D. Zerbino

发表

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

E. Birney, D. Zerbino, 2008, Genome research.

Ensembl regulation resources

Daniel R. Zerbino, Ewan Birney, Michael Nuhn, 2016, Database J. Biol. Databases Curation.

The Ensembl Regulatory Build

P. Flicek, D. Zerbino, P. Flicek, 2015, Genome Biology.

Ensembl 2015

Alessandro Vullo, Daniel R. Zerbino, Laurent Gil, 2014, Nucleic Acids Res..

Comprehensive molecular characterization of human colon and rectal cancer

Steven J. M. Jones, Joshua M. Stuart, Brian D. O’Connor, 2012, Nature.

Comprehensive genomic characterization of squamous cell lung cancers

Steven J. M. Jones, Joshua M. Stuart, Brian D. O’Connor, 2012, Nature.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Nuno A. Fonseca, Shaun D. Jackman, David R. Kelley, 2011, Genome research.

A Quantitative Proteome Map of the Human Body

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2019, Cell.

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

Andrew D. Yates, Manoj Pandian Sakthivel, D. Zerbino, 2020, bioRxiv.

FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community

Peter W. Harrison, G. Cochrane, P. Flicek, 2018, Animal genetics.

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Steven J. M. Jones, Marcel H. Schulz, Richard A. Moore, 2016, Cell.

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Jonathan M. Cairns, Cameron S. Osborne, D. Zerbino, 2015, Genome Biology.

An analysis of core deformations in protein superfamilies.

D. Zerbino, A. Ortiz, P. López-Romero, 2005, Biophysical journal.

Cactus: Algorithms for genome multiple sequence alignment.

David Haussler, Ngan Nguyen, Dent Earl, 2011, Genome research.

Progress, Challenges, and Surprises in Annotating the Human Genome

A. Frankish, P. Flicek, D. Zerbino, 2020, Annual review of genomics and human genetics.

Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies

Daniel R Zerbino, D. Zerbino, 2010, Current protocols in bioinformatics.

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

Daniel R. Zerbino, Ewan Birney, Elliott H. Margulies, 2009, PloS one.

Ensembl 2020

Astrid Gall, Alessandro Vullo, James E. Allen, 2019, Nucleic Acids Res..

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

Jonathan M. Cairns, D. Zerbino, P. Freire-Pritchett, 2015, bioRxiv.

Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids

D. Zerbino, M. Zilbauer, D. Jones, 2022, bioRxiv.

Transcription and DNA Methylation Patterns of Blood-Derived CD8+ T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis

D. Zerbino, J. Satsangi, P. Sarkies, 2020, Gastroenterology.

Core deformations in protein families: a physical perspective.

D. Zerbino, A. Ortiz, P. López-Romero, 2005, Biophysical chemistry.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

Jonathan M. Cairns, D. Zerbino, W. Ouwehand, 2016, Cell.

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data

Andrew D. Yates, Carla A. Cummins, Denye N. Ogeh, 2020, bioRxiv.

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

Maria Cerezo, Paul Flicek, Yaniv Erlich, 2016, Nature Genetics.

ORIGINAL RESEARCH Culture-Associated Q2 DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids

D. Zerbino, M. Zilbauer, R. Foster, 2022 .

An algebraic framework to sample the rearrangement histories of a cancer metagenome with double cut and join, duplication and deletion events

D. Haussler, D. Zerbino, B. Paten, 2013 .

Ensembl 2018

Astrid Gall, Alessandro Vullo, Jane Loveland, 2017, Nucleic Acids Res..

Genetic effects on gene expression across human tissues

Nicola J. Rinaldi, Ian C. McDowell, Christopher D. Brown, 2017, Nature.

An efficient conformational sampling method for homology modeling

Alejandra Leo-Macias, Daniel Zerbino, Ugo Bastolla, 2008, Proteins.

Ensembl 2014

Daniel R. Zerbino, Laurent Gil, Ewan Birney, 2013, Nucleic Acids Res..

GENCODE reference annotation for the human and mouse genomes

Mark Gerstein, Tomás Di Domenico, Jane Loveland, 2018, Nucleic Acids Res..

Ensembl 2017

Alessandro Vullo, Matthew R. Laird, Daniel R. Zerbino, 2016, Nucleic Acids Res..

The impact of rare variation on gene expression across tissues

Gao Wang, Mary Goldman, Brian Craft, 2016, Nature.

Ensembl 2021

Astrid Gall, James E. Allen, Daniel R. Zerbino, 2020, Nucleic Acids Res..

Improvements to services at the European Nucleotide Archive

Ying Cheng, Rodrigo Lopez, Guy Cochrane, 2009, Nucleic Acids Res..

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2021, Cell.

Ensembl 2019

Astrid Gall, Alessandro Vullo, Jane Loveland, 2018, Nucleic Acids Res..

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

Andrew D. Yates, Manoj Pandian Sakthivel, D. Zerbino, 2021, Nature Genetics.

Ensembl 2016

Daniel R. Zerbino, Laurent Gil, Ewan Birney, 2015, Nucleic Acids Res..

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

David Haussler, Glenn Hickey, Daniel R. Zerbino, 2013, BMC Bioinformatics.

Comparative analysis of neutrophil and monocyte epigenomes

Thomas Lengauer, A. Valencia, R. Guigó, 2017, bioRxiv.

GENCODE 2021

James C. Wright, Jonathan M. Mudge, Andrew D. Yates, 2020, Nucleic Acids Res..

Building a Pan-Genome Reference for a Population

David Haussler, Ngan Nguyen, Glenn Hickey, 2015, J. Comput. Biol..

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Martin Vingron, Marcel H. Schulz, Daniel R. Zerbino, 2012, Bioinform..

graphsAlgorithms for de novo short read assembly using de Bruijn

Daniel R. Zerbino, Ewan Birney, E. Birney, 2010 .

The Ensembl Regulatory Build

P. Flicek, D. Zerbino, Nathan Johnson, 2015, Genome Biology.

A Quantitative Proteome Map of the Human Body

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2019, Cell.

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Jonathan M. Cairns, D. Zerbino, P. Freire-Pritchett, 2016, Genome Biology.

The open targets post-GWAS analysis pipeline

William Jones, Gareth Peat, Michael Nuhn, 2020, Bioinform..

Ensembl 2022

James E. Allen, Jonathan M. Mudge, Andrew D. Yates, 2021, Nucleic Acids Res..

The Gene Regulation Knowledge Commons: The action area of GREEKC.

Juan M. Vaquerizas, Pedro T. Monteiro, D. Zerbino, 2021, Biochimica et biophysica acta. Gene regulatory mechanisms.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Building a Pangenome Reference for a Population

David Haussler, Ngan Nguyen, Glenn Hickey, 2014, RECOMB.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

Alessandro Vullo, Matthew R. Laird, Daniel R. Zerbino, 2016, bioRxiv.

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

Daniel R. Zerbino, Paul Flicek, Nathan Johnson, 2013, Bioinform..

HAL: a hierarchical format for storing and analyzing multiple genome alignments

David Haussler, Glenn Hickey, Daniel R. Zerbino, 2013, Bioinform..

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

Dan M. Bolser, Maria Victoria Schneider, Daniel R. Zerbino, 2013, Briefings Bioinform..

CD8+ T-cell transcription and DNA methylation show age specific differences and lack correlation with clinical outcome in pediatric Inflammatory Bowel Disease

D. Zerbino, P. Sarkies, A. Ross, 2020, bioRxiv.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Nicola J. Rinaldi, Ian C. McDowell, Christopher D. Brown, 2018, Nature Communications.

The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes

Peter W. Harrison, G. Cochrane, D. Zerbino, 2021, Frontiers in Genetics.

Sequence tube maps: making graph genomes intuitive to commuters

Benedict Paten, Glenn Hickey, Vanessa H. Tan, 2019, Bioinform..

Recommendations for the FAIRification of genomic track metadata

Finn Drabløs, Daniel R. Zerbino, Eivind Hovig, 2021, F1000Research.

A new strategy for genome assembly using short sequence reads and reduced representation libraries.

Ewan Birney, James C Mullikin, E. Birney, 2010, Genome research.

Integrating Genomes

D. Haussler, B. Paten, D. Haussler, 2012, Science.

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

D. Haussler, D. Zerbino, B. Paten, 2013, BMC Bioinformatics.

A Unifying Parsimony Model of Genome Evolution

David Haussler, Daniel R. Zerbino, Benedict Paten, 2013 .

A unifying model of genome evolution under parsimony

David Haussler, Glenn Hickey, Daniel R. Zerbino, 2013, BMC Bioinformatics.

Additional File 3 : The CHiCAGO R package vignette

Jonathan M. Cairns, Plagnol, D. Zerbino, 2016 .

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Mary Goldman, Brian Craft, Jingchun Zhu, 2016, Nature Communications.

Sequence ontology terminology for gene regulation.

D. Zerbino, C. Mungall, S. Schulz, 2021, Biochimica et biophysica acta. Gene regulatory mechanisms.