Publications for 2019

2019

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Integrated evolutionary and structural analysis reveals xenobiotics and pathogens as the major drivers of mammalian adaptation
Slodkowicz G, Goldman N. Preprint DOI: 10.1101/762690
p13CMFA: Parsimonious 13C metabolic flux analysis.
Foguet C, Jayaraman A, Marin S, Selivanov VA, Moreno P, Messeguer R, de Atauri P, Cascante M. PLoS computational biology Volume 15 (2019) p.e1007310 DOI: 10.1371/journal.pcbi.1007310
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Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers
Shome S, Parra RG, Fatima N, Monzon AM, Cuypers B, Moosa Y, Coimbra NDR, Assis J, Giner-Delgado C, Dönertaş HM, Cuesta-Astroz Y, Saarunya G, Allali I, Gupta S, Srivastava A, Kalsan M, Valdivia C, J. Olguin-Orellana G, Papadimitriou S, Parisi D, Kristensen NP, Rib L, Guebila MB, Bauer E, Zaffaroni G, Bekkar A, Ashano E, Paladin L, Necci M, Moreyra NN, Rydén M, Villalobos-Solís J, Papadopoulos N, Rafael C, Karakulak T, Kaya Y, Gladbach Y, Dhanda SK, Šoštarić N, Alex A, DeBlasio D, Rahman F. Preprint DOI: 10.12688/f1000research.20408.1
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers.
Shome S, Parra RG, Fatima N, Monzon AM, Cuypers B, Moosa Y, Coimbra NDR, Assis J, Giner-Delgado C, Dönertaş HM, Cuesta-Astroz Y, Saarunya G, Allali I, Gupta S, Srivastava A, Kalsan M, Valdivia C, J Olguin-Orellana G, Papadimitriou S, Parisi D, Kristensen NP, Rib L, Guebila MB, Bauer E, Zaffaroni G, Bekkar A, Ashano E, Paladin L, Necci M, Moreyra NN, Rydén M, Villalobos-Solís J, Papadopoulos N, Rafael C, Karakulak T, Kaya Y, Gladbach Y, Dhanda SK, Šoštarić N, Alex A, DeBlasio D, Rahman F. F1000Research Volume 8 (2019) DOI: 10.12688/f1000research.20408.1
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
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
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
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Robustness and applicability of functional genomics tools on scRNA-seq data
Holland CH, Tanevski J, Gleixner J, Kumar MP, Mereu E, Perales-Patón J, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Preprint DOI: 10.1101/753319
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Gene networks in cancer are biased by aneuploidies and sample impurities
Schubert M, Colomé-Tatché M, Foijer F. Preprint DOI: 10.1101/752816
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Dynamical rearrangement of human epidermal growth factor receptor 2 upon antibody binding: effects on the dimerization
Magalhães PR, Machuqueiro M, Almeida JG, Melo A, Cordeiro MNDS, Verde SC, Gümüş ZH, Moreira IS, Correia JDG, Melo R. Preprint DOI: 10.1101/752980
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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
Leveraging European infrastructures to access 1 million human genomes by 2022.
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Nature reviews. Genetics (2019) DOI: 10.1038/s41576-019-0156-9
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 (2019) DOI: 10.1038/s41590-019-0471-5
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
Laehnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Stephan-Otto Attolini C, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Jessurun Lobo T, Keizer EM, Khatri I, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, de Ridder J, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Preprint DOI: 10.7287/peerj.preprints.27885
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
HENA, heterogeneous network-based data set for Alzheimer's disease.
Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, Vilo J, Simonneau M, Peterson H. Scientific data Volume 6 (2019) p.151 DOI: 10.1038/s41597-019-0152-0
Emerging concepts in pseudoenzyme classification, evolution, and signaling.
Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Science signaling Volume 12 (2019) DOI: 10.1126/scisignal.aat9797
The bio.tools registry of software tools and data resources for the life sciences.
Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. Genome biology Volume 20 (2019) p.164 DOI: 10.1186/s13059-019-1772-6
Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus.
Silva Martins WF, Wilding CS, Isaacs AT, Rippon EJ, Megy K, Donnelly MJ. Scientific reports Volume 9 (2019) p.11406 DOI: 10.1038/s41598-019-47850-w
Quantifying the impact of public omics data.
Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H. Nature communications Volume 10 (2019) p.3512 DOI: 10.1038/s41467-019-11461-w
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A Galaxy-based training resource for single-cell RNA-seq quality control and analyses
Etherington GJ, Soranzo N, Mohammed S, Haerty W, Davey RP, Di Palma F. Preprint DOI: 10.1101/724047
Assessment of protein assembly prediction in CASP13.
Guzenko D, Lafita A, Monastyrskyy B, Kryshtafovych A, Duarte JM. Proteins (2019) DOI: 10.1002/prot.25795
Origins of peptidases.
Rawlings ND, Bateman A. Biochimie (2019) 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
Correction: 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.1897-1898 DOI: 10.1038/s41436-018-0327-7
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Systematic characterization and prediction of post-translational modification cross-talk between proteins.
Huang R, Huang Y, Guo Y, Ji S, Lu M, Li T. Bioinformatics (Oxford, England) Volume 35 (2019) p.2626-2633 DOI: 10.1093/bioinformatics/bty1033
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
An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.
Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. Molecular ecology resources (2019) DOI: 10.1111/1755-0998.13070
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 the high-pathogenicity island (HPI) in the intrinsic extra-intestinal virulence of Escherichia coli revealed by a genome-wide association study
Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. Preprint DOI: 10.1101/712034
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Rora regulates activated T helper cells during inflammation
Haim-Vilmovsky L, Walker JA, Henriksson J, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie AN, Teichmann SA. Preprint DOI: 10.1101/709998
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A simple approach for accurate peptide quantification in MS-based proteomics
Maia TM, Staes A, Plasman K, Pauwels J, Boucher K, Argentini A, Martens L, Montoye T, Gevaert K, Impens F. Preprint DOI: 10.1101/703397
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Proteome-wide inference of protein kinase regulatory circuits
Invergo BM, Petursson B, Bradley D, Giudice G, Petsalaki E, Beltrao P. Preprint DOI: 10.1101/703157
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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Meta-Analysis of Cancer Triploidy: Whole-Genome Rearrangements in Male Human Tumours Are Characterised by XXY Karyotypes
Vainshelbaum NM, Zayakin P, Kleina R, Giuliani A, Erenpreisa J. Preprint DOI: 10.20944/preprints201904.0085.v2
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Detection of simple and complex de novo mutations without, with, or with multiple reference sequences
Garimella KV, Iqbal Z, Krause MA, Campino S, Kekre M, Drury E, Kwiatkowski D, Sa JM, Wellems TE, McVean G. Preprint DOI: 10.1101/698910
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
TADOSS: computational estimation of tandem domain swap stability.
Lafita A, Tian P, Best RB, Bateman A. Bioinformatics (Oxford, England) Volume 35 (2019) p.2507-2508 DOI: 10.1093/bioinformatics/bty974
Autism-associated missense genetic variants impact locomotion and neurodevelopment in Caenorhabditis elegans.
Wong WR, Brugman KI, Maher S, Oh JY, Howe K, Kato M, Sternberg PW. Human molecular genetics Volume 28 (2019) p.2271-2281 DOI: 10.1093/hmg/ddz051
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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, Ibba M, Hinton JCD. Preprint DOI: 10.1101/689075
A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity.
Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB. Bioinformatics (Oxford, England) Volume 35 (2019) p.2315-2317 DOI: 10.1093/bioinformatics/bty960
The EMBL-EBI search and sequence analysis tools APIs in 2019.
Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, Lopez R. Nucleic acids research Volume 47 (2019) p.W636-W641 DOI: 10.1093/nar/gkz268
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Mutational signatures are jointly shaped by DNA damage and repair
Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. Preprint DOI: 10.1101/686295
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Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank
Denaxas S, Parkinson H, Fitzpatrick N, Sudlow C, Hemingway H. Preprint DOI: 10.1101/685156
From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.
McGrath A, Champ K, Shang CA, van Dam E, Brooksbank C, Morgan SL. PLoS computational biology Volume 15 (2019) p.e1006923 DOI: 10.1371/journal.pcbi.1006923
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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, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD, Quest for Orthologs Consortium . Molecular biology and evolution (2019) DOI: 10.1093/molbev/msz150
Common and distinct transcriptional signatures of mammalian embryonic lethality.
Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Nature communications Volume 10 (2019) p.2792 DOI: 10.1038/s41467-019-10642-x
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The future of peptide-centric Data-Independent Acquisition is predicted
Van Puyvelde B, Willems S, Gabriels R, Daled S, De Clerck L, Staes A, Vande Casteele S, Impens F, Deforce D, Deforce D, Martens L, Degroeve S, Dhaenens M. Preprint DOI: 10.1101/681429
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.
Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P. Molecular & cellular proteomics : MCP Volume 18 (2019) p.S114-S125 DOI: 10.1074/mcp.RA118.001280
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Human and mouse essentiality screens as a resource for disease gene discovery
Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LM, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu C, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon A, Lloyd KK, Brown SD, Parkinson H, Meehan TF, Smedley D, on behalf of the Genomics England Research Consortium and the International Mouse Phenotyping Consortium. Preprint DOI: 10.1101/678250
Evolution of protein kinase substrate recognition at the active site.
Bradley D, Beltrao P. PLoS biology Volume 17 (2019) p.e3000341 DOI: 10.1371/journal.pbio.3000341
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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, Thornton J, Raymond FL, NIHR BioResource. Preprint DOI: 10.1101/678219
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F. Journal of integrative bioinformatics Volume 16 (2019) DOI: 10.1515/jib-2019-0021
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Nature communications Volume 10 (2019) p.2674 DOI: 10.1038/s41467-019-09799-2
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Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data
Haselimashhadi H, Jeremy MC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu C, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy M, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SD, Smedley D, Flicek P, Mallon A, Parkinson H, Meehan TF. Preprint DOI: 10.1101/656678
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Robust summarization and inference in proteome-wide label-free quantification
Sticker A, Goeminne L, Martens L, Clement L. Preprint DOI: 10.1101/668863
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Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Preprint DOI: 10.1101/668855
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An integrated landscape of protein expression in human cancer
Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA. Preprint DOI: 10.1101/665968
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Integration of genomic variation and phenotypic data using HmtPhenome
Preste R, Attimonelli M. Preprint DOI: 10.1101/660282
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.
Breeze CE, Reynolds AP, van Dongen J, Dunham I, Lazar J, Neph S, Vierstra J, Bourque G, Teschendorff AE, Stamatoyannopoulos JA, Beck S. Bioinformatics (Oxford, England) (2019) DOI: 10.1093/bioinformatics/btz456
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J. Nature biotechnology Volume 37 (2019) p.592-600 DOI: 10.1038/s41587-019-0140-0
Applications of machine learning in drug discovery and development.
Vamathevan J, Clark D, Czodrowski P, Dunham I, Ferran E, Lee G, Li B, Madabhushi A, Shah P, Spitzer M, Zhao S. Nature reviews. Drug discovery Volume 18 (2019) p.463-477 DOI: 10.1038/s41573-019-0024-5
Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping.
Thomas SE, Collins P, James RH, Mendes V, Charoensutthivarakul S, Radoux C, Abell C, Coyne AG, Floto RA, von Delft F, Blundell TL. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Volume 377 (2019) p.20180422 DOI: 10.1098/rsta.2018.0422
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Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets
Bossini-Castillo L, Glinos DA, Kunowska N, Golda G, Lamikanra A, Spitzer M, Soskic B, Cano-Gamez E, Smyth DJ, Cattermole C, Alasoo K, Mann A, Kundu K, Soranzo N, Dunham I, Roberts D, Trynka G. Preprint DOI: 10.1101/654632
Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.
Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, Dunlop MG, Hurles ME, Wright CF, Firth HV, Cunningham F, FitzPatrick DR. Nature communications Volume 10 (2019) p.2373 DOI: 10.1038/s41467-019-10016-3
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Stochastic semi-supervised learning to prioritise genes from high-throughput genomic screens
Vitsios D, Petrovski S. Preprint DOI: 10.1101/655449
A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila.
Durmaz E, Rajpurohit S, Betancourt N, Fabian DK, Kapun M, Schmidt P, Flatt T. Evolution; international journal of organic evolution Volume 73 (2019) p.1774-1792 DOI: 10.1111/evo.13759
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
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Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.
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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
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
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
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
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
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
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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
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
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
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
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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 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
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
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
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The Gene Ontology Resource: 20 years and still GOing strong.
The Gene Ontology Consortium. Nucleic acids research Volume 47 (2019) p.D330-D338 DOI: 10.1093/nar/gky1055
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Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.
Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, Del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. Acta crystallographica. Section F, Structural biology communications Volume 75 (2019) p.19-32 DOI: 10.1107/s2053230x18015108
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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
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
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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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
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
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
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
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
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
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
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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UniProt: a worldwide hub of protein knowledge.
UniProt Consortium. Nucleic acids research Volume 47 (2019) p.D506-D515 DOI: 10.1093/nar/gky1049
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
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
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
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
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