Daniel Zerbino

Daniel Zerbino

Team Leader, Genome Analysis

Daniel Zerbino leads the Genome Analysis team, which focuses on the functional annotation of sequence variants and non-genic regions. Daniel completed his PhD at EMBL-EBI, studying de novo assembly of next-generation sequencing data, and developed the Velvet assembler. After a postdoc at the University of California Santa Cruz analysing RNA-Seq data and studying the mathematics of sequence rearrangements, he returned to EMBL-EBI to lead Ensembl Regulation before leading the Genome Analysis team. Daniel's background is in mathematics and computer engineering, and he holds a joint degree from the École Polytechnique and the École des Mines in France.

ORCID iD: 0000-0001-5350-3056

Tel:+44 (0)1223 494 130 / Fax:+44 (0)1223 494 468

Zerbino team

The Genome Analysis team focuses on phenotypic changes, at molecular and organism levels, that are caused by the genome and its variants. This includes the functional annotation of non-coding variants, a field which we have only started to investigate but which will likely help advance a large number of genetic association studies.



The ensembl regulatory build.
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR.
Genome Biol Volume 16 (2015) p.56
DOI: 10.1186/s13059-015-0621-5

Ensembl 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, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P.
Nucleic Acids Res Volume 43 (2015) p.d662-9
DOI: 10.1093/nar/gku1010

Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B.
J Comput Biol Volume 22 (2015) p.387-401
DOI: 10.1089/cmb.2014.0146


WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P.
Bioinformatics Volume 30 (2014) p.1008-1009
DOI: 10.1093/bioinformatics/btt737

Ensembl 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, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SM.
Nucleic Acids Res Volume 42 (2014) p.d749-55
DOI: 10.1093/nar/gkt1196

A unifying model of genome evolution under parsimony.
Paten B, Zerbino DR, Hickey G, Haussler D.
BMC Bioinformatics Volume 15 (2014) p.206
DOI: 10.1186/1471-2105-15-206


Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P, RGASP Consortium.
Nat Methods Volume 10 (2013) p.1177-1184
DOI: 10.1038/nmeth.2714

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV.
Brief Bioinform Volume 14 (2013) p.548-555
DOI: 10.1093/bib/bbt045

HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Hickey G, Paten B, Earl D, Zerbino D, Haussler D.
Bioinformatics Volume 29 (2013) p.1341-1342
DOI: 10.1093/bioinformatics/btt128


Comprehensive molecular characterization of human colon and rectal cancer.
Cancer Genome Atlas Network.
Nature Volume 487 (2012) p.330-337
DOI: 10.1038/nature11252

Integrating genomes.
Zerbino DR, Paten B, Haussler D.
Science Volume 336 (2012) p.179-182
DOI: 10.1126/science.1216830

Comprehensive genomic characterization of squamous cell lung cancers.
Cancer Genome Atlas Research Network.
Nature Volume 489 (2012) p.519-525
DOI: 10.1038/nature11404

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E.
Bioinformatics Volume 28 (2012) p.1086-1092
DOI: 10.1093/bioinformatics/bts094


Assemblathon 1: a competitive assessment of de novo short read assembly methods.
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, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.
Genome Res Volume 21 (2011) p.2224-2241
DOI: 10.1101/gr.126599.111

Cactus: Algorithms for genome multiple sequence alignment.
Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.
Genome Res Volume 21 (2011) p.1512-1528
DOI: 10.1101/gr.123356.111

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics Volume 27 (2011) p.2156-2158
DOI: 10.1093/bioinformatics/btr330


A new strategy for genome assembly using short sequence reads and reduced representation libraries.
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.
Genome Res Volume 20 (2010) p.249-256
DOI: 10.1101/gr.097956.109

Using the Velvet de novo assembler for short-read sequencing technologies.
Zerbino DR.
Curr Protoc Bioinformatics Volume Chapter 11 (2010) p.unit 11.5
DOI: 10.1002/0471250953.bi1105s31

Improvements to services at the European Nucleotide Archive.
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, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G.
Nucleic Acids Res Volume 38 (2010) p.d39-45
DOI: 10.1093/nar/gkp998


Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
Zerbino DR, McEwen GK, Margulies EH, Birney E.
PLoS One Volume 4 (2009) p.e8407
DOI: 10.1371/journal.pone.0008407


Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E.
Genome Res Volume 18 (2008) p.821-829
DOI: 10.1101/gr.074492.107

An efficient conformational sampling method for homology modeling.
Han R, Leo-Macias A, Zerbino D, Bastolla U, Contreras-Moreira B, Ortiz AR.
Proteins Volume 71 (2008) p.175-188
DOI: 10.1002/prot.21672


Core deformations in protein families: a physical perspective.
Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR.
Biophys Chem Volume 115 (2005) p.125-128
DOI: 10.1016/j.bpc.2004.12.016

An analysis of core deformations in protein superfamilies.
Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR.
Biophys J Volume 88 (2005) p.1291-1299
DOI: 10.1529/biophysj.104.052449


Team members

Fiona Cunningham
Laurent Gil
Sarah Hunt
Thomas Juettemann
Ilias Lavidas
William McLaren
Michael Nuhn
Anja Thormann
Steven Wilder