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Daniel R. Zerbino, PhD - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 
 European Bioinformatics Institute University of Cambridge, Cambridge, England, United Kingdom 
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47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, ... ... Zerbino DR, et al. Ensembl 2022. Nucleic Acids Research. PMID 34791404 DOI: 10.1093/nar/gkab1049  0.513
2021 De Silva NH, Bhai J, Chakiachvili M, Contreras-Moreira B, Cummins C, Frankish A, Gall A, Genez T, Howe KL, Hunt SE, Martin FJ, Moore B, Ogeh D, Parker A, Parton A, ... ... Zerbino DR, et al. The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. Nucleic Acids Research. PMID 34634797 DOI: 10.1093/nar/gkab889  0.416
2021 Gundersen S, Boddu S, Capella-Gutierrez S, Drabløs F, Fernández JM, Kompova R, Taylor K, Titov D, Zerbino D, Hovig E. Recommendations for the FAIRification of genomic track metadata. F1000research. 10. PMID 34249331 DOI: 10.12688/f1000research.28449.1  0.46
2021 Harrison PW, Sokolov A, Nayak A, Fan J, Zerbino D, Cochrane G, Flicek P. The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes. Frontiers in Genetics. 12: 639238. PMID 34220930 DOI: 10.3389/fgene.2021.639238  0.405
2021 Gundersen S, Boddu S, Capella-Gutierrez S, Drabløs F, Fernández JM, Kompova R, Taylor K, Titov D, Zerbino D, Hovig E. Recommendations for the FAIRification of genomic track metadata F1000research. 10: 268. DOI: 10.12688/F1000RESEARCH.28449.1  0.459
2020 Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, ... ... Zerbino D, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087  0.69
2020 Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, ... ... Zerbino DR, et al. Ensembl 2021. Nucleic Acids Research. PMID 33137190 DOI: 10.1093/nar/gkaa942  0.548
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, ... ... Zerbino DR, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8  0.355
2020 Zerbino DR, Frankish A, Flicek P. Progress, Challenges, and Surprises in Annotating the Human Genome. Annual Review of Genomics and Human Genetics. PMID 32421357 DOI: 10.1146/Annurev-Genom-121119-083418  0.572
2020 Peat G, Jones W, Nuhn M, Marugán JC, Newell W, Dunham I, Zerbino D. The Open Targets Post-GWAS analysis pipeline. Bioinformatics (Oxford, England). PMID 31930349 DOI: 10.1093/Bioinformatics/Btaa020  0.393
2019 Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, ... ... Zerbino DR, et al. Ensembl 2020. Nucleic Acids Research. PMID 31691826 DOI: 10.1093/nar/gkz966  0.531
2019 Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino DR. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics (Oxford, England). PMID 31368484 DOI: 10.1093/Bioinformatics/Btz597  0.706
2019 Titov D, Gundersen S, Kompova R, Capella-Gutierrez S, Drabløs F, Fernández JM, Taylor K, Zerbino D, Hovig E. TrackFind – FAIR search of genomic tracks F1000research. 8. DOI: 10.7490/F1000Research.1117098.1  0.506
2018 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, ... ... Zerbino DR, et al. Ensembl 2019. Nucleic Acids Research. PMID 30407521 DOI: 10.1093/nar/gky1113  0.502
2018 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, ... ... Zerbino D, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955  0.695
2018 Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. Animal Genetics. PMID 30311252 DOI: 10.1111/Age.12736  0.414
2017 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, et al. Ensembl 2018. Nucleic Acids Research. PMID 29155950 DOI: 10.1093/nar/gkx1098  0.53
2017 Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Database : the Journal of Biological Databases and Curation. 2017. PMID 28365736 DOI: 10.1093/Database/Bax020  0.608
2017 Corbett S, Juettemann T, Kostadima M, Cunningham F, Zerbino DR, Flicek P. The EMBL-EBI CRISPR archive F1000research. 6. DOI: 10.7490/F1000Research.1113950.1  0.312
2016 Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, ... ... Zerbino DR, et al. Ensembl 2017. Nucleic Acids Research. PMID 27899575 DOI: 10.1093/nar/gkw1104  0.509
2016 Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, ... ... Zerbino DR, et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell. 167: 1369-1384.e19. PMID 27863249 DOI: 10.1016/J.Cell.2016.09.037  0.402
2016 Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. Bmc Bioinformatics. 17: 400. PMID 27687569 DOI: 10.1186/S12859-016-1258-4  0.696
2016 Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, ... ... Zerbino DR, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics. PMID 27111036 DOI: 10.1038/Ng.3559  0.453
2016 Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, et al. Ensembl regulation resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 26888907 DOI: 10.1093/Database/Bav119  0.607
2016 Zerbino D. Integrative analysis of genomic function in Ensembl F1000research. 5. DOI: 10.7490/F1000Research.1111374.1  0.509
2015 Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, ... ... Zerbino DR, et al. Ensembl 2016. Nucleic Acids Research. PMID 26687719 DOI: 10.1093/nar/gkv1157  0.627
2015 Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. The ensembl regulatory build. Genome Biology. 16: 56. PMID 25887522 DOI: 10.1186/S13059-015-0621-5  0.485
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 387-401. PMID 25565268 DOI: 10.1089/Cmb.2014.0146  0.728
2015 Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, ... ... Zerbino DR, et al. Ensembl 2015. Nucleic Acids Research. 43: D662-9. PMID 25352552 DOI: 10.1093/nar/gku1010  0.611
2015 Ballinger TJ, Zerbino D, Paten B, Haussler D. Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-11  0.668
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population Journal of Computational Biology. 22: 387-401. DOI: 10.1089/cmb.2014.0146  0.641
2014 Paten B, Zerbino DR, Hickey G, Haussler D. A unifying model of genome evolution under parsimony Bmc Bioinformatics. 15. PMID 24946830 DOI: 10.1186/1471-2105-15-206  0.676
2014 Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics (Oxford, England). 30: 1008-9. PMID 24363377 DOI: 10.1093/Bioinformatics/Btt737  0.515
2014 Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, ... ... Zerbino DR, et al. Ensembl 2014. Nucleic Acids Research. 42: D749-55. PMID 24316576 DOI: 10.1093/nar/gkt1196  0.611
2014 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Haussler D, Paten B. Building a pangenome reference for a population Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8394: 207-221. DOI: 10.1007/978-3-319-05269-4-17  0.464
2013 Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Briefings in Bioinformatics. 14: 548-55. PMID 23793381 DOI: 10.1093/Bib/Bbt045  0.387
2013 Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: A hierarchical format for storing and analyzing multiple genome alignments Bioinformatics. 29: 1341-1342. PMID 23505295 DOI: 10.1093/Bioinformatics/Btt128  0.734
2012 Zerbino DR, Paten B, Haussler D. Integrating genomes Science. 336: 179-182. PMID 22499938 DOI: 10.1126/science.1216830  0.682
2012 Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (Oxford, England). 28: 1086-92. PMID 22368243 DOI: 10.1093/Bioinformatics/Bts094  0.629
2011 Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111  0.731
2011 Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment Genome Research. 21: 1512-1528. PMID 21665927 DOI: 10.1101/Gr.123356.111  0.684
2011 Radenbaugh A, Sanborn JZ, Zerbino D, Wilks C, Stuart JM, Haussler D. Abstract 59: Identification of RNA editing events in cancer using high-throughput sequencing data Cancer Research. 71: 59-59. DOI: 10.1158/1538-7445.Am2011-59  0.404
2010 Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies Current Protocols in Bioinformatics. 11.5.1-11.5.12. PMID 20836074 DOI: 10.1002/0471250953.Bi1105S31  0.42
2010 Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Research. 20: 249-56. PMID 20123915 DOI: 10.1101/Gr.097956.109  0.715
2010 Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, ... ... Zerbino D, et al. Improvements to services at the European Nucleotide Archive. Nucleic Acids Research. 38: D39-45. PMID 19906712 DOI: 10.1093/Nar/Gkp998  0.591
2009 Zerbino DR, McEwen GK, Margulies EH, Birney E. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. Plos One. 4: e8407. PMID 20027311 DOI: 10.1371/Journal.Pone.0008407  0.618
2008 Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. 18: 821-9. PMID 18349386 DOI: 10.1101/Gr.074492.107  0.612
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