Daniel R. Zerbino, PhD - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 
 European Bioinformatics Institute University of Cambridge, Cambridge, England, United Kingdom 

28 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
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  0.36
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  0.36
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  0.4
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  0.4
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  0.4
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  0.4
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  0.36
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
2013 Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods. 10: 1177-84. PMID 24185837 DOI: 10.1038/Nmeth.2714  0.4
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  0.4
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  0.4
2012 Zerbino DR, Paten B, Haussler D. Integrating genomes Science. 336: 179-182. PMID 22499938 DOI: 10.1126/science.1216830  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
2008 Han R, Leo-Macias A, Zerbino D, Bastolla U, Contreras-Moreira B, Ortiz AR. An efficient conformational sampling method for homology modeling Proteins: Structure, Function and Genetics. 71: 175-188. PMID 17985353 DOI: 10.1002/Prot.21672  0.4
2005 Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. Core deformations in protein families: A physical perspective Biophysical Chemistry. 115: 125-128. PMID 15752593 DOI: 10.1016/J.Bpc.2004.12.016  0.4
2005 Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. An analysis of core deformations in protein superfamilies Biophysical Journal. 88: 1291-1299. PMID 15542556 DOI: 10.1529/Biophysj.104.052449  0.4
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