.1038/s41598-018-32053-6
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Optimal Piecewise Linear Regression Algorithm for QSAR Modelling.
Cardoso-Silva J, Papadatos G, Papageorgiou LG, Tsoka S. Molecular informatics Volume 38 (2019) p.e1800028 DOI: 10.1002/minf.201800028
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Protein inference using PIA workflows and PSI standard file formats
Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M. Preprint DOI: 10.1101/424473
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C Silva AS, Palmer A, Kovalev V, Tarasov A, Alexandrov T, Martens L, Degroeve S. Analytical chemistry Volume 90 (2018) p.11636-11642 DOI: 10.1021/acs.analchem.8b03224
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Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
Eduati F, Jaaks P, Merten CA, Garnett MJ, Rodriguez JS. Preprint DOI: 10.1101/422998
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ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature.
Dalkiran A, Rifaioglu AS, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. BMC bioinformatics Volume 19 (2018) p.334 DOI: 10.1186/s12859-018-2368-y
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Discovery of potent and selective Spleen Tyrosine Kinase inhibitors for the topical treatment of inflammatory skin disease.
Barker MD, Liddle J, Atkinson FL, Wilson DM, Dickson MC, Ramirez-Molina C, Lewis H, Davis RP, Somers DO, Neu M, Jones E, Watson R. Bioorganic & medicinal chemistry letters Volume 28 (2018) p.3458-3462 DOI: 10.1016/j.bmcl.2018.09.022
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IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients.
Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, Nava C, Jacquemont ML, Tallot M, Milh M, Edery P, Marzin P, Barcia G, Barnerias C, Besmond C, Bienvenu T, Bruel AL, Brunga L, Ceulemans B, Coubes C, Cristancho AG, Cunningham F, Dehouck MB, Donner EJ, Duban-Bedu B, Dubourg C, Gardella E, Gauthier J, Geneviève D, Gobin-Limballe S, Goldberg EM, Hagebeuk E, Hamdan FF, Hančárová M, Hubert L, Ioos C, Ichikawa S, Janssens S, Journel H, Kaminska A, Keren B, Koopmans M, Lacoste C, Laššuthová P, Lederer D, Lehalle D, Marjanovic D, Métreau J, Michaud JL, Miller K, Minassian BA, Morales J, Moutard ML, Munnich A, Ortiz-Gonzalez XR, Pinard JM, Prchalová D, Putoux A, Quelin C, Rosen AR, Roume J, Rossignol E, Simon MEH, Smol T, Shur N, Shelihan I, Štěrbová K, Vyhnálková E, Vilain C, Soblet J, Smits G, Yang SP, van der Smagt JJ, van Hasselt PM, van Kempen M, Weckhuysen S, Helbig I, Villard L, Héron D, Koeleman B, Møller RS, Lesca G, Helbig KL, Nabbout R, Verbeek NE, Depienne C. Genetics in medicine : official journal of the American College of Medical Genetics Volume 21 (2019) p.837-849 DOI: 10.1038/s41436-018-0268-1
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TRIM21 mediates antibody inhibition of adenovirus-based gene delivery and vaccination.
Bottermann M, Foss S, van Tienen LM, Vaysburd M, Cruickshank J, O'Connell K, Clark J, Mayes K, Higginson K, Hirst JC, McAdam MB, Slodkowicz G, Hutchinson E, Kozik P, Andersen JT, James LC. Proceedings of the National Academy of Sciences of the United States of America Volume 115 (2018) p.10440-10445 DOI: 10.1073/pnas.1806314115
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Metabolic profiling and targeted lipidomics reveals a disturbed lipid profile in mothers and fetuses with intrauterine growth restriction.
Miranda J, Simões RV, Paules C, Cañueto D, Pardo-Cea MA, García-Martín ML, Crovetto F, Fuertes-Martin R, Domenech M, Gómez-Roig MD, Eixarch E, Estruch R, Hansson SR, Amigó N, Cañellas N, Crispi F, Gratacós E. Scientific reports Volume 8 (2018) p.13614 DOI: 10.1038/s41598-018-31832-5
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Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA, HipSci Consortium. Preprint DOI: 10.1101/413047
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Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Scientific reports Volume 8 (2018) p.13537 DOI: 10.1038/s41598-018-31659-0
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COMRADES determines in vivo RNA structures and interactions.
Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA. Nature methods Volume 15 (2018) p.785-788 DOI: 10.1038/s41592-018-0121-0
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HLA-DQA1*05 is associated with the development of antibodies to anti-TNF therapy
Sazonovs A, Kennedy N, Moutsianas L, Heap GA, Rice DL, Reppell M, Bewshea C, Walker G, Perry MH, McDonald TJ, Lees C, Cummings F, Parkes M, Mansfield J, Barrett JC, McGovern D, Goodhand J, Anderson CA, Ahmad T, PANTS consortium. Preprint DOI: 10.1101/410035
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In silico Prioritization of Transporter-Drug Relationships From Drug Sensitivity Screens.
César-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G. Frontiers in pharmacology Volume 9 (2018) p.1011 DOI: 10.3389/fphar.2018.01011
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Dietary supplementation with ferric tyrosine improves zootechnical performance and reduces caecal Campylobacter spp. load in broilers.
Currie D, Green M, Dufailu OA, Matthaios P, Soultanas P, McCartney E, Lester H, Van Den Eede L, Apajalahti J, Mahdavi J. British poultry science Volume 59 (2018) p.646-653 DOI: 10.1080/00071668.2018.1507015
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Visualisation and analysis of RNA-Seq assembly graphs
Nazarie FW, Shih B, Angus T, Barnett MW, Chen S, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen Sv, Enright AJ, Freeman TC. Preprint DOI: 10.1101/409573
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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Guenther U, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Khonsari PE, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O’Donovan C, Pearce JT, Peluso A, Pireddu L, Piras ME, Reed MA, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone S, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. Preprint DOI: 10.1101/409151
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DES-Mutation: System for Exploring Links of Mutations and Diseases.
Kordopati V, Salhi A, Razali R, Radovanovic A, Tifratene F, Uludag M, Li Y, Bokhari A, AlSaieedi A, Bin Raies A, Van Neste C, Essack M, Bajic VB. Scientific reports Volume 8 (2018) p.13359 DOI: 10.1038/s41598-018-31439-w
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Cross-tissue eQTL enrichment of associations in schizophrenia.
Bettella F, Brown AA, Smeland OB, Wang Y, Witoelar A, Buil Demur AA, Thompson WK, Zuber V, Dale AM, Djurovic S, Andreassen OA. PloS one Volume 13 (2018) p.e0202812 DOI: 10.1371/journal.pone.0202812
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Genome Wide Association Mapping of Grain and Straw Biomass Traits in the Rice Bengal and Assam Aus Panel (BAAP) Grown Under Alternate Wetting and Drying and Permanently Flooded Irrigation.
Norton GJ, Travis AJ, Douglas A, Fairley S, Alves EP, Ruang-Areerate P, Naredo MEB, McNally KL, Hossain M, Islam MR, Price AH. Frontiers in plant science Volume 9 (2018) p.1223 DOI: 10.3389/fpls.2018.01223
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Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.
Farmery JHR, Smith ML, NIHR BioResource - Rare Diseases, Lynch AG. Scientific reports Volume 8 (2018) p.13376 DOI: 10.1038/s41598-018-31524-0
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Evaluation of the bacterial diversity of Spanish-type chorizo during the ripening process using high-throughput sequencing and physicochemical characterization.
Juárez-Castelán C, García-Cano I, Escobar-Zepeda A, Azaola-Espinosa A, Álvarez-Cisneros Y, Ponce-Alquicira E. Meat science Volume 150 (2019) p.7-13 DOI: 10.1016/j.meatsci.2018.09.001
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RAFTS3G – An efficient and versatile clustering software to analyses in large protein datasets
Lima Nichio BTd, de Oliveira AMR, de Pierri CR, Costa Santos LG, Vialle RA, Marchaukoski JN, Oliveira Pedrosa Fd, Raittz RT. Preprint DOI: 10.1101/407437
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Two Distinct Patterns of Clostridium difficile Diversity Across Europe Indicating Contrasting Routes of Spread.
Eyre DW, Davies KA, Davis G, Fawley WN, Dingle KE, De Maio N, Karas A, Crook DW, Peto TEA, Walker AS, Wilcox MH, EUCLID Study Group. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Volume 67 (2018) p.1035-1044 DOI: 10.1093/cid/ciy252
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships.
Meyer HV, Birney E. Bioinformatics (Oxford, England) Volume 34 (2018) p.2951-2956 DOI: 10.1093/bioinformatics/bty197
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Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades.
Vialle RA, de Souza JES, Lopes KP, Teixeira DG, Alves Sobrinho PA, Ribeiro-Dos-Santos AM, Furtado C, Sakamoto T, Oliveira Silva FA, Herculano Corrêa de Oliveira E, Hamoy IG, Assumpção PP, Ribeiro-Dos-Santos Â, Santos Lima JPM, Seuánez HN, de Souza SJ, Santos S. Genome biology and evolution Volume 10 (2018) p.2366-2379 DOI: 10.1093/gbe/evy130
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Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.
Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, Gut M, Yaspo ML, Linser M, Lowy E, Datta A, Clarke L, Flicek P, Vingron M, Roos D, van den Berg TK, Heath S, Rico D, Frontini M, Kostadima M, Gut I, Valencia A, Ouwehand WH, Stunnenberg HG, Martens JHA, Kuijpers TW. Cell reports Volume 24 (2018) p.2784-2794 DOI: 10.1016/j.celrep.2018.08.018
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Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins.
Jakubec D, Kratochvíl M, Vymĕtal J, Vondrášek J. PloS one Volume 13 (2018) p.e0203085 DOI: 10.1371/journal.pone.0203085
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Ten simple rules for measuring the impact of workshops.
Sufi S, Nenadic A, Silva R, Duckles B, Simera I, de Beyer JA, Struthers C, Nurmikko-Fuller T, Bellis L, Miah W, Wilde A, Emsley I, Philippe O, Balzano M, Coelho S, Ford H, Jones C, Higgins V. PLoS computational biology Volume 14 (2018) p.e1006191 DOI: 10.1371/journal.pcbi.1006191
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A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours.
Redford L, Alhilal G, Needham S, O'Brien O, Coaker J, Tyson J, Amorim LM, Middleton I, Izuogu O, Arends M, Oniscu A, Alonso ÁM, Laguna SM, Gallon R, Sheth H, Santibanez-Koref M, Jackson MS, Burn J. PloS one Volume 13 (2018) p.e0203052 DOI: 10.1371/journal.pone.0203052
Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.
Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA. Cell systems Volume 7 (2018) p.284-294.e12 DOI: 10.1016/j.cels.2018.06.011
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Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences.
Mason A, Foster D, Bradley P, Golubchik T, Doumith M, Gordon NC, Pichon B, Iqbal Z, Staves P, Crook D, Walker AS, Kearns A, Peto T. Journal of clinical microbiology Volume 56 (2018) DOI: 10.1128/jcm.01815-17
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ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1.
Liu D, Skomorovska Y, Song J, Bowler E, Harris R, Ravasz M, Bai S, Ayati M, Tamai K, Koyuturk M, Yuan X, Wang Z, Wang Y, Ewing RM. Cancer biology & therapy Volume 20 (2019) p.90-100 DOI: 10.1080/15384047.2018.1507256
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Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts.
Sawas T, Killcoyne S, Iyer PG, Wang KK, Smyrk TC, Kisiel JB, Qin Y, Ahlquist DA, Rustgi AK, Costa RJ, Gerstung M, Fitzgerald RC, Katzka DA, OCCAMS Consortium. Gastroenterology Volume 155 (2018) p.1720-1728.e4 DOI: 10.1053/j.gastro.2018.08.036
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Zooplankton monitoring to contribute towards addressing global biodiversity conservation challenges.
Chiba S, Batten S, Martin CS, Ivory S, Miloslavich P, Weatherdon LV. Journal of plankton research Volume 40 (2018) p.509-518 DOI: 10.1093/plankt/fby030
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Approaches for containerized scientific workflows in cloud environments with applications in life science
Spjuth O, Capuccini M, Carone M, Larsson A, Schaal W, Novella J, Di Tommaso P, Notredame C, Moreno P, Khoonsari PE, Herman S, Kultima K, Lampa S. Preprint DOI: 10.7287/peerj.preprints.27141v1
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The germline genetic component of drug sensitivity in cancer cell lines.
Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O. Nature communications Volume 9 (2018) p.3385 DOI: 10.1038/s41467-018-05811-3
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Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol.
Murillo JR, Pla I, Goto-Silva L, Nogueira FCS, Domont GB, Perez-Riverol Y, Sánchez A, Junqueira M. Analytical biochemistry Volume 559 (2018) p.51-54 DOI: 10.1016/j.ab.2018.08.013
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The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus.
Morales-Hojas R, Hinsley M, Armean IM, Silk R, Harrup LE, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick WJ, Kersey P, Carpenter S, Fife M. BMC genomics Volume 19 (2018) p.624 DOI: 10.1186/s12864-018-5014-1
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Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape
Park J, Polański K, Meyer K, Teichmann SA. Preprint DOI: 10.1101/397042
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Selecting causal risk factors from high-throughput experiments using multivariable Mendelian randomization
Zuber V, Colijn JM, Klaver C, Burgess S. Preprint DOI: 10.1101/396333
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Evolution of Protein Ductility in Duplicated Genes of Plants.
Yruela I, Contreras-Moreira B, Dunker AK, Niklas KJ. Frontiers in plant science Volume 9 (2018) p.1216 DOI: 10.3389/fpls.2018.01216
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Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation.
Hanson RM, Musacchio S, Mayfield JW, Vainio MJ, Yerin A, Redkin D. Journal of chemical information and modeling Volume 58 (2018) p.1755-1765 DOI: 10.1021/acs.jcim.8b00324
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High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms.
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The first single particle analysis Map Challenge: A summary of the assessments.
Heymann JB, Marabini R, Kazemi M, Sorzano COS, Holmdahl M, Mendez JH, Stagg SM, Jonic S, Palovcak E, Armache JP, Zhao J, Cheng Y, Pintilie G, Chiu W, Patwardhan A, Carazo JM. Journal of structural biology Volume 204 (2018) p.291-300 DOI: 10.1016/j.jsb.2018.08.010
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. BMC genomics Volume 19 (2018) p.604 DOI: 10.1186/s12864-018-4989-y
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Terminal uridylyltransferases target RNA viruses as part of the innate immune system.
Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA. Nature structural & molecular biology Volume 25 (2018) p.778-786 DOI: 10.1038/s41594-018-0106-9
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Conserved phosphorylation hotspots in eukaryotic protein domain families
Strumillo MJ, Oplová M, Viéitez C, Ochoa D, Shahraz M, Busby BP, Sopko R, Studer RA, Perrimon N, Panse VG, Beltrao P. Preprint DOI: 10.1101/391185
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Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
Lee K, Famiglietti ML, McMahon A, Wei CH, MacArthur JAL, Poux S, Breuza L, Bridge A, Cunningham F, Xenarios I, Lu Z. PLoS computational biology Volume 14 (2018) p.e1006390 DOI: 10.1371/journal.pcbi.1006390
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Genomic landscape and chronological reconstruction of driver events in multiple myeloma
Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JMC, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, Campbell PJ. Preprint DOI: 10.1101/388611
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The Standard Output: A Tool-Agnostic Modeling Storage Format.
Terranova N, Smith MK, Nordgren R, Comets E, Lavielle M, Harling K, Hooker AC, Sarr C, Mentré F, Yvon F, Swat MJ. CPT: pharmacometrics & systems pharmacology Volume 7 (2018) p.543-546 DOI: 10.1002/psp4.12339
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A molecular signature for delayed graft function.
McGuinness D, Mohammed S, Monaghan L, Wilson PA, Kingsmore DB, Shapter O, Stevenson KS, Coley SM, Devey L, Kirkpatrick RB, Shiels PG. Aging cell Volume 17 (2018) p.e12825 DOI: 10.1111/acel.12825
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Adaptation of proteins to the cold in Antarctic fish: A role for Methionine?
Berthelot C, Clarke J, Desvignes T, Detrich HW, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Preprint DOI: 10.1101/388900
Gene expression-based drug repurposing to target aging.
Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM. Aging cell Volume 17 (2018) p.e12819 DOI: 10.1111/acel.12819
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Improving sample classification by harnessing the potential of 1H-NMR signal chemical shifts.
Cañueto D, Salek RM, Correig X, Cañellas N. Scientific reports Volume 8 (2018) p.11886 DOI: 10.1038/s41598-018-30351-7
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Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach.
Brandizi M, Singh A, Rawlings C, Hassani-Pak K. Journal of integrative bioinformatics Volume 15 (2018) DOI: 10.1515/jib-2018-0023
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Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history
Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane T, Hubbard T, Harrow J, Gerstein M. Preprint DOI: 10.1101/386656
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Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
Boroviak T, Stirparo GG, Dietmann S, Hernando-Herraez I, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P. Preprint DOI: 10.1101/385815
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Disruption of TWIST1 translation by 5' UTR variants in Saethre-Chotzen syndrome.
Zhou Y, Koelling N, Fenwick AL, McGowan SJ, Calpena E, Wall SA, Smithson SF, Wilkie AOM, Twigg SRF. Human mutation Volume 39 (2018) p.1360-1365 DOI: 10.1002/humu.23598
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CTCF maintains regulatory homeostasis of cancer pathways.
Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT. Genome biology Volume 19 (2018) p.106 DOI: 10.1186/s13059-018-1484-3
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Genome-wide identification of directed gene networks using large-scale population genomics data.
Luijk R, Dekkers KF, van Iterson M, Arindrarto W, Claringbould A, Hop P, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, Franke L, 't Hoen PAC, Jansen R, van Meurs J, Mei H, Slagboom PE, Heijmans BT, van Zwet EW, BIOS (Biobank-based Integrative Omics Study) Consortium. Nature communications Volume 9 (2018) p.3097 DOI: 10.1038/s41467-018-05452-6
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Common ELIXIR Service for Researcher Authentication and Authorisation
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BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq.
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Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.
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A roadmap for restoring trust in Big Data.
Lawler M, Morris AD, Sullivan R, Birney E, Middleton A, Makaroff L, Knoppers BM, Horgan D, Eggermont A. The Lancet. Oncology Volume 19 (2018) p.1014-1015 DOI: 10.1016/s1470-2045(18)30425-x
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The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
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Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes.
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NonA and CPX Link the Circadian Clockwork to Locomotor Activity in Drosophila.
Luo W, Guo F, McMahon A, Couvertier S, Jin H, Diaz M, Fieldsend A, Weerapana E, Rosbash M. Neuron Volume 99 (2018) p.768-780.e3 DOI: 10.1016/j.neuron.2018.07.001
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Kipoi: accelerating the community exchange and reuse of predictive models for genomics
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Functional confirmation that the R1488* variant in SCN9A results in complete loss-of-function of Nav1.7.
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PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping
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A recent advance in the intracellular and extracellular redox post-translational modification of proteins in plants.
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Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study.
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T cell cytolytic capacity is independent of initial stimulation strength.
Richard AC, Lun ATL, Lau WWY, Göttgens B, Marioni JC, Griffiths GM. Nature immunology Volume 19 (2018) p.849-858 DOI: 10.1038/s41590-018-0160-9
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An enhanced CRISPR repressor for targeted mammalian gene regulation.
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Expanding the Rubterolone Family: Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans.
Guo H, Benndorf R, König S, Leichnitz D, Weigel C, Peschel G, Berthel P, Kaiser M, Steinbeck C, Werz O, Poulsen M, Beemelmanns C. Chemistry (Weinheim an der Bergstrasse, Germany) Volume 24 (2018) p.11319-11324 DOI: 10.1002/chem.201802066
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The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.
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A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity.
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Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates.
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Cancer incidence and mortality rates and trends in Trinidad and Tobago.
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Nearly all new protein-coding predictions in the CHESS database are not protein-coding
Jungreis I, Tress ML, Mudge J, Sisu C, Hunt T, Johnson R, Uszczynska-Ratajczak B, Lagarde J, Wright J, Muir P, Gerstein M, Guigo R, Kellis M, Frankish A, Flicek P, The GENCODE Consortium. Preprint DOI: 10.1101/360602
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UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites.
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A High-Resolution Genetic Map for the Laboratory Rat.
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Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J, Medina-Rivera A, Thomas-Chollier M. Nucleic acids research Volume 46 (2018) p.W209-W214 DOI: 10.1093/nar/gky317
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Vialle RA, Tamuri AU, Goldman N. Molecular biology and evolution Volume 35 (2018) p.1783-1797 DOI: 10.1093/molbev/msy055
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Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
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Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.
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The Human Cell Atlas: Technical approaches and challenges.
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Zhao L, Hansard M, Cavallaro A. IEEE transactions on visualization and computer graphics Volume 24 (2018) p.2167-2179 DOI: 10.1109/tvcg.2017.2708108
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The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.
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The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis.
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Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders.
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A correction for sample overlap in genome-wide association studies in a polygenic pleiotropy-informed framework.
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HmtVar: a brand-new resource for human mitochondrial variations and pathogenicity data
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Understanding trivial challenges of microbial genomics: An assembly example
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The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.
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Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy
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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
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In vivo and in vitro identification of Z-BOX C - a new bilirubin oxidation end product.
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A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.
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Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.
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GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.
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Defective germline reprogramming rewires the spermatogonial transcriptome.
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Protease Activities Triggered by Ralstonia solanacearum Infection in Susceptible and Tolerant Tomato Lines.
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PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
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A comprehensive genomic history of extinct and living elephants.
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A functional landscape of chronic kidney disease entities from public transcriptomic data
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Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction
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NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.
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The development and application of bioinformatics core competencies to improve bioinformatics training and education.
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The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
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rDolphin: a GUI R package for proficient automatic profiling of 1D 1H-NMR spectra of study datasets.
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LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies
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Computational modelling of atherosclerosis: developing a community resource
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Genome watch: Keeping tally in the microbiome.
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Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.
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Spatiotemporal patterning of EpCAM is important for murine embryonic endo- and mesodermal differentiation.
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Spin Crossover in a Hexaamineiron(II) Complex: Experimental Confirmation of a Computational Prediction.
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A SNP panel for identification of DNA and RNA specimens.
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CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation.
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Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping.
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Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution.
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Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.
Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Nature genetics Volume 50 (2018) p.307-316 DOI: 10.1038/s41588-017-0029-0
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Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.
Farmery JHR, Smith ML, NIHR BioResource - Rare Diseases, Lynch AG. Scientific reports Volume 8 (2018) p.1300 DOI: 10.1038/s41598-017-14403-y
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Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
Bonàs-Guarch S, Guindo-Martínez M, Miguel-Escalada I, Grarup N, Sebastian D, Rodriguez-Fos E, Sánchez F, Planas-Fèlix M, Cortes-Sánchez P, González S, Timshel P, Pers TH, Morgan CC, Moran I, Atla G, González JR, Puiggros M, Martí J, Andersson EA, Díaz C, Badia RM, Udler M, Leong A, Kaur V, Flannick J, Jørgensen T, Linneberg A, Jørgensen ME, Witte DR, Christensen C, Brandslund I, Appel EV, Scott RA, Luan J, Langenberg C, Wareham NJ, Pedersen O, Zorzano A, Florez JC, Hansen T, Ferrer J, Mercader JM, Torrents D. Nature communications Volume 9 (2018) p.321 DOI: 10.1038/s41467-017-02380-9
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MIRO: guidelines for minimum information for the reporting of an ontology.
Matentzoglu N, Malone J, Mungall C, Stevens R. Journal of biomedical semantics Volume 9 (2018) p.6 DOI: 10.1186/s13326-017-0172-7
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Identification of genetic elements in metabolism by high-throughput mouse phenotyping.
Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H, IMPC Consortium, Hough T, Mallon AM, Wells S, Santos L, Lelliott CJ, White JK, Sorg T, Champy MF, Bower LR, Reynolds CL, Flenniken AM, Murray SA, Nutter LMJ, Svenson KL, West D, Tocchini-Valentini GP, Beaudet AL, Bosch F, Braun RB, Dobbie MS, Gao X, Herault Y, Moshiri A, Moore BA, Kent Lloyd KC, McKerlie C, Masuya H, Tanaka N, Flicek P, Parkinson HE, Sedlacek R, Seong JK, Wang CL, Moore M, Brown SD, Tschöp MH, Wurst W, Klingenspor M, Wolf E, Beckers J, Machicao F, Peter A, Staiger H, Häring HU, Grallert H, Campillos M, Maier H, Fuchs H, Gailus-Durner V, Werner T, Hrabe de Angelis M. Nature communications Volume 9 (2018) p.288 DOI: 10.1038/s41467-017-01995-2
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Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.
Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM. eLife Volume 7 (2018) DOI: 10.7554/elife.30224
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Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle.
Villarreal-Ramos B, Berg S, Whelan A, Holbert S, Carreras F, Salguero FJ, Khatri BL, Malone K, Rue-Albrecht K, Shaughnessy R, Smyth A, Ameni G, Aseffa A, Sarradin P, Winter N, Vordermeier M, Gordon SV. Scientific reports Volume 8 (2018) p.894 DOI: 10.1038/s41598-017-18575-5
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The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for Bluetongue virus
Morales-Hojas R, Hinsley M, Armean IM, Silk R, Harrup LE, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick WJ, Kersey P, Carpenter S, Fife M. Preprint DOI: 10.1101/249482
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Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient.
Brener J, Gall A, Hurst J, Batorsky R, Lavandier N, Chen F, Edwards A, Bolton C, Dsouza R, Allen T, Pybus OG, Kellam P, Matthews PC, Goulder PJR. Retrovirology Volume 15 (2018) p.7 DOI: 10.1186/s12977-018-0390-9
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A quantitative and temporal map of proteostasis during heat shock in Saccharomyces cerevisiae.
Jarnuczak AF, Albornoz MG, Eyers CE, Grant CM, Hubbard SJ. Molecular omics Volume 14 (2018) p.37-52 DOI: 10.1039/c7mo00050b
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Identification of shared genetic variants between schizophrenia and lung cancer.
Zuber V, Jönsson EG, Frei O, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Smeland OB, Dieset I, Fanous AH, Desikan RS, Küry S, Bézieau S, Dale AM, Mills IG, Andreassen OA. Scientific reports Volume 8 (2018) p.674 DOI: 10.1038/s41598-017-16481-4
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.
Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G, Lönnberg T. Scientific reports Volume 8 (2018) p.685 DOI: 10.1038/s41598-017-19100-4
Designing an intuitive web application for drug discovery scientists.
Karamanis N, Pignatelli M, Carvalho-Silva D, Rowland F, Cham JA, Dunham I. Drug discovery today Volume 23 (2018) p.1169-1174 DOI: 10.1016/j.drudis.2018.01.032
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DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing.
Anson LW, Chau K, Sanderson N, Hoosdally S, Bradley P, Iqbal Z, Phan H, Foster D, Oakley S, Morgan M, Peto TEA, Modernizing Medical Microbiology Informatics Group Mmmig, Crook DW, Pankhurst LJ. Journal of medical microbiology Volume 67 (2018) p.347-357 DOI: 10.1099/jmm.0.000664
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Improving communication for interdisciplinary teams working on storage of digital information in DNA.
Hesketh EE, Sayir J, Goldman N. F1000Research Volume 7 (2018) p.39 DOI: 10.12688/f1000research.13482.1
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Polygenic hazard score to guide screening for aggressive prostate cancer: development and validation in large scale cohorts.
Seibert TM, Fan CC, Wang Y, Zuber V, Karunamuni R, Parsons JK, Eeles RA, Easton DF, Kote-Jarai Z, Al Olama AA, Garcia SB, Muir K, Grönberg H, Wiklund F, Aly M, Schleutker J, Sipeky C, Tammela TL, Nordestgaard BG, Nielsen SF, Weischer M, Bisbjerg R, Røder MA, Iversen P, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Brenner H, Cuk K, Saum KU, Park JY, Sellers TA, Slavov C, Kaneva R, Mitev V, Batra J, Clements JA, Spurdle A, Teixeira MR, Paulo P, Maia S, Pandha H, Michael A, Kierzek A, Karow DS, Mills IG, Andreassen OA, Dale AM, PRACTICAL Consortium*. BMJ (Clinical research ed.) Volume 360 (2018) p.j5757 DOI: 10.1136/bmj.j5757
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Integrated omics dissection of proteome dynamics during cardiac remodeling.
Lau E, Cao Q, Lam MPY, Wang J, Ng DCM, Bleakley BJ, Lee JM, Liem DA, Wang D, Hermjakob H, Ping P. Nature communications Volume 9 (2018) p.120 DOI: 10.1038/s41467-017-02467-3
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Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.
Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Nature cell biology Volume 20 (2018) p.127-134 DOI: 10.1038/s41556-017-0013-z
Evolution, dynamics and dysregulation of kinase signalling.
Ochoa D, Bradley D, Beltrao P. Current opinion in structural biology Volume 48 (2018) p.133-140 DOI: 10.1016/j.sbi.2017.12.008
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A systematic atlas of chaperome deregulation topologies across the human cancer landscape.
Hadizadeh Esfahani A, Sverchkova A, Saez-Rodriguez J, Schuppert AA, Brehme M. PLoS computational biology Volume 14 (2018) p.e1005890 DOI: 10.1371/journal.pcbi.1005890
Perturbation-response genes reveal signaling footprints in cancer gene expression.
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Nature communications Volume 9 (2018) p.20 DOI: 10.1038/s41467-017-02391-6
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A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity.
Buryska T, Babkova P, Vavra O, Damborsky J, Prokop Z. Applied and environmental microbiology Volume 84 (2018) DOI: 10.1128/aem.01684-17
Data visualisation 101: A practical introduction to designing scientific Figures
Karamanis N. DOI: 10.6019/tol.datavis-w.2018.00001.1
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Kersey PJ, Allen JE, Allot A, Barba M, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Grabmueller C, Kumar N, Liu Z, Maurel T, Moore B, McDowall MD, Maheswari U, Naamati G, Newman V, Ong CK, Paulini M, Pedro H, Perry E, Russell M, Sparrow H, Tapanari E, Taylor K, Vullo A, Williams G, Zadissia A, Olson A, Stein J, Wei S, Tello-Ruiz M, Ware D, Luciani A, Potter S, Finn RD, Urban M, Hammond-Kosack KE, Bolser DM, De Silva N, Howe KL, Langridge N, Maslen G, Staines DM, Yates A. Nucleic acids research Volume 46 (2018) p.D802-D808 DOI: 10.1093/nar/gkx1011
EMBL-EBI resources: An introduction
Gopalasingam P. DOI: 10.6019/tol.intr-ebi-res-w.2015.00001.1
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A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.
Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH. Stem cell reports Volume 10 (2018) p.1-6 DOI: 10.1016/j.stemcr.2017.12.002
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PITDB: a database of translated genomic elements.
Saha S, Chatzimichali EA, Matthews DA, Bessant C. Nucleic acids research Volume 46 (2018) p.D1223-D1228 DOI: 10.1093/nar/gkx906
Europe PMC in 2017.
Levchenko M, Gou Y, Graef F, Hamelers A, Huang Z, Ide-Smith M, Iyer A, Kilian O, Katuri J, Kim JH, Marinos N, Nambiar R, Parkin M, Pi X, Rogers F, Talo F, Vartak V, Venkatesan A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1254-D1260 DOI: 10.1093/nar/gkx1005
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WormBase 2017: molting into a new stage.
Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C, Kishore R, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers F, Russell M, Schindelman G, Tuli MA, Van Auken K, Wang Q, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW. Nucleic acids research Volume 46 (2018) p.D869-D874 DOI: 10.1093/nar/gkx998
AmyPro: a database of proteins with validated amyloidogenic regions.
Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R. Nucleic acids research Volume 46 (2018) p.D387-D392 DOI: 10.1093/nar/gkx950
HMMER: Fast and sensitive sequence similarity searches
Finn R. DOI: 10.6019/tol.hmmer-w.2018.00001.1
Extracting gene-disease evidence from literature, genetics, genomics and more
Carvalho-Silva D, Levchenko M. DOI: 10.6019/tol.gene-disease-w.2018.00001.1
The European Bioinformatics Institute in 2017: data coordination and integration.
Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E. Nucleic acids research Volume 46 (2018) p.D21-D29 DOI: 10.1093/nar/gkx1154
Analysing and visualising microbiome-derived datasets using the MGnify Web API
Tarkowska O. DOI: 10.6019/tol.mgnify-w.2018.00001.1
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Antibody-mediated modulation of cytokinins in tobacco: organ-specific changes in cytokinin homeostasis.
Gelová Z, Ten Hoopen P, Novák O, Motyka V, Pernisová M, Dabravolski S, Didi V, Tillack I, Okleštková J, Strnad M, Hause B, Haruštiaková D, Conrad U, Janda L, Hejátko J. Journal of experimental botany Volume 69 (2018) p.441-454 DOI: 10.1093/jxb/erx426
Ensembl variation resources.
Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P, Cunningham F. Database : the journal of biological databases and curation Volume 2018 (2018) DOI: 10.1093/database/bay119
The BioStudies database-one stop shop for all data supporting a life sciences study.
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1266-D1270 DOI: 10.1093/nar/gkx965
Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.
Bolt BJ, Rodgers FH, Shafie M, Kersey PJ, Berriman M, Howe KL. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.471-491 DOI: 10.1007/978-1-4939-7737-6_15
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The SysteMHC Atlas project.
Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E. Nucleic acids research Volume 46 (2018) p.D1237-D1247 DOI: 10.1093/nar/gkx664
Automatic annotation systems in UniProt
Pichler K, Renaux A. DOI: 10.6019/tol.uniprot_annot-w.2018.00001.1
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Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.
Grove C, Cain S, Chen WJ, Davis P, Harris T, Howe KL, Kishore R, Lee R, Paulini M, Raciti D, Tuli MA, Van Auken K, Williams G, WormBase Consortium. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.399-470 DOI: 10.1007/978-1-4939-7737-6_14
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The international nucleotide sequence database collaboration.
Karsch-Mizrachi I, Takagi T, Cochrane G, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 46 (2018) p.D48-D51 DOI: 10.1093/nar/gkx1097
Bringing data to life: data management for the biomolecular sciences
Teperek M, Türkyilmaz-van der Velden Y, Birney E, Busch-Nentwich E, George N, Cochrane K, Levchenko M, Sarntivijai S, Jones S, Hooft R, Morgan S, Burke M. DOI: 10.6019/tol.data_management-w.2018.00001.1
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Saccharomyces genome database informs human biology.
Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM. Nucleic acids research Volume 46 (2018) p.D736-D742 DOI: 10.1093/nar/gkx1112
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The Encyclopedia of DNA elements (ENCODE): data portal update.
Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK, Narayanan AK, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Cherry JM. Nucleic acids research Volume 46 (2018) p.D794-D801 DOI: 10.1093/nar/gkx1081
Ensembl 2018.
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P. Nucleic acids research Volume 46 (2018) p.D754-D761 DOI: 10.1093/nar/gkx1098
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Nucleic acids research Volume 46 (2018) p.D618-D623 DOI: 10.1093/nar/gkx1012
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Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes.
Cornelissen M, Gall A, van der Kuyl A, Wymant C, Blanquart F, Fraser C, Berkhout B. Methods in molecular biology (Clifton, N.J.) Volume 1746 (2018) p.55-61 DOI: 10.1007/978-1-4939-7683-6_5
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In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson's Disease.
Lemos A, Melo R, Preto AJ, Almeida JG, Moreira IS, Dias Soeiro Cordeiro MN. Current neuropharmacology Volume 16 (2018) p.786-848 DOI: 10.2174/1570159x16666180308161642
The European Nucleotide Archive in 2017.
Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 46 (2018) p.D36-D40 DOI: 10.1093/nar/gkx1125
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Computational Approaches in Antibody-drug Conjugate Optimization for Targeted Cancer Therapy.
Melo R, Lemos A, Preto AJ, Almeida JG, Correia JDG, Sensoy O, Moreira IS. Current topics in medicinal chemistry Volume 18 (2018) p.1091-1109 DOI: 10.2174/1568026618666180731165222
The eukaryotic linear motif resource - 2018 update.
Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. Nucleic acids research Volume 46 (2018) p.D428-D434 DOI: 10.1093/nar/gkx1077
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S. Nucleic acids research Volume 46 (2018) p.D486-D492 DOI: 10.1093/nar/gkx1070
Repeats in Pfam
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam_repeats-t.2018.00001.1
EBI Search as a service
Park Y. DOI: 10.6019/tol.ebi_search-w.2018.00001.1
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DISNOR: a disease network open resource.
Lo Surdo P, Calderone A, Iannuccelli M, Licata L, Peluso D, Castagnoli L, Cesareni G, Perfetto L. Nucleic acids research Volume 46 (2018) p.D527-D534 DOI: 10.1093/nar/gkx876
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A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules.
Demirel HC, Dogan T, Tuncbag N. Current topics in medicinal chemistry Volume 18 (2018) p.700-713 DOI: 10.2174/1568026618666180601080824
Detection and evolution of repetitive proteins
Laifta Masip A. DOI: 10.6019/tol.evol-prot-w.2018.00001.1
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S, Boland MA, Hunter FMI, Ten Hoopen P, Alako B, Amid C, Wilkinson DJ, Curtis TP, Cochrane G, Finn RD. Nucleic acids research Volume 46 (2018) p.D726-D735 DOI: 10.1093/nar/gkx967
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Nucleic acids research Volume 46 (2018) p.D335-D342 DOI: 10.1093/nar/gkx1038
Pfam Database: Creating Protein Families
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam_fams-t.2018.00001.1
Genome Properties: Tutorial
Richardson L. DOI: 10.6019/tol.genprop-t.2018.00001.1
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ChannelsDB: database of biomacromolecular tunnels and pores.
Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J. Nucleic acids research Volume 46 (2018) p.D399-D405 DOI: 10.1093/nar/gkx868
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Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C, BEEHIVE Collaboration. Virus evolution Volume 4 (2018) p.vey007 DOI: 10.1093/ve/vey007
PhenoMeNal: Metabolomics data analysis in the cloud
Pireddu L, Moreno P. DOI: 10.6019/tol.phenomenal-w.2017.00001.1
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Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.
Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD. Nucleic acids research Volume 46 (2018) p.D221-D228 DOI: 10.1093/nar/gkx1031
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Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK. Database : the journal of biological databases and curation Volume 2018 (2018) DOI: 10.1093/database/bay002
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Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites.
Atas H, Tuncbag N, Doğan T. Methods in molecular biology (Clifton, N.J.) Volume 1762 (2018) p.51-69 DOI: 10.1007/978-1-4939-7756-7_4
Mouse strains in Ensembl
Haskell E. DOI: 10.6019/tol.ensembl_mouse-w.2018.00001.1
Expression Atlas: gene and protein expression across multiple studies and organisms.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Nucleic acids research Volume 46 (2018) p.D246-D251 DOI: 10.1093/nar/gkx1158
Bioinformatics Sequence Analysis Web Services with Job Dispatcher
Madeira F. DOI: 10.6019/tol.bio_seq-w.2018.00001.1
The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data.
Newman V, Moore B, Sparrow H, Perry E. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.115-139 DOI: 10.1007/978-1-4939-7737-6_6
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Evaluation of Protein-Ligand Docking by Cyscore.
Cao Y, Dai W, Miao Z. Methods in molecular biology (Clifton, N.J.) Volume 1762 (2018) p.233-243 DOI: 10.1007/978-1-4939-7756-7_12
Ensembl REST API
Perry E. DOI: 10.6019/tol.ensembl_api-t.2018.00001.1
BioModels: expanding horizons to include more modelling approaches and formats.
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H. Nucleic acids research Volume 46 (2018) p.D1248-D1253 DOI: 10.1093/nar/gkx1023
ProteomeXchange submissions via PRIDE
Vizcaino JA, Ternent T, Sehra M, Csordas A. DOI: 10.6019/tol.pxd-t.2014.00001.1
The Reactome Pathway Knowledgebase.
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 46 (2018) p.D649-D655 DOI: 10.1093/nar/gkx1132
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Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. Nucleic acids research Volume 46 (2018) p.D1181-D1189 DOI: 10.1093/nar/gkx1111
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S, Quest for Orthologs Consortium . Bioinformatics (Oxford, England) Volume 34 (2018) p.323-329 DOI: 10.1093/bioinformatics/btx542
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Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes.
Graham AM, Lavretsky P, Muñoz-Fuentes V, Green AJ, Wilson RE, McCracken KG. Genome biology and evolution Volume 10 (2018) p.14-32 DOI: 10.1093/gbe/evx253
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. Nucleic acids research Volume 46 (2018) p.D624-D632 DOI: 10.1093/nar/gkx1134
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Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.
Wirbel J, Cutillas P, Saez-Rodriguez J. Methods in molecular biology (Clifton, N.J.) Volume 1711 (2018) p.103-132 DOI: 10.1007/978-1-4939-7493-1_6
Searching and Extracting Data from the EMBL-EBI Complex Portal.
Meldal BHM, Orchard S. Methods in molecular biology (Clifton, N.J.) Volume 1764 (2018) p.377-390 DOI: 10.1007/978-1-4939-7759-8_24
Complex Portal: Quick tour
Meldal B. DOI: 10.6019/tol.comport-w.2015.00001.1
Preprint discovery 101: Tips & tricks for authors and readers
Levchenko M. DOI: 10.6019/tol.preprint-w.2018.00001.1
Effective Literature Research with Europe PMC
Levchenko M. DOI: 10.6019/tol.europepmc-w.2018.00001.1
Hands-on on Protein Function Prediction with Machine Learning and Interactive Analytics
Saidi R. DOI: 10.6019/tol.unip_machine-w.2018.00001.1

2017

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A Novel Long Non-Coding RNA in the hTERT Promoter Region Regulates hTERT Expression.
Malhotra S, Freeberg MA, Winans SJ, Taylor J, Beemon KL. Non-coding RNA Volume 4 (2017) DOI: 10.3390/ncrna4010001
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Genome-wide evolutionary dynamics of influenza B viruses on a global scale.
Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ. PLoS pathogens Volume 13 (2017) p.e1006749 DOI: 10.1371/journal.ppat.1006749
Phenotype inference in an Escherichia coli strain panel.
Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. eLife Volume 6 (2017) DOI: 10.7554/elife.31035
A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it.
Spicer RA, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 14 (2018) p.16 DOI: 10.1007/s11306-017-1309-5
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Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
Rheinbay E, Nielsen MM, Abascal F, Tiao G, Hornshøj H, Hess JM, Pedersen RI, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bertl J, Dhingra P, Diamanti K, Gonzalez-Perez A, Guo Q, Haradhvala NJ, Isaev K, Juul M, Komorowski J, Kumar S, Lee D, Lochovsky L, Liu EM, Pich O, Tamborero D, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Zhang J, Boroevich KA, Carlevaro-Fita J, Chakravarty D, Chan CW, Fonseca NA, Hamilton MP, Hong C, Kahles A, Kim Y, Lehmann K, Johnson TA, Kahraman A, Park K, Saksena G, Sieverling L, Sinnott-Armstrong NA, Campbell PJ, Hobolth A, Kellis M, Lawrence MS, Raphael B, Rubin MA, Sander C, Stein L, Stuart J, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein MB, Khurana E, López-Bigas N, Martincorena I, Pedersen JS, Getz G. Preprint DOI: 10.1101/237313
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CYRI1-mediated inhibition of RAC1 signalling restricts Salmonella Typhimurium infection
Yuki KE, Marei H, Fiskin E, Eva MM, Gopal AA, Schwartzentruber JA, Majewski J, Cellier M, Mandl JN, Vidal SM, Malo D, Dikic I. Preprint DOI: 10.1101/238733
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.
Martín-Gálvez D, Dunoyer de Segonzac D, Ma MCJ, Kwitek AE, Thybert D, Flicek P. BMC genomics Volume 18 (2017) p.986 DOI: 10.1186/s12864-017-4351-9
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Comparative analysis of neutrophil and monocyte epigenomes
Rico D, Martens JH, Downes K, Carrillo-de-Santa-Pau E, Pancaldi V, Breschi A, Richardson D, Heath S, Saeed S, Frontini M, Chen L, Watt S, Müller F, Clarke L, Kerstens HH, Wilder SP, Palumbo E, Djebali S, Raineri E, Merkel A, Esteve-Codina A, Sultan M, van Bommel A, Gut M, Yaspo M, Rubio M, Fernandez JM, Attwood A, de la Torre V, Royo R, Fragkogianni S, Gelpí JL, Torrents D, Iotchkova V, Logie C, Aghajanirefah A, Singh AA, Janssen-Megens EM, Berentsen K, Erber W, Rendon A, Kostadima M, Loos R, van der Ent MA, Kaan A, Sharifi N, Paul DS, Ifrim DC, Quintin J, Love MI, Pisano DG, Burden F, Foad N, Farrow S, Zerbino DR, Dunham I, Kuijpers T, Lehrach H, Lengauer T, Bertone P, Netea MG, Vingron M, Beck S, Flicek P, Gut I, Ouwehand WH, Bock C, Soranzo N, Guigo R, Valencia A, Stunnenberg HG. Preprint DOI: 10.1101/237784
Cell ontology in an age of data-driven cell classification.
Osumi-Sutherland D. BMC bioinformatics Volume 18 (2017) p.558 DOI: 10.1186/s12859-017-1980-6
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Usage of cell nomenclature in biomedical literature.
Kafkas Ş, Sarntivijai S, Hoehndorf R. BMC bioinformatics Volume 18 (2017) p.561 DOI: 10.1186/s12859-017-1978-0
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RNA-Seq Analysis of an Antisense Sequence Optimized for Exon Skipping in Duchenne Patients Reveals No Off-Target Effect.
Domenger C, Allais M, François V, Léger A, Lecomte E, Montus M, Servais L, Voit T, Moullier P, Audic Y, Le Guiner C. Molecular therapy. Nucleic acids Volume 10 (2018) p.277-291 DOI: 10.1016/j.omtn.2017.12.008
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Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Cell chemical biology Volume 25 (2018) p.224-229.e2 DOI: 10.1016/j.chembiol.2017.11.009
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Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
Ong E, Xie J, Ni Z, Liu Q, Sarntivijai S, Lin Y, Cooper D, Terryn R, Stathias V, Chung C, Schürer S, He Y. BMC bioinformatics Volume 18 (2017) p.556 DOI: 10.1186/s12859-017-1981-5
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
Sarntivijai S, Diehl AD, He Y. BMC bioinformatics Volume 18 (2017) p.560 DOI: 10.1186/s12859-017-1976-2
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Comparison, alignment, and synchronization of cell line information between CLO and EFO.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y. BMC bioinformatics Volume 18 (2017) p.557 DOI: 10.1186/s12859-017-1979-z
Accurate and fast feature selection workflow for high-dimensional omics data.
Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP, Audain E. PloS one Volume 12 (2017) p.e0189875 DOI: 10.1371/journal.pone.0189875
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Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines.
Turner TR, Hayhurst JD, Hayward DR, Bultitude WP, Barker DJ, Robinson J, Madrigal JA, Mayor NP, Marsh SGE. HLA Volume 91 (2018) p.88-101 DOI: 10.1111/tan.13184
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A protein standard that emulates homology for the characterization of protein inference algorithms
The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. Preprint DOI: 10.1101/236471
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Severe infections emerge from commensal bacteria by adaptive evolution.
Young BC, Wu CH, Gordon NC, Cole K, Price JR, Liu E, Sheppard AE, Perera S, Charlesworth J, Golubchik T, Iqbal Z, Bowden R, Massey RC, Paul J, Crook DW, Peto TE, Walker AS, Llewelyn MJ, Wyllie DH, Wilson DJ. eLife Volume 6 (2017) DOI: 10.7554/elife.30637
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MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.
Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY. Analytical chemistry Volume 90 (2018) p.685-689 DOI: 10.1021/acs.analchem.7b03544
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Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD. Genome research Volume 28 (2018) p.203-213 DOI: 10.1101/gr.225615.117
Expression Atlas: Quick tour
Huerta L. DOI: 10.6019/tol.exatlas-qt.2017.00001.1
Open Targets: Mining gene and disease associations for improved drug target identification
Carvalho-Silva D. DOI: 10.6019/tol.opentargets-w.2017.00001.1
Finding the best data for your needs in the PDB archive
Conroy M. DOI: 10.6019/tol.pdbenov17-w.2017.00001.1
Enzymes in UniProt
Zaru R. DOI: 10.6019/tol.unip-enzymes-w.2017.00001.1
GWAS Catalog: Exploring SNP-trait associations
Emery L, MacArthur J. DOI: 10.6019/tol.gwas-t.2017.00001.1
Navigating the data-rich literature: finding evidence in biomedical publications
Levchenko M. DOI: 10.6019/tol.epmc_oct-w.2017.00001.1
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The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
Pramanik J, Chen X, Kar G, Gomes T, Henriksson J, Miao Z, Natarajan K, McKenzie ANJ, Mahata B, Teichmann SA. Preprint DOI: 10.1101/235010
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Real-time search of all bacterial and viral genomic data
Bradley P, Den Bakker HC, Rocha EPC, McVean G, Iqbal Z. Preprint DOI: 10.1101/234955
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Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging
Severo MS, Landry JJ, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA, Levashina EA. Preprint DOI: 10.1101/234492
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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Preprint DOI: 10.1101/234930
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The Metabolic Response of Skeletal Muscle to Endurance Exercise Is Modified by the ACE-I/D Gene Polymorphism and Training State.
Valdivieso P, Vaughan D, Laczko E, Brogioli M, Waldron S, Rittweger J, Flück M. Frontiers in physiology Volume 8 (2017) p.993 DOI: 10.3389/fphys.2017.00993
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Sharing and reuse of individual participant data from clinical trials: principles and recommendations.
Ohmann C, Banzi R, Canham S, Battaglia S, Matei M, Ariyo C, Becnel L, Bierer B, Bowers S, Clivio L, Dias M, Druml C, Faure H, Fenner M, Galvez J, Ghersi D, Gluud C, Groves T, Houston P, Karam G, Kalra D, Knowles RL, Krleža-Jerić K, Kubiak C, Kuchinke W, Kush R, Lukkarinen A, Marques PS, Newbigging A, O'Callaghan J, Ravaud P, Schlünder I, Shanahan D, Sitter H, Spalding D, Tudur-Smith C, van Reusel P, van Veen EB, Visser GR, Wilson J, Demotes-Mainard J. BMJ open Volume 7 (2017) p.e018647 DOI: 10.1136/bmjopen-2017-018647
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nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. Analytical chemistry Volume 90 (2018) p.649-656 DOI: 10.1021/acs.analchem.7b02795
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In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. Nature communications Volume 8 (2017) p.2109 DOI: 10.1038/s41467-017-00686-2
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Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.
Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP. Journal of chemical information and modeling Volume 57 (2017) p.2976-2985 DOI: 10.1021/acs.jcim.7b00338
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Molecular and functional variation in iPSC-derived sensory neurons.
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, HIPSCI Consortium, Gutteridge A, Gaffney DJ. Nature genetics Volume 50 (2018) p.54-61 DOI: 10.1038/s41588-017-0005-8
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History-driven population structure and asymmetric gene flow in a recovering large carnivore at the rear-edge of its European range.
Karamanlidis AA, Skrbinšek T, de Gabriel Hernando M, Krambokoukis L, Munoz-Fuentes V, Bailey Z, Nowak C, Stronen AV. Heredity Volume 120 (2018) p.168-182 DOI: 10.1038/s41437-017-0031-4
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Cancer research Volume 78 (2018) p.769-780 DOI: 10.1158/0008-5472.can-17-1679
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Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.
Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT. Nature communications Volume 8 (2017) p.2128 DOI: 10.1038/s41467-017-02001-5
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
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Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Preprint DOI: 10.1101/231118
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Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses.
Mata CP, Luque D, Gómez-Blanco J, Rodríguez JM, González JM, Suzuki N, Ghabrial SA, Carrascosa JL, Trus BL, Castón JR. PLoS pathogens Volume 13 (2017) p.e1006755 DOI: 10.1371/journal.ppat.1006755
Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M. Seminars in cancer biology Volume 52 (2018) p.75-85 DOI: 10.1016/j.semcancer.2017.12.001
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Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. Cell systems Volume 5 (2017) p.604-619.e7 DOI: 10.1016/j.cels.2017.11.002
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Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms.
Jespers W, Schiedel AC, Heitman LH, Cooke RM, Kleene L, van Westen GJP, Gloriam DE, Müller CE, Sotelo E, Gutiérrez-de-Terán H. Trends in pharmacological sciences Volume 39 (2018) p.75-89 DOI: 10.1016/j.tips.2017.11.001
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model.
Sundaram V, Wang T. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 40 (2018) DOI: 10.1002/bies.201700155
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Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.
Sancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. The New phytologist Volume 218 (2018) p.1631-1644 DOI: 10.1111/nph.14926
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The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
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Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling.
Vlot AHC, de Witte WEA, Danhof M, van der Graaf PH, van Westen GJP, de Lange ECM. The AAPS journal Volume 20 (2017) p.11 DOI: 10.1208/s12248-017-0172-7
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Functional SNP allele discovery (fSNPd): an approach to find highly penetrant, environmental-triggered genotypes underlying complex human phenotypes.
Stouffer K, Nahorski M, Moreno P, Sarveswaran N, Menon D, Lee M, Geoffrey Woods C. BMC genomics Volume 18 (2017) p.944 DOI: 10.1186/s12864-017-4325-y
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clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003 DOI: 10.1093/bioinformatics/btx532
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.
Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ. Nucleic acids research Volume 45 (2017) p.e177 DOI: 10.1093/nar/gkx836
Editorial overview: Catalysis and regulation.
Thornton J, Orengo C. Current opinion in structural biology Volume 47 (2017) p.vi-viii DOI: 10.1016/j.sbi.2017.11.005
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Using bio.tools to generate and annotate workbench tool descriptions.
Hillion KH, Kuzmin I, Khodak A, Rasche E, Crusoe M, Peterson H, Ison J, Ménager H. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12974.1
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DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
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Nbeal2 interacts with Dock7, Sec16a, and Vac14.
Mayer L, Jasztal M, Pardo M, Aguera de Haro S, Collins J, Bariana TK, Smethurst PA, Grassi L, Petersen R, Nurden P, Favier R, Yu L, Meacham S, Astle WJ, Choudhary J, Yue WW, Ouwehand WH, Guerrero JA. Blood Volume 131 (2018) p.1000-1011 DOI: 10.1182/blood-2017-08-800359
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Genetic diversity of the African malaria vector Anopheles gambiae.
Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya:, Uganda:, Crosses:, Sequencing and data production, Web application development, Project coordination. Nature Volume 552 (2017) p.96-100 DOI: 10.1038/nature24995
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Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen H, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Rätsch G, Schwarz R, Stegle O, PCAWG Group 3. Preprint DOI: 10.1101/225441
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Community-driven data analysis training for biology
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Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway.
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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
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Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
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Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
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Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP.
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Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani.
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Scipion web tools: Easy to use cryo-EM image processing over the web.
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A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing
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Whole Exome Sequencing allows the identification of two novel groups of Xeroderma pigmentosum in Tunisia, XP-D and XP-E: Impact on molecular diagnosis.
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Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.
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Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting
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StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites.
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On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
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cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
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PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
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Wagih O. Bioinformatics (Oxford, England) Volume 33 (2017) p.3645-3647 DOI: 10.1093/bioinformatics/btx469
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Germline determinants of the somatic mutation landscape in 2,642 cancer genomes
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ComplexViewer: visualization of curated macromolecular complexes.
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An epigenome-wide association study meta-analysis of educational attainment.
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Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.
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The future of metabolomics in ELIXIR
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Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes.
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PDBsum: Structural summaries of PDB entries.
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. Protein science : a publication of the Protein Society Volume 27 (2018) p.129-134 DOI: 10.1002/pro.3289
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Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development.
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Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals
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Report of the International Stem Cell Banking Initiative Workshop Activity: Current Hurdles and Progress in Seed-Stock Banking of Human Pluripotent Stem Cells.
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Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.
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Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
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Single-cell transcriptomics to explore the immune system in health and disease.
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Kelsey G, Stegle O, Reik W. Science (New York, N.Y.) Volume 358 (2017) p.69-75 DOI: 10.1126/science.aan6826
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A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination
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Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach.
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Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome.
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UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants
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Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology.
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Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles.
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clusterSeq: methods for identifying co-expression in high-throughput sequencing data
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Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data
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BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing
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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays.
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The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence