Publications for 2018

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.
Jeffryes M, Bateman A. F1000Research Volume 7 (2018) DOI: 10.12688/f1000research.17315.1
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Identification of genes required for eye development by high-throughput screening of mouse knockouts.
Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, International Mouse Phenotyping Consortium, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Lloyd KCK, Murphy CJ, Moshiri A. Communications biology Volume 1 (2018) p.236 DOI: 10.1038/s42003-018-0226-0
A resource of variant effect predictions of single nucleotide variants in model organisms.
Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P. Molecular systems biology Volume 14 (2018) p.e8430 DOI: 10.15252/msb.20188430
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A test metric for assessing single-cell RNA-seq batch correction.
Büttner M, Miao Z, Wolf FA, Teichmann SA, Theis FJ. Nature methods Volume 16 (2019) p.43-49 DOI: 10.1038/s41592-018-0254-1
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From prioritisation to understanding: mechanistic predictions of variant effects.
Slodkowicz G, Babu MM. Molecular systems biology Volume 14 (2018) p.e8741 DOI: 10.15252/msb.20188741
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6'-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations.
Frei S, Istrate A, Leumann CJ. Beilstein journal of organic chemistry Volume 14 (2018) p.3088-3097 DOI: 10.3762/bjoc.14.288
Identifying Potential Ageing-Modulating Drugs In Silico.
Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Trends in endocrinology and metabolism: TEM Volume 30 (2019) p.118-131 DOI: 10.1016/j.tem.2018.11.005
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Plant genome sequences: past, present, future.
Kersey PJ. Current opinion in plant biology Volume 48 (2019) p.1-8 DOI: 10.1016/j.pbi.2018.11.001
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SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.
Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M, Robson SC, Hermida-Prado F, Yang YH, Babaei-Jadidi R, Garyfallos DA, Ponstingl H, Dias JML, Gallipoli P, Seiler M, Buonamici S, Vick B, Bannister AJ, Rad R, Prinjha RK, Marioni JC, Huntly B, Batson J, Morris JC, Pina C, Bradley A, Jeremias I, Bates DO, Yusa K, Kouzarides T, Vassiliou GS. Nature communications Volume 9 (2018) p.5378 DOI: 10.1038/s41467-018-07620-0
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Minimum Information about an Uncultivated Virus Genome (MIUViG).
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Nature biotechnology Volume 37 (2019) p.29-37 DOI: 10.1038/nbt.4306
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Scop3D: Online Visualization of Mutation Rates on Protein Structure.
Kreft L, Turan D, Hulstaert N, Botzki A, Martens L, Vandermarliere E. Journal of proteome research Volume 18 (2019) p.765-769 DOI: 10.1021/acs.jproteome.8b00681
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A rapid and robust method for single cell chromatin accessibility profiling.
Chen X, Miragaia RJ, Natarajan KN, Teichmann SA. Nature communications Volume 9 (2018) p.5345 DOI: 10.1038/s41467-018-07771-0
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Update on the moFF Algorithm for Label-Free Quantitative Proteomics.
Argentini A, Staes A, Grüning B, Mehta S, Easterly C, Griffin TJ, Jagtap P, Impens F, Martens L. Journal of proteome research Volume 18 (2019) p.728-731 DOI: 10.1021/acs.jproteome.8b00708
Eleven quick tips to build a usable REST API for life sciences.
Tarkowska A, Carvalho-Silva D, Cook CE, Turner E, Finn RD, Yates AD. PLoS computational biology Volume 14 (2018) p.e1006542 DOI: 10.1371/journal.pcbi.1006542
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Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes.
Mavaddat N, Michailidou K, Dennis J, Lush M, Fachal L, Lee A, Tyrer JP, Chen TH, Wang Q, Bolla MK, Yang X, Adank MA, Ahearn T, Aittomäki K, Allen J, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Auer PL, Auvinen P, Barrdahl M, Beane Freeman LE, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Børresen-Dale AL, Brauch H, Bremer M, Brenner H, Brentnall A, Brock IW, Brooks-Wilson A, Brucker SY, Brüning T, Burwinkel B, Campa D, Carter BD, Castelao JE, Chanock SJ, Chlebowski R, Christiansen H, Clarke CL, Collée JM, Cordina-Duverger E, Cornelissen S, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Dörk T, Dos-Santos-Silva I, Dumont M, Durcan L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Ellberg C, Engel C, Eriksson M, Evans DG, Fasching PA, Figueroa J, Fletcher O, Flyger H, Försti A, Fritschi L, Gabrielson M, Gago-Dominguez M, Gapstur SM, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Gilyazova IR, Glendon G, Goldberg MS, Goldgar DE, González-Neira A, Grenaker Alnæs GI, Grip M, Gronwald J, Grundy A, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hankinson SE, Harkness EF, Hart SN, He W, Hein A, Heyworth J, Hillemanns P, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Howell A, Huang G, Humphreys K, Hunter DJ, Jakimovska M, Jakubowska A, Janni W, John EM, Johnson N, Jones ME, Jukkola-Vuorinen A, Jung A, Kaaks R, Kaczmarek K, Kataja V, Keeman R, Kerin MJ, Khusnutdinova E, Kiiski JI, Knight JA, Ko YD, Kosma VM, Koutros S, Kristensen VN, Krüger U, Kühl T, Lambrechts D, Le Marchand L, Lee E, Lejbkowicz F, Lilyquist J, Lindblom A, Lindström S, Lissowska J, Lo WY, Loibl S, Long J, Lubiński J, Lux MP, MacInnis RJ, Maishman T, Makalic E, Maleva Kostovska I, Mannermaa A, Manoukian S, Margolin S, Martens JWM, Martinez ME, Mavroudis D, McLean C, Meindl A, Menon U, Middha P, Miller N, Moreno F, Mulligan AM, Mulot C, Muñoz-Garzon VM, Neuhausen SL, Nevanlinna H, Neven P, Newman WG, Nielsen SF, Nordestgaard BG, Norman A, Offit K, Olson JE, Olsson H, Orr N, Pankratz VS, Park-Simon TW, Perez JIA, Pérez-Barrios C, Peterlongo P, Peto J, Pinchev M, Plaseska-Karanfilska D, Polley EC, Prentice R, Presneau N, Prokofyeva D, Purrington K, Pylkäs K, Rack B, Radice P, Rau-Murthy R, Rennert G, Rennert HS, Rhenius V, Robson M, Romero A, Ruddy KJ, Ruebner M, Saloustros E, Sandler DP, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schürmann P, Schwentner L, Scott C, Scott RJ, Seynaeve C, Shah M, Sherman ME, Shrubsole MJ, Shu XO, Slager S, Smeets A, Sohn C, Soucy P, Southey MC, Spinelli JJ, Stegmaier C, Stone J, Swerdlow AJ, Tamimi RM, Tapper WJ, Taylor JA, Terry MB, Thöne K, Tollenaar RAEM, Tomlinson I, Truong T, Tzardi M, Ulmer HU, Untch M, Vachon CM, van Veen EM, Vijai J, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett W, Winqvist R, Wolk A, Yang XR, Yannoukakos D, Zhang Y, Zheng W, Ziogas A, ABCTB Investigators, kConFab/AOCS Investigators, NBCS Collaborators, Dunning AM, Thompson DJ, Chenevix-Trench G, Chang-Claude J, Schmidt MK, Hall P, Milne RL, Pharoah PDP, Antoniou AC, Chatterjee N, Kraft P, García-Closas M, Simard J, Easton DF. American journal of human genetics Volume 104 (2019) p.21-34 DOI: 10.1016/j.ajhg.2018.11.002
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CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines.
Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y. iScience Volume 10 (2018) p.247-264 DOI: 10.1016/j.isci.2018.11.029
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DEEPScreen: High Performance Drug-Target Interaction Prediction with Convolutional Neural Networks Using 2-D Structural Compound Representations
Rifaioglu AS, Atalay V, Martin MJ, Cetin-Atalay R, Dogan T. Preprint DOI: 10.1101/491365
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Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing.
Sanchis-Juan A, Stephens J, French CE, Gleadall N, Mégy K, Penkett C, Shamardina O, Stirrups K, Delon I, Dewhurst E, Dolling H, Erwood M, Grozeva D, Stefanucci L, Arno G, Webster AR, Cole T, Austin T, Branco RG, Ouwehand WH, Raymond FL, Carss KJ. Genome medicine Volume 10 (2018) p.95 DOI: 10.1186/s13073-018-0606-6
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Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
Moreno P, Pireddu L, Roger P, Goonasekera N, Afgan E, van den Beek M, He S, Larsson A, Schober D, Ruttkies C, Johnson D, Rocca-Serra P, Weber RJ, Gruening B, Salek RM, Kale N, Perez-Riverol Y, Papatheodorou I, Spjuth O, Neumann S. Preprint DOI: 10.1101/488643
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Cohesin-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation.
Chen Z, Amro EM, Becker F, Hölzer M, Rasa SMM, Njeru SN, Han B, Di Sanzo S, Chen Y, Tang D, Tao S, Haenold R, Groth M, Romanov VS, Kirkpatrick JM, Kraus JM, Kestler HA, Marz M, Ori A, Neri F, Morita Y, Rudolph KL. The Journal of experimental medicine Volume 216 (2019) p.152-175 DOI: 10.1084/jem.20181505
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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan K, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J, Naas T, O'Grady J, Paracchini V, Rossen JW, Ruppé E, Vamathevan J, Venturi V, Van den Eede G. Preprint DOI: 10.12688/f1000research.14509.2
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The RNA-binding proteins Zfp36l1 and Zfp36l2 act redundantly in myogenesis.
Bye-A-Jee H, Pugazhendhi D, Woodhouse S, Brien P, Watson R, Turner M, Pell J. Skeletal muscle Volume 8 (2018) p.37 DOI: 10.1186/s13395-018-0183-9
The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest.
Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. Cell Volume 176 (2019) p.391-403.e19 DOI: 10.1016/j.cell.2018.11.004
Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs.
Saidi R, Dhifli W, Maddouri M, Mephu Nguifo E. Journal of computational biology : a journal of computational molecular cell biology Volume 26 (2019) p.561-571 DOI: 10.1089/cmb.2018.0171
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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. Journal of proteome research Volume 18 (2019) p.741-747 DOI: 10.1021/acs.jproteome.8b00723
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Predicting eukaryotic protein secretion without signals.
Nielsen H, Petsalaki EI, Zhao L, Stühler K. Biochimica et biophysica acta. Proteins and proteomics Volume 1867 (2019) p.140174 DOI: 10.1016/j.bbapap.2018.11.011
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Unipept 4.0: Functional Analysis of Metaproteome Data.
Gurdeep Singh R, Tanca A, Palomba A, Van der Jeugt F, Verschaffelt P, Uzzau S, Martens L, Dawyndt P, Mesuere B. Journal of proteome research Volume 18 (2019) p.606-615 DOI: 10.1021/acs.jproteome.8b00716
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RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns.
Brennan GP, Vitsios DM, Casey S, Looney AM, Hallberg B, Henshall DC, Boylan GB, Murray DM, Mooney C. PloS one Volume 13 (2018) p.e0207952 DOI: 10.1371/journal.pone.0207952
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GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes.
Franceschini N, Giambartolomei C, de Vries PS, Finan C, Bis JC, Huntley RP, Lovering RC, Tajuddin SM, Winkler TW, Graff M, Kavousi M, Dale C, Smith AV, Hofer E, van Leeuwen EM, Nolte IM, Lu L, Scholz M, Sargurupremraj M, Pitkänen N, Franzén O, Joshi PK, Noordam R, Marioni RE, Hwang SJ, Musani SK, Schminke U, Palmas W, Isaacs A, Correa A, Zonderman AB, Hofman A, Teumer A, Cox AJ, Uitterlinden AG, Wong A, Smit AJ, Newman AB, Britton A, Ruusalepp A, Sennblad B, Hedblad B, Pasaniuc B, Penninx BW, Langefeld CD, Wassel CL, Tzourio C, Fava C, Baldassarre D, O'Leary DH, Teupser D, Kuh D, Tremoli E, Mannarino E, Grossi E, Boerwinkle E, Schadt EE, Ingelsson E, Veglia F, Rivadeneira F, Beutner F, Chauhan G, Heiss G, Snieder H, Campbell H, Völzke H, Markus HS, Deary IJ, Jukema JW, de Graaf J, Price J, Pott J, Hopewell JC, Liang J, Thiery J, Engmann J, Gertow K, Rice K, Taylor KD, Dhana K, Kiemeney LALM, Lind L, Raffield LM, Launer LJ, Holdt LM, Dörr M, Dichgans M, Traylor M, Sitzer M, Kumari M, Kivimaki M, Nalls MA, Melander O, Raitakari O, Franco OH, Rueda-Ochoa OL, Roussos P, Whincup PH, Amouyel P, Giral P, Anugu P, Wong Q, Malik R, Rauramaa R, Burkhardt R, Hardy R, Schmidt R, de Mutsert R, Morris RW, Strawbridge RJ, Wannamethee SG, Hägg S, Shah S, McLachlan S, Trompet S, Seshadri S, Kurl S, Heckbert SR, Ring S, Harris TB, Lehtimäki T, Galesloot TE, Shah T, de Faire U, Plagnol V, Rosamond WD, Post W, Zhu X, Zhang X, Guo X, Saba Y, MEGASTROKE Consortium, Dehghan A, Seldenrijk A, Morrison AC, Hamsten A, Psaty BM, van Duijn CM, Lawlor DA, Mook-Kanamori DO, Bowden DW, Schmidt H, Wilson JF, Wilson JG, Rotter JI, Wardlaw JM, Deanfield J, Halcox J, Lyytikäinen LP, Loeffler M, Evans MK, Debette S, Humphries SE, Völker U, Gudnason V, Hingorani AD, Björkegren JLM, Casas JP, O'Donnell CJ. Nature communications Volume 9 (2018) p.5141 DOI: 10.1038/s41467-018-07340-5
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The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury.
Späth MR, Bartram MP, Palacio-Escat N, Hoyer KJR, Debes C, Demir F, Schroeter CB, Mandel AM, Grundmann F, Ciarimboli G, Beyer A, Kizhakkedathu JN, Brodesser S, Göbel H, Becker JU, Benzing T, Schermer B, Höhne M, Burst V, Saez-Rodriguez J, Huesgen PF, Müller RU, Rinschen MM. Kidney international Volume 95 (2019) p.333-349 DOI: 10.1016/j.kint.2018.08.037
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Association of Genetic Variants Related to Gluteofemoral vs Abdominal Fat Distribution With Type 2 Diabetes, Coronary Disease, and Cardiovascular Risk Factors.
Lotta LA, Wittemans LBL, Zuber V, Stewart ID, Sharp SJ, Luan J, Day FR, Li C, Bowker N, Cai L, De Lucia Rolfe E, Khaw KT, Perry JRB, O'Rahilly S, Scott RA, Savage DB, Burgess S, Wareham NJ, Langenberg C. JAMA Volume 320 (2018) p.2553-2563 DOI: 10.1001/jama.2018.19329
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Neutral tumor evolution?
Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P. Nature genetics Volume 50 (2018) p.1630-1633 DOI: 10.1038/s41588-018-0258-x
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Identification of new allosteric sites and modulators of AChE through computational and experimental tools.
Roca C, Requena C, Sebastián-Pérez V, Malhotra S, Radoux C, Pérez C, Martinez A, Antonio Páez J, Blundell TL, Campillo NE. Journal of enzyme inhibition and medicinal chemistry Volume 33 (2018) p.1034-1047 DOI: 10.1080/14756366.2018.1476502
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Author Correction: 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.1752 DOI: 10.1038/s41588-018-0275-9
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Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.
Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. Science translational medicine Volume 10 (2018) DOI: 10.1126/scitranslmed.aap8914
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Sequana coverage: detection and characterization of genomic variations using running median and mixture models.
Desvillechabrol D, Bouchier C, Kennedy S, Cokelaer T. GigaScience Volume 7 (2018) DOI: 10.1093/gigascience/giy110
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Structural progression of amyloid-β Arctic mutant aggregation in cells revealed by multiparametric imaging.
Lu M, Williamson N, Mishra A, Michel CH, Kaminski CF, Tunnacliffe A, Kaminski Schierle GS. The Journal of biological chemistry Volume 294 (2019) p.1478-1487 DOI: 10.1074/jbc.ra118.004511
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Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.
Venkatesan A, Tagny Ngompe G, Hassouni NE, Chentli I, Guignon V, Jonquet C, Ruiz M, Larmande P. PloS one Volume 13 (2018) p.e0198270 DOI: 10.1371/journal.pone.0198270
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Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.
Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Genes Volume 9 (2018) DOI: 10.3390/genes9120593
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Strategies and opportunities for promoting bioinformatics in Zimbabwe.
Shoko R, Manasa J, Maphosa M, Mbanga J, Mudziwapasi R, Nembaware V, Sanyika WT, Tinago T, Chikwambi Z, Mawere C, Matimba A, Mugumbate G, Mufandaedza J, Mulder N, Patterton H, Patterton H. PLoS computational biology Volume 14 (2018) p.e1006480 DOI: 10.1371/journal.pcbi.1006480
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Biallelic Loss-of-Function Variants in AIMP1 Cause a Rare Neurodegenerative Disease.
Accogli A, Guerrero K, D'Agostino MD, Tran L, Cieuta-Walti C, Thiffault I, Chénier S, Schwartzentruber J, Majewski J, Care4Rare Canada Consortium, Bernard G. Journal of child neurology Volume 34 (2019) p.74-80 DOI: 10.1177/0883073818811223
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Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach.
De Anda V, Zapata-Peñasco I, Blaz J, Poot-Hernández AC, Contreras-Moreira B, González-Laffitte M, Gámez-Tamariz N, Hernández-Rosales M, Eguiarte LE, Souza V. Frontiers in microbiology Volume 9 (2018) p.2606 DOI: 10.3389/fmicb.2018.02606
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Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth
Chen H, Eling N, Martinez-Jimenez CP, O’Brien LM, Marioni JC, Odom DT, la Roche Md. Preprint DOI: 10.1101/480327
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Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue.
Pellegrinelli V, Peirce VJ, Howard L, Virtue S, Türei D, Senzacqua M, Frontini A, Dalley JW, Horton AR, Bidault G, Severi I, Whittle A, Rahmouni K, Saez-Rodriguez J, Cinti S, Davies AM, Vidal-Puig A. Nature communications Volume 9 (2018) p.4974 DOI: 10.1038/s41467-018-07453-x
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A linear mixed-model approach to study multivariate gene-environment interactions.
Moore R, Casale FP, Jan Bonder M, Horta D, BIOS Consortium, Franke L, Barroso I, Stegle O. Nature genetics Volume 51 (2019) p.180-186 DOI: 10.1038/s41588-018-0271-0
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Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.
McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. Natural product reports Volume 36 (2019) p.248-249 DOI: 10.1039/c8np90041h
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Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.
Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS. Journal of molecular biology Volume 431 (2019) p.336-350 DOI: 10.1016/j.jmb.2018.11.018
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Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury.
Souza T, Trairatphisan P, Piñero J, Furlong LI, Saez-Rodriguez J, Kleinjans J, Jennen D. Frontiers in genetics Volume 9 (2018) p.527 DOI: 10.3389/fgene.2018.00527
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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.
Garaud S, Zayakin P, Buisseret L, Rulle U, Silina K, de Wind A, Van den Eyden G, Larsimont D, Willard-Gallo K, Linē A. Frontiers in immunology Volume 9 (2018) p.2660 DOI: 10.3389/fimmu.2018.02660
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A reference set of curated biomedical data and metadata from clinical case reports.
Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, Ping P. Scientific data Volume 5 (2018) p.180258 DOI: 10.1038/sdata.2018.258
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A well-ordered nanoflow LC-MS/MS approach for proteome profiling using 200 cm long micro pillar array columns
De Beeck JO, Pauwels J, Van Landuyt N, Jacobs P, De Malsche W, Desmet G, Argentini A, Staes A, Martens L, Impens F, Gevaert K. Preprint DOI: 10.1101/472134
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BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis
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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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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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A synthesis approach of mouse studies to identify genes and proteins in arterial thrombosis and bleeding.
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Transform-MinER: transforming molecules in enzyme reactions.
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Publisher Correction: Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.
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DNA G-quadruplex structures mold the DNA methylome.
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Minimum Information for Reusable Arthropod Abundance Data (MIReAAD)
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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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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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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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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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Discovery of potent and selective Spleen Tyrosine Kinase inhibitors for the topical treatment of inflammatory skin disease.
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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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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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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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Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
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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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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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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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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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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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Evaluation of the bacterial diversity of Spanish-type chorizo during the ripening process using high-throughput sequencing and physicochemical characterization.
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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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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
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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
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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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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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.
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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 7 (2018) p.284-294.e12 DOI: 10.1016/j.cels.2018.06.011
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Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts.
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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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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.
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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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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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Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape
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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.
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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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Terminal uridylyltransferases target RNA viruses as part of the innate immune system.
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Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
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The first single particle analysis Map Challenge: A summary of the assessments.
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Conserved phosphorylation hotspots in eukaryotic protein domain families
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Genomic landscape and chronological reconstruction of driver events in multiple myeloma
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Adaptation of proteins to the cold in Antarctic fish: A role for Methionine?
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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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Improving sample classification by harnessing the potential of 1H-NMR signal chemical shifts.
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Disruption of TWIST1 translation by 5' UTR variants in Saethre-Chotzen syndrome.
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Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history
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Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
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Publisher Correction: Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
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The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
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Bimolecular Coupling as a Vector for Decomposition of Fast-Initiating Olefin Metathesis Catalysts.
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Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.
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Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia.
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Variants in ACTG2 underlie a substantial number of Australasian patients with primary chronic intestinal pseudo-obstruction.
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The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.
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Aberration hubs in protein interaction networks highlight actionable targets in cancer.
Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y. Oncotarget Volume 9 (2018) p.25166-25180 DOI: 10.18632/oncotarget.25382
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Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy
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The burden of prostate cancer in Trinidad and Tobago: one of the highest mortality rates in the world.
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NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.
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GOA and QuickGO: Quick tour
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Ensembl - Analysing Linkage Disequilibrium: webinar
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Current Challenges in Plant Eco-Metabolomics.
Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. International journal of molecular sciences Volume 19 (2018) DOI: 10.3390/ijms19051385
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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher S, Fan Y, Fittall M, Drews RM, Yao X, Lee J, Schlesner M, Zhu H, Adams DJ, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, on behalf of the PCAWG Evolution and Heterogeneity Working Groupthe PCAWG consortium, the PCAWG consortium. Preprint DOI: 10.1101/312041
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Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes
Maher GJ, Ralph HK, Ding Z, Koelling N, Mlcochova H, Giannoulatou E, Dhami P, Paul DS, Stricker SH, Beck S, McVean G, Wilkie AO, Goriely A. Preprint DOI: 10.1101/314815
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Comprehensive variant effect predictions of single nucleotide variants in model organisms
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Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.
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Alternative models for sharing confidential biomedical data.
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In vivo and in vitro identification of Z-BOX C - a new bilirubin oxidation end product.
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Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.
Almeida A, Mitchell AL, Tarkowska A, Finn RD. GigaScience Volume 7 (2018) DOI: 10.1093/gigascience/giy054
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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.
Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. Frontiers in microbiology Volume 9 (2018) p.771 DOI: 10.3389/fmicb.2018.00771
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Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.
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Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.
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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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Macrophage-Derived Extracellular Succinate Licenses Neural Stem Cells to Suppress Chronic Neuroinflammation.
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Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
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A survey of metastasis suppressors in Metazoa.
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A functional landscape of chronic kidney disease entities from public transcriptomic data
Tajti F, Kuppe C, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland C, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. Preprint DOI: 10.1101/265447
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Condensed Tannins Affect Bacterial and Fungal Microbiomes and Mycotoxin Production during Ensiling and upon Aerobic Exposure.
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Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci
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Mapping human development at single-cell resolution.
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Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction
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Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.
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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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Genome watch: Keeping tally in the microbiome.
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Computational modelling of atherosclerosis: developing a community resource
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Spin Crossover in a Hexaamineiron(II) Complex: Experimental Confirmation of a Computational Prediction.
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Spatiotemporal patterning of EpCAM is important for murine embryonic endo- and mesodermal differentiation.
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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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Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
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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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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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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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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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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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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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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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Polygenic hazard score to guide screening for aggressive prostate cancer: development and validation in large scale cohorts.
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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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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 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
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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
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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
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
Data visualisation 101: A practical introduction to designing scientific Figures
Karamanis N. DOI: 10.6019/tol.datavis-w.2018.00001.1
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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 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
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
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
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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
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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
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
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
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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
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
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
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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
Effective Literature Research with Europe PMC
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Bioinformatics Sequence Analysis Web Services with Job Dispatcher
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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
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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
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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
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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
Detection and evolution of repetitive proteins
Laifta Masip A. DOI: 10.6019/tol.evol-prot-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
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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
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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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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
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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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
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
EMBL-EBI resources: An introduction
Gopalasingam P. DOI: 10.6019/tol.intr-ebi-res-w.2015.00001.1
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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
PhenoMeNal: Metabolomics data analysis in the cloud
Pireddu L, Moreno P. DOI: 10.6019/tol.phenomenal-w.2017.00001.1
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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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
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
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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
Genome Properties: Tutorial
Richardson L. DOI: 10.6019/tol.genprop-t.2018.00001.1
Mouse strains in Ensembl
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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
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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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
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
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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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
Hands-on on Protein Function Prediction with Machine Learning and Interactive Analytics
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Preprint discovery 101: Tips & tricks for authors and readers
Levchenko M. DOI: 10.6019/tol.preprint-w.2018.00001.1
Pfam Database: Creating Protein Families
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam_fams-t.2018.00001.1
Repeats in Pfam
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam_repeats-t.2018.00001.1
HMMER: Fast and sensitive sequence similarity searches
Finn R. DOI: 10.6019/tol.hmmer-w.2018.00001.1
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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
EBI Search as a service
Park Y. DOI: 10.6019/tol.ebi_search-w.2018.00001.1
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
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
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
Complex Portal: Quick tour
Meldal B. DOI: 10.6019/tol.comport-w.2015.00001.1
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
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
Automatic annotation systems in UniProt
Pichler K, Renaux A. DOI: 10.6019/tol.uniprot_annot-w.2018.00001.1
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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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
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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