Publications for 2018

2018

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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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) (2018) DOI: 10.1093/bioinformatics/bty1033
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Rapid identification of novel protein families using similarity searches
Jeffryes M, Bateman A. Preprint DOI: 10.12688/f1000research.17315.1
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Population-wide copy number variation calling using variant call format files from 6,898 individuals
Png G, Suveges D, Park Y, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E, Gilly A. Preprint DOI: 10.1101/504209
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
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
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
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
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 (2018) DOI: 10.1038/nbt.4306
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Multi-omics characterization of interaction-mediated control of human protein abundance levels
Sousa A, Goncalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P. Preprint DOI: 10.1101/499434
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Skewed X-inactivation is common in the general female population.
Shvetsova E, Sofronova A, Monajemi R, Gagalova K, Draisma HHM, White SJ, Santen GWE, Chuva de Sousa Lopes SM, Heijmans BT, van Meurs J, Jansen R, Franke L, Kiełbasa SM, den Dunnen JT, 't Hoen PAC, BIOS consortium, GoNL consortium. European journal of human genetics : EJHG Volume 27 (2019) p.455-465 DOI: 10.1038/s41431-018-0291-3
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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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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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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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, Ruttkies C, Schober D, Johnson D, Rocca-Serra P, Weber RJ, Gruening B, Salek R, Kale N, Perez-Riverol Y, Papatheodorou I, Spjuth O, Neumann S. Preprint DOI: 10.1101/488643
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
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
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 (2018) DOI: 10.1089/cmb.2018.0171
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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Metabolic engineering strategies for improvement of ethanol production in cellulolytic Saccharomyces cerevisiae.
Song X, Li Y, Wu Y, Cai M, Liu Q, Gao K, Zhang X, Bai Y, Xu H, Qiao M. FEMS yeast research Volume 18 (2018) DOI: 10.1093/femsyr/foy090
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
TADOSS: computational estimation of tandem domain swap stability.
Lafita A, Tian P, Best RB, Bateman A. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty974
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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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, de la Roche M. Preprint DOI: 10.1101/480327
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
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
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) (2018) DOI: 10.1093/bioinformatics/bty960
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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BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A, Heled J, Jones G, Kuhnert D, de Maio N, Matschiner M, Mendes FK, Muller N, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard M, Wu C, Xie D, Zhang C, Stadler T, Drummond AJ. Preprint DOI: 10.1101/474296
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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. Preprint DOI: 10.1101/473231
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Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster
Betancourt N, Rajpurohit S, Durmaz E, Fabian D, Kapun M, Flatt T, Schmidt P. Preprint DOI: 10.1101/471565
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Tumors induce de novo steroid biosynthesis in T cells to evade immunity:
Mahata B, Pramanik J, Weyden Lvd, Kar G, Riedel A, Fonseca NA, Kundu K, Ryder E, Duddy G, Walczak I, Davidson S, Okkenhaug K, Adams DJ, Shields JD, Teichmann SA. Preprint DOI: 10.1101/471359
Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars.
Carvalho-Silva D, Garcia L, Morgan SL, Brooksbank C, Dunham I. PLoS computational biology Volume 14 (2018) p.e1006419 DOI: 10.1371/journal.pcbi.1006419
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Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap.
Giuffra E, Tuggle CK, FAANG Consortium. Annual review of animal biosciences Volume 7 (2019) p.65-88 DOI: 10.1146/annurev-animal-020518-114913
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Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease
Konki M, Malonzo M, Karlsson I, Lindgren N, Ghimire B, Smolander J, Scheinin N, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen N, Kaprio J, Lähdesmäki H, Rinne J, Lund RJ. Preprint DOI: 10.1101/468470
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Single-cell RNA sequencing reveals a dynamic stromal niche within the evolving tumour microenvironment
Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R, Hagai T, Chen X, A. Haniffa M, D. Shields J, A. Teichmann S. Preprint DOI: 10.1101/467225
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Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay:
Pervouchine D, Popov I, Berry A, Borsari B, Frankish A, Guigo R. Preprint DOI: 10.1101/464404
Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency.
Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W. Cell systems Volume 7 (2018) p.482-495.e10 DOI: 10.1016/j.cels.2018.09.003
The official unified nomenclature adopted by the HGNC calls for the use of the acronyms, CCN1-6, and discontinuation in the use of CYR61, CTGF, NOV and WISP 1-3 respectively.
Perbal B, Tweedie S, Bruford E. Journal of cell communication and signaling Volume 12 (2018) p.625-629 DOI: 10.1007/s12079-018-0491-1
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Comparative genomics of the major parasitic worms.
International Helminth Genomes Consortium. Nature genetics Volume 51 (2019) p.163-174 DOI: 10.1038/s41588-018-0262-1
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Comparative analysis of sequencing technologies platforms for single-cell transcriptomics
Natarajan KN, Miao Z, Jiang M, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L, Li B, Hou Y, Liu S, Teichmann S. Preprint DOI: 10.1101/463117
ClinGen advancing genomic data-sharing standards as a GA4GH driver project.
Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. Human mutation Volume 39 (2018) p.1686-1689 DOI: 10.1002/humu.23625
Publisher Correction: Image Data Resource: a bioimage data integration and publication platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. Nature methods Volume 15 (2018) p.984 DOI: 10.1038/s41592-018-0169-x
A call for public archives for biological image data.
Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. Nature methods Volume 15 (2018) p.849-854 DOI: 10.1038/s41592-018-0195-8
Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis.
Schor IE, Bussotti G, Maleš M, Forneris M, Viales RR, Enright AJ, Furlong EEM. Current biology : CB Volume 28 (2018) p.3547-3561.e9 DOI: 10.1016/j.cub.2018.09.026
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Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction:
Szalai B, Subramanian V, Alfoldi R, Puskas LG, Saez-Rodriguez J. Preprint DOI: 10.1101/454348
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Identification of RNA-associated peptides, iRAP, defines precise sites of protein-RNA interaction
Peil L, Waghmare S, Fischer L, Spitzer M, Tollervey D, Rappsilber J. Preprint DOI: 10.1101/456111
Parents in science.
Perry E, Tessmar-Raible K, Raible F. Genome biology Volume 19 (2018) p.180 DOI: 10.1186/s13059-018-1549-3
Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data.
Invergo BM, Beltrao P. Essays in biochemistry Volume 62 (2018) p.525-534 DOI: 10.1042/EBC20180019
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Bacterial contribution to genesis of the novel germ line determinant oskar
Blondel L, Jones TEM, Extavour CG. Preprint DOI: 10.1101/453514
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Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank
Tachmazidou I, Hatzikotoulas K, Southam L, Esparza-Gordillo J, Haberland V, Zheng J, Johnson T, Koprulu M, Zengini E, Steinberg J, Wilkinson JM, Bhatnagar S, Hoffman J, Buchan N, Suveges D, arcOGEN Consortium, Yerges Armstrong L, Davey Smith G, Gaunt TR, Scott RA, McCarthy LC, Zeggini E. Preprint DOI: 10.1101/453530
Gene expression variability across cells and species shapes innate immunity.
Hagai T, Chen X, Miragaia RJ, Rostom R, Gomes T, Kunowska N, Henriksson J, Park JE, Proserpio V, Donati G, Bossini-Castillo L, Vieira Braga FA, Naamati G, Fletcher J, Stephenson E, Vegh P, Trynka G, Kondova I, Dennis M, Haniffa M, Nourmohammad A, Lässig M, Teichmann SA. Nature Volume 563 (2018) p.197-202 DOI: 10.1038/s41586-018-0657-2
A large-scale dataset of in vivo pharmacology assay results.
Hunter FMI, L Atkinson F, Bento AP, Bosc N, Gaulton A, Hersey A, Leach AR. Scientific data Volume 5 (2018) p.180230 DOI: 10.1038/sdata.2018.230
Chromosome assembly of large and complex genomes using multiple references.
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Genome research Volume 28 (2018) p.1720-1732 DOI: 10.1101/gr.236273.118
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Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis
Võsa U, Claringbould A, Westra H, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Kasela S, Pervjakova N, Alvaes I, Fave M, Agbessi M, Christiansen M, Jansen R, Seppälä I, Tong L, Teumer A, Schramm K, Hemani G, Verlouw J, Yaghootkar H, Sönmez R, Andrew AA, Kukushkina V, Kalnapenkis A, Rüeger S, Porcu E, Kronberg-Guzman J, Kettunen J, Powell J, Lee B, Zhang F, Arindrarto W, Beutner F, Brugge H, Dmitrieva J, Elansary M, Fairfax BP, Georges M, Heijmans BT, Kähönen M, Kim Y, Knight JC, Kovacs P, Krohn K, Li S, Loeffler M, Marigorta UM, Mei H, Momozawa Y, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Pritchard J, Raitakari O, Rotzschke O, Slagboom EP, Stehouwer CD, Stumvoll M, Sullivan P, 't Hoen PA, Thiery J, Tönjes A, van Dongen J, van Iterson M, Veldink J, Völker U, Wijmenga C, Swertz M, Andiappan A, Montgomery GW, Ripatti S, Perola M, Kutalik Z, Dermitzakis E, Bergmann S, Frayling T, van Meurs J, Prokisch H, Ahsan H, Pierce B, Lehtimäki T, Boomsma D, Psaty BM, Gharib SA, Awadalla P, Milani L, Ouwehand WH, Downes K, Stegle O, Battle A, Yang J, Visscher PM, Scholz M, Gibson G, Esko T, Franke L, BIOS Consortium, i2QTL Consortium. Preprint DOI: 10.1101/447367
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Publishing peer review materials
Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M. Preprint DOI: 10.12688/f1000research.16460.1
Publishing peer review materials.
Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M. F1000Research Volume 7 (2018) p.1655 DOI: 10.12688/f1000research.16460.1
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.
Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. Animal genetics Volume 49 (2018) p.520-526 DOI: 10.1111/age.12736
Expanding the Use of Spectral Libraries in Proteomics.
Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Journal of proteome research Volume 17 (2018) p.4051-4060 DOI: 10.1021/acs.jproteome.8b00485
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Population-scale proteome variation in human induced pluripotent stem cells
Mirauta B, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, Stegle O, Lamond A, HipSci consortium. Preprint DOI: 10.1101/439216
Haplosaurus computes protein haplotypes for use in precision drug design.
Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Nature communications Volume 9 (2018) p.4128 DOI: 10.1038/s41467-018-06542-1
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Using the drug-protein interactome to identify anti-ageing compounds for humans
Fuentealba Valenzuela M, Donertas HM, Williams R, Labbadia J, Thornton J, Partridge L. Preprint DOI: 10.1101/438234
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions: Supporting Information
C. Silva AS, Martens L, Degroeve S. Preprint DOI: 10.1101/428805
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 (2018) DOI: 10.1038/s41436-018-0327-7
Classification and Personalized Prognosis in Myeloproliferative Neoplasms.
Grinfeld J, Nangalia J, Baxter EJ, Wedge DC, Angelopoulos N, Cantrill R, Godfrey AL, Papaemmanuil E, Gundem G, MacLean C, Cook J, O'Neil L, O'Meara S, Teague JW, Butler AP, Massie CE, Williams N, Nice FL, Andersen CL, Hasselbalch HC, Guglielmelli P, McMullin MF, Vannucchi AM, Harrison CN, Gerstung M, Green AR, Campbell PJ. The New England journal of medicine Volume 379 (2018) p.1416-1430 DOI: 10.1056/nejmoa1716614
Transform-MinER: transforming molecules in enzyme reactions.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Bioinformatics (Oxford, England) Volume 34 (2018) p.3597-3599 DOI: 10.1093/bioinformatics/bty394
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Nature genetics Volume 50 (2018) p.1574-1583 DOI: 10.1038/s41588-018-0223-8
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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
Human genes: Time to follow the roads less traveled?
Dunham I. PLoS biology Volume 16 (2018) p.e3000034 DOI: 10.1371/journal.pbio.3000034
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Process-specific somatic mutation distributions vary with three-dimensional genome structure
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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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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
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Meyer HV, Birney E. Bioinformatics (Oxford, England) Volume 34 (2018) p.2951-2956 DOI: 10.1093/bioinformatics/bty197
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The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus.
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Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA. Nature structural & molecular biology Volume 25 (2018) p.778-786 DOI: 10.1038/s41594-018-0106-9
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Heymann JB, Marabini R, Kazemi M, Sorzano COS, Holmdahl M, Mendez JH, Stagg SM, Jonic S, Palovcak E, Armache JP, Zhao J, Cheng Y, Pintilie G, Chiu W, Patwardhan A, Carazo JM. Journal of structural biology Volume 204 (2018) p.291-300 DOI: 10.1016/j.jsb.2018.08.010
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Genomic landscape and chronological reconstruction of driver events in multiple myeloma
Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JM, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, Campbell PJ. Preprint DOI: 10.1101/388611
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Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM. Aging cell Volume 17 (2018) p.e12819 DOI: 10.1111/acel.12819
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Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT. Genome biology Volume 19 (2018) p.106 DOI: 10.1186/s13059-018-1484-3
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Physicochemical amino acid properties better describe substitution rates in large populations
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A roadmap for restoring trust in Big Data.
Lawler M, Morris AD, Sullivan R, Birney E, Middleton A, Makaroff L, Knoppers BM, Horgan D, Eggermont A. The Lancet. Oncology Volume 19 (2018) p.1014-1015 DOI: 10.1016/s1470-2045(18)30425-x
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A locus at 7p14.3 predisposes to refractory celiac disease progression from celiac disease.
Hrdlickova B, Mulder CJ, Malamut G, Meresse B, Platteel M, Kamatani Y, Ricaño-Ponce I, van Wanrooij RLJ, Zorro MM, Jan Bonder M, Gutierrez-Achury J, Cellier C, Zhernakova A, Nijeboer P, Galan P, Withoff S, Lathrop M, Bouma G, Xavier RJ, Jabri B, Bensussan NC, Wijmenga C, Kumar V. European journal of gastroenterology & hepatology Volume 30 (2018) p.828-837 DOI: 10.1097/MEG.0000000000001168
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
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The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
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Microarray-Based quality assessment as a supporting criterion for de novo transcriptome assembly selection.
Carvajal-Lopez P, Von Borstel FD, Torres A, Rustici G, Gutierrez J, Romero-Vivas E. IEEE/ACM transactions on computational biology and bioinformatics (2018) DOI: 10.1109/tcbb.2018.2860997
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Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes.
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NonA and CPX Link the Circadian Clockwork to Locomotor Activity in Drosophila.
Luo W, Guo F, McMahon A, Couvertier S, Jin H, Diaz M, Fieldsend A, Weerapana E, Rosbash M. Neuron Volume 99 (2018) p.768-780.e3 DOI: 10.1016/j.neuron.2018.07.001
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PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping
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Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study.
Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N, Ojal J, Shebe M, Awuondo KO, Mturi N, Tsofa B, Sepúlveda N, Clark TG, Band G, Clarke G, Rowlands K, Hubbart C, Jeffreys A, Kariuki S, Marsh K, Mackinnon M, Maitland K, Kwiatkowski DP, Rockett KA, Williams TN, MalariaGEN Consortium. The Lancet. Haematology Volume 5 (2018) p.e333-e345 DOI: 10.1016/S2352-3026(18)30107-8
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Nearly all new protein-coding predictions in the CHESS database are not protein-coding
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Vialle RA, Tamuri AU, Goldman N. Molecular biology and evolution Volume 35 (2018) p.1783-1797 DOI: 10.1093/molbev/msy055
The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.
Bornelöv S, Reynolds N, Xenophontos M, Gharbi S, Johnstone E, Floyd R, Ralser M, Signolet J, Loos R, Dietmann S, Bertone P, Hendrich B. Molecular cell Volume 71 (2018) p.56-72.e4 DOI: 10.1016/j.molcel.2018.06.003
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HmtVar: a brand-new resource for human mitochondrial variations and pathogenicity data
Preste R, Vitale O, Clima R, Attimonelli M. Preprint DOI: 10.1101/355461
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Lee JY, Choi H, Colangelo CM, Davis D, Hoopmann MR, Käll L, Lam H, Payne SH, Perez-Riverol Y, The M, Wilson R, Weintraub ST, Palmblad M. Journal of biomolecular techniques : JBT Volume 29 (2018) p.39-45 DOI: 10.7171/jbt.18-2902-003
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Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Preprint DOI: 10.1101/350868
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Understanding trivial challenges of microbial genomics: An assembly example
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Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set
The IMEx Consortium curators, del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Pinero J, Kotlyar M, Chiara P, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras Millan P. Preprint DOI: 10.1101/346833
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Optimally designed vs intuition-driven inputs: the study case of promoter activity modelling
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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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Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
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PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery
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Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Nature biotechnology Volume 36 (2018) p.421-427 DOI: 10.1038/nbt.4091
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Integrative analysis of pharmacogenomics in major cancer cell line databases using CellMinerCDB
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Sharma S, Petsalaki E. International journal of molecular sciences Volume 19 (2018) DOI: 10.3390/ijms19040933
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Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors
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Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis.
Steely CJ, Baker JN, Walker JA, Loupe CD, Baboon Genome Analysis Consortium, Batzer MA. Mobile DNA Volume 9 (2018) p.10 DOI: 10.1186/s13100-018-0115-6
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. Nature microbiology Volume 3 (2018) p.514-522 DOI: 10.1038/s41564-018-0123-9
SpatialDE: identification of spatially variable genes.
Svensson V, Teichmann SA, Stegle O. Nature methods Volume 15 (2018) p.343-346 DOI: 10.1038/nmeth.4636
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A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources
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Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.
Tyzack JD, Fernando L, Ribeiro AJM, Borkakoti N, Thornton JM. Structure (London, England : 1993) Volume 26 (2018) p.565-571.e3 DOI: 10.1016/j.str.2018.02.009
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Quantifying the impact of public omics data
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Cabili MN, Carey K, Dyke SOM, Brookes AJ, Fiume M, Jeanson F, Kerry G, Lash A, Sofia H, Spalding D, Tasse AM, Varma S, Pandya R. Scientific data Volume 5 (2018) p.180039 DOI: 10.1038/sdata.2018.39
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.
Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E. PLoS computational biology Volume 14 (2018) p.e1006002 DOI: 10.1371/journal.pcbi.1006002
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Journal of integrative bioinformatics Volume 15 (2018) DOI: 10.1515/jib-2017-0081
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The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis
Melamed A, Yaguchi H, Miura M, Witkover A, Fitzgerald TW, Birney E, Bangham CRM. Preprint DOI: 10.1101/277335
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Tian AL, Lu M, Calderón-Mantilla G, Petsalaki E, Dottorini T, Tian X, Wang Y, Huang SY, Hou JL, Li X, Elsheikha HM, Zhu XQ. Parasites & vectors Volume 11 (2018) p.152 DOI: 10.1186/s13071-018-2745-4
Convergent genomic signatures of domestication in sheep and goats.
Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, Joost S, Ajmone-Marsan P, Negrini R, Orlando L, Rezaei HR, Naderi S, Clarke L, Flicek P, Wincker P, Coissac E, Kijas J, Tosser-Klopp G, Chikhi A, Bruford MW, Taberlet P, Pompanon F. Nature communications Volume 9 (2018) p.813 DOI: 10.1038/s41467-018-03206-y
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Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
Berndt N, Egners A, Mastrobuoni G, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Olde Damink S, Erdem M, Saez-Rodriguez J, Holzhuetter H, Kempa S, Cramer T. Preprint DOI: 10.1101/275040
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CELLector: Genomics Guided Selection of Cancer in vitro Models
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Molecular Genetic Analysis Subdivided by Adversity Exposure Suggests Etiologic Heterogeneity in Major Depression.
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Gene Unprediction with Spurio: A tool to identify spurious protein sequences.
Höps W, Jeffryes M, Bateman A. F1000Research Volume 7 (2018) p.261 DOI: 10.12688/f1000research.14050.1
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Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S. Acta crystallographica. Section D, Structural biology Volume 74 (2018) p.237-244 DOI: 10.1107/S2059798318003303
ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.
Pineda SS, Chaumeil PA, Kunert A, Kaas Q, Thang MWC, Le L, Nuhn M, Herzig V, Saez NJ, Cristofori-Armstrong B, Anangi R, Senff S, Gorse D, King GF. Bioinformatics (Oxford, England) Volume 34 (2018) p.1074-1076 DOI: 10.1093/bioinformatics/btx661
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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
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Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Menden MP, Cheng Y, Calzone L, Martignetti L, Ori A, Iskar M, Gillet L, Zhong Q, Varma S, Schmitt U, Qiu P, Sun Y, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Saez-Rodriguez J, Reinhold WC, Sander C, Pommier Y, Aebersold R. Preprint DOI: 10.1101/268953
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Jupe S, Ray K, Roca CD, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H. The Journal of allergy and clinical immunology Volume 141 (2018) p.1411-1416 DOI: 10.1016/j.jaci.2017.12.992
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A High-Resolution Genetic Map for the Laboratory Rat
Littrell J, Tsaih S, Baud A, Rastas PM, Solberg-Woods L, Flister M. Preprint DOI: 10.1101/268227
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Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT
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Exploring autophagy with Gene Ontology.
Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. Autophagy Volume 14 (2018) p.419-436 DOI: 10.1080/15548627.2017.1415189
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog.
Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL. Genome biology Volume 19 (2018) p.21 DOI: 10.1186/s13059-018-1396-2
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Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D, The DREAM Module Identification Challenge Consortium. Preprint DOI: 10.1101/265553
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Lees J, Galardini M, Bentley SD, Weiser JN, Corander J. Preprint DOI: 10.1101/266312
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Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis
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Peng K, Jin L, Niu YD, Huang Q, McAllister TA, Yang HE, Denise H, Xu Z, Acharya S, Wang S, Wang Y. Applied and environmental microbiology Volume 84 (2018) DOI: 10.1128/AEM.02274-17
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A functional landscape of chronic kidney disease entities from public transcriptomic data
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Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.
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ProForma: A Standard Proteoform Notation.
LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO. Journal of proteome research Volume 17 (2018) p.1321-1325 DOI: 10.1021/acs.jproteome.7b00851
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Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci
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Correction: Pockets as structural descriptors of EGFR kinase conformations.
Hasenahuer MA, Barletta GP, Fernandez-Alberti S, Parisi G, Fornasari MS. PloS one Volume 13 (2018) p.e0192815 DOI: 10.1371/journal.pone.0192815
Harmonising phenomics information for a better interoperability in the rare disease field.
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Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction
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Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
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The development and application of bioinformatics core competencies to improve bioinformatics training and education.
Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L. PLoS computational biology Volume 14 (2018) p.e1005772 DOI: 10.1371/journal.pcbi.1005772
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.
Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP. Circulation. Genomic and precision medicine Volume 11 (2018) p.e001813 DOI: 10.1161/CIRCGEN.117.001813
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Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors
Wagih O, Merico D, Delong A, Frey BJ. Preprint DOI: 10.1101/253427
NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.
Gaude E, Schmidt C, Gammage PA, Dugourd A, Blacker T, Chew SP, Saez-Rodriguez J, O'Neill JS, Szabadkai G, Minczuk M, Frezza C. Molecular cell Volume 69 (2018) p.581-593.e7 DOI: 10.1016/j.molcel.2018.01.034
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
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LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies
Hannah MV, Casale FP, Stegle O, Birney E. Preprint DOI: 10.1101/255497
Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.
Pratas MI, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP. Scientific reports Volume 8 (2018) p.1717 DOI: 10.1038/s41598-018-19820-1
Reactome graph database: Efficient access to complex pathway data.
Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H. PLoS computational biology Volume 14 (2018) p.e1005968 DOI: 10.1371/journal.pcbi.1005968
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Dawn and photoperiod sensing by phytochrome A
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A SNP panel for identification of DNA and RNA specimens.
Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, BIOS consortium, 't Hoen PAC. BMC genomics Volume 19 (2018) p.90 DOI: 10.1186/s12864-018-4482-7
Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains.
Monk D, Morales J, den Dunnen JT, Russo S, Court F, Prawitt D, Eggermann T, Beygo J, Buiting K, Tümer Z, Nomenclature group of the European Network for Human Congenital Imprinting Disorders. Epigenetics Volume 13 (2018) p.117-121 DOI: 10.1080/15592294.2016.1264561
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Gene Expression-Based Drug Repurposing to Target Ageing
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Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution.
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Identification of genetic elements in metabolism by high-throughput mouse phenotyping.
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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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FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies
Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister A, Thurston M, Batista D, Granell R, Adekale M, Dauga D, Ganley E, Hodson S, Lawrence R, Khodiyar V, Tenenbaum J, Axton JM, Ball M, Besson S, Bloom T, Bonazzi V, Jimenez R, Carr D, Chan WM, Chung C, Clement-Stoneham G, Cousijn H, Dayalan S, Dumontier M, Dzale Yeumo E, Edmunds S, Everitt N, Fripp D, Goble C, Golebiewski M, Hall N, Hanisch R, Hucka M, Huerta M, Kenall A, Kiley R, Klenk J, Koureas D, Larkin J, Lemberger T, Lynch N, Schriml L, Ma'ayan A, MacCallum C, Mons B, Moore J, Muller W, Murray H, Nobusada T, Noesgaard D, Paxton-Boyd J, Orchard S, Rustici G, Schurer S, Sharples K, Soares e Silva M, Stanford NJ, Subirats-Coll I, Swedlow J, Tong W, Wilkinson M, Wise J, Yilmaz P. Preprint DOI: 10.1101/245183
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The genome of the biting midgeCulicoides sonorensisand 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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Mutation accumulation differentially impacts ageing in mammalian tissues
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Beyond the ribosome: proteome-wide secretability studies using SECRiFY
Boone M, Ramasamy P, Maddelein D, Turan D, Vandermarliere E, Vranken W, Callewaert N. Preprint DOI: 10.1101/241349
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
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
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
Perturbation-response genes reveal signaling footprints in cancer gene expression.
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Nature communications Volume 9 (2018) p.20 DOI: 10.1038/s41467-017-02391-6
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Biotea: semantics for Pubmed Central.
Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. PeerJ Volume 6 (2018) p.e4201 DOI: 10.7717/peerj.4201
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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Proteomic Profiling of Secreted Proteins, Exosomes, and Microvesicles in Cell Culture Conditioned Media.
Sinha A, Principe S, Alfaro J, Ignatchenko A, Ignatchenko V, Kislinger T. Methods in molecular biology (Clifton, N.J.) Volume 1722 (2018) p.91-102 DOI: 10.1007/978-1-4939-7553-2_6
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
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
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S, Boland MA, Hunter FMI, Ten Hoopen P, Alako B, Amid C, Wilkinson DJ, Curtis TP, Cochrane G, Finn RD. Nucleic acids research Volume 46 (2018) p.D726-D735 DOI: 10.1093/nar/gkx967
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Nucleic acids research Volume 46 (2018) p.D335-D342 DOI: 10.1093/nar/gkx1038
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 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
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 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
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
Ensembl variation resources.
Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P, Cunningham F. Database : the journal of biological databases and curation Volume 2018 (2018) DOI: 10.1093/database/bay119
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
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Three-dimensional cardiovascular imaging-genetics: a mass univariate framework.
Biffi C, de Marvao A, Attard MI, Dawes TJW, Whiffin N, Bai W, Shi W, Francis C, Meyer H, Buchan R, Cook SA, Rueckert D, O'Regan DP. Bioinformatics (Oxford, England) Volume 34 (2018) p.97-103 DOI: 10.1093/bioinformatics/btx552
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
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
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
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
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
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
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
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
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
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
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
Ensembl 2018.
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P. Nucleic acids research Volume 46 (2018) p.D754-D761 DOI: 10.1093/nar/gkx1098
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
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
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
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
Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes.
Graham AM, Lavretsky P, Muñoz-Fuentes V, Green AJ, Wilson RE, McCracken KG. Genome biology and evolution Volume 10 (2018) p.14-32 DOI: 10.1093/gbe/evx253
The 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
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