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List of works by Ewan Birney

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

scientific article

A Draft Sequence of the Neandertal Genome

scientific article

A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.

scientific article published on August 2017

A SNP map of the rat genome generated from cDNA sequences

scientific article

A call for public archives for biological image data

scientific article published on 01 November 2018

A database and API for variation, dense genotyping and resequencing data

scientific article

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

scientific article published in April 2022

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

scientific article

A physical map of the mouse genome

scientific article

A putative homolog of U2AF65 in S. cerevisiae

scientific article (publication date: 11 September 1992)

A putative homology of U2AF65 in S. cerevisiae

scientific article published in March 1993

A roadmap for restoring trust in Big Data

article by Mark Lawler et al published August 2018 in Lancet Oncology Commission

A small-cell lung cancer genome with complex signatures of tobacco exposure

scientific article

A survey of homozygous deletions in human cancer genomes

scientific article

A transcription factor collective defines cardiac cell fate and reflects lineage history

scientific article

Advanced genomic data mining

scientific article

Allele-specific and heritable chromatin signatures in humans

scientific article published on 16 September 2010

An effective model for natural selection in promoters

scientific article

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

scientific article

An overview of Ensembl

scientific article (publication date: May 2004)

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Analysis of variation at transcription factor binding sites in Drosophila and humans

scientific article published in 2012

Apollo: a sequence annotation editor

scientific article

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

scientific article published on April 2008

Arabidopsis reactome: a foundation knowledgebase for plant systems biology

article

Archaic humans: Four makes a party.

scientific article published on 18 December 2013

Assemblies: the good, the bad, the ugly ⬇️

scientific article published on January 1, 2011

Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences

scientific article published on 01 February 2019

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 01 November 2019

Automated generation of heuristics for biological sequence comparison

scientific article published in 2005

Biological database design and implementation

scientific article

Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science

scientific article published on 15 May 2019

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration

scientific article published on 26 September 2016

COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records

scientific article published in 2022

Cancer and genomics

scientific article

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

scientific article

Challenges and standards in integrating surveys of structural variation

scientific article published on July 2007

Chromatin and heritability: how epigenetic studies can complement genetic approaches ⬇️

scientific article published on March 16, 2011

ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.

scientific article published on 9 March 2018

ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

scientific article

Common genetic variation drives molecular heterogeneity in human iPSCs

Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs

scientific article

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

scientific article (publication date: 4 October 2002)

Comparative genomics: genome-wide analysis in metazoan eukaryotes

scientific article

Comparison of Associations with Different Macular Inner Retinal Thickness Parameters in a Large Cohort: The UK Biobank

scientific article published on 21 August 2019

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment

scientific article published on 12 April 2004

Confounding between recombination and selection, and the Ped/Pop method for detecting selection

scientific article published on 10 July 2008

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses ⬇️

scientific article published on February 21, 2011

Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association

scientific article published on 28 April 2015

Correction: Reactome: a knowledge base of biologic pathways and processes.

scientific article published on 4 February 2009

Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

scientific article published in October 2017

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published in Nature

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Databases and tools for browsing genomes

scientific article

Defining functional DNA elements in the human genome

scientific article

Discovering novel cis-regulatory motifs using functional networks

scientific article published in May 2003

Double Dutch for duplications

Dry work in a wet world: computation in systems biology

scientific article

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison

scientific article published on January 1, 1997

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

EMMA--mouse mutant resources for the international scientific community

scientific article

ENFIN - An Integrative Structure for Systems Biology

article

ENFIN a network to enhance integrative systems biology

scientific article published on 12 October 2007

ENFIN--A European network for integrative systems biology

scientific article

Efficient storage of high throughput DNA sequencing data using reference-based compression

scientific article

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

scientific article

EnsMart: a generic system for fast and flexible access to biological data

scientific article (publication date: 2004)

Ensembl 2002: accommodating comparative genomics

scientific article published on January 2003

Ensembl 2004

scientific article (publication date: 2004)

Ensembl 2005

scientific article

Ensembl 2006.

scientific article

Ensembl 2007

scientific article

Ensembl 2008

scientific article

Ensembl 2009

scientific article (publication date: 2009)

Ensembl 2011

scientific article

Ensembl 2012

scientific article

Ensembl 2013

scientific article

Ensembl 2014

scientific article

Ensembl 2015

scientific article (publication date: 2015)

Ensembl 2016

scientific article

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

scientific article

Ensembl Genomes: extending Ensembl across the taxonomic space

scientific article

Ensembl regulation resources

scientific article published on 17 February 2016

Ensembl variation resources

scientific article published in 2010

Ensembl's 10th year

scientific article

Ensembl: a genome infrastructure

scientific article published on January 2003

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

scientific article

Epigenome-wide Association Studies and the Interpretation of Disease -Omics

scientific article

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Estimating the neutral rate of nucleotide substitution using introns

scientific article published in February 2007

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria

scientific article

Evolutionary genomics: come fly with us.

scientific article published in November 2007

FORGE : A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions

FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

scientific article

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

scientific article

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

article

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals

scientific article published on 28 January 2019

GREENER principles for environmentally sustainable computational science

Gene finding in the chicken genome

scientific article

GeneWise and Genomewise

scientific article published in May 2004

Genetic and functional insights into the fractal structure of the heart

scientific article published on 19 August 2020

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

scientific article

Genetic variants regulating expression levels and isoform diversity during embryogenesis

scientific article published on 26 December 2016

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome annotation techniques: new approaches and challenges

scientific article

Genome browsing with Ensembl: a practical overview.

scientific article

Genome information resources - developments at Ensembl

scientific article published on June 2004

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome wide association analysis of the heart using high-resolution 3D cardiac MRI identifies new genetic loci underlying cardiac structure and function

scientific article published on 27 January 2016

Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Genome-wide meta-analysis identifies new susceptibility loci for migraine

scientific article

Genome-wide nucleotide-level mammalian ancestor reconstruction

scientific article (publication date: November 2008)

Genomic analysis reveals a functional role for myocardial trabeculae in adults

Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish

scientific article published on 20 March 2014

Genomic information infrastructure after the deluge

scientific article

Genomic reconstruction of the SARS-CoV-2 epidemic in England

scientific article

Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase

scientific article

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

scientific article published on 21 February 2022

Genomics in healthcare: GA4GH looks to 2022

article

Heritable individual-specific and allele-specific chromatin signatures in humans

scientific article

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

scientific article

Highly accurate protein structure prediction for the human proteome

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

scientific article published on 7 February 2013

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of domains from protein sequences

scientific article published on 01 January 2000

Identification of novel peptide hormones in the human proteome by hidden Markov model screening.

scientific article published on 6 February 2007

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors

Immunity-related genes and gene families in Anopheles gambiae

scientific article published in October 2002

Improvements to services at the European Nucleotide Archive

scientific article

In vivo validation of a computationally predicted conserved Ath5 target gene set

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integrating Genomics into Healthcare: A Global Responsibility

scientific article published on 01 January 2019

Integrating biological data--the Distributed Annotation System

scientific article

Integration of cytogenetic landmarks into the draft sequence of the human genome

scientific article published in Nature

Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle

scientific article published on 10 May 2019

Integrative annotation of chromatin elements from ENCODE data

scientific article

Integrative knowledge management to enhance pharmaceutical R&D

scientific article

InterPro--an integrated documentation resource for protein families, domains and functional sites

scientific article (publication date: December 2000)

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

article

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

scientific article published on 16 April 2018

International network of cancer genome projects

scientific article

Journey to the genetic interior. Interview by Stephen S Hall

scientific article published on October 1, 2012

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

scientific article

Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 27 August 2019

Levers and fulcrums: progress in cis-regulatory motif models

scientific article published in April 2008

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

scientific article

MAPU 2.0: high-accuracy proteomes mapped to genomes

scientific article published on 23 October 2008

Major submissions tool developments at the European Nucleotide Archive

scientific article

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

scientific article

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

scientific article

MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.

scientific article published on 31 May 2017

Mining the draft human genome

scientific article

Modeling gene expression using chromatin features in various cellular contexts

scientific article (publication date: 13 June 2012)

Mouse genomic variation and its effect on phenotypes and gene regulation

scientific article (publication date: 14 September 2011)

Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs

scientific article published on 01 April 2022

Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels ⬇️

scientific article (publication date: 15 April 2012)

Open Targets: a platform for therapeutic target identification and validation

scientific article

Open annotation offers a democratic solution to genome sequencing

scientific article published in Nature

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

scientific article

Optimising oligonucleotide array design for ChIP-on-chip.

scientific article

Optimized design and assessment of whole genome tiling arrays.

scientific article published on July 2007

PH domain: the first anniversary

scientific article (publication date: September 1994)

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames

scientific article published on 15 July 1996

Paralogous annotation of disease-causing variants in long QT syndrome genes

scientific article

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler

scientific article

Petabyte-scale innovations at the European Nucleotide Archive

scientific article

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

scientific article

Pfam: multiple sequence alignments and HMM-profiles of protein domains

scientific article published in January 1998

PhenotypeSimulator: a comprehensive framework for multi-trait, multi-locus phenotype to genotype simulation

scientific article published on 29 March 2018

Picking pyknons out of the human genome

scientific article published on 2 June 2006

Policy challenges of clinical genome sequencing

scientific article published in the British Medical Journal

Prepublication data sharing

scientific article

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database

scientific article (publication date: 2008)

Progress in Medicine: Experts Take Stock

scientific article published on 29 December 2015

Progress in sequencing the mouse genome

article

Promoter shape varies across populations and affects promoter evolution and expression noise

scientific article published on 13 February 2017

ProtEST: protein multiple sequence alignments from expressed sequence tags

scientific article published in February 2000

Protein Sequence Analysis and Domain Identification

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association

scientific article

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

scientific article published on 21 May 2021

RNA modifications detection by comparative Nanopore direct RNA sequencing

scientific article

RNA modifications detection by comparative Nanopore direct RNA sequencing

scientific article published on 10 December 2021

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

Reactome knowledgebase of human biological pathways and processes

scientific article (publication date: 2009)

Reactome – a knowledgebase of human biological pathways

Reactome – a knowledgebase of human biological pathways

Reactome: a database of reactions, pathways and biological processes

scientific article

Reactome: a knowledge base of biologic pathways and processes

scientific article

Reactome: a knowledgebase of biological pathways

scientific article

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004.

scientific article published on June 2005

SNP and haplotype mapping for genetic analysis in the rat.

scientific article

SPEM: a parser for EMBL style flat file database entries

scientific article

Searching databases to find protein domain organization

scientific article

Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription

scientific article published on 29 April 2022

Sense from sequence reads: methods for alignment and assembly

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

scientific article published on September 2012

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

scientific article

Sockeye: a 3D environment for comparative genomics

scientific article

Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

The Anopheles gambiae genome: an update

scientific article published on February 2004

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The Bioperl project

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The Convergence of Research and Clinical Genomics

scientific article published on 01 May 2019

The Distributed Annotation System for Integration of Biological Data

The EBI RDF platform: linked open data for the life sciences

scientific article

The EMBL-EBI channel

scientific article

The Ensembl core software libraries

scientific article

The Ensembl genome database project

scientific article

The European Bioinformatics Institute (EMBL-EBI) in 2021

scientific article published on 25 November 2021

The European Bioinformatics Institute in 2016: Data growth and integration

scientific article

The European Bioinformatics Institute in 2017: data coordination and integration

scientific article published on 25 November 2017

The European Bioinformatics Institute in 2018: tools, infrastructure and training

scientific article published on 01 January 2019

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences

scientific article published on 01 January 2020

The European Bioinformatics Institute's data resources 2014

scientific article

The European Bioinformatics Institute's data resources.

scientific article

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis

scientific article published on 27 November 2020

The European Nucleotide Archive

scientific article

The Genome Knowledgebase: a resource for biologists and bioinformaticists

scientific article published in January 2003

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

scientific article

The HGNC Database in 2008: a resource for the human genome

scientific article

The Human Cell Atlas

scientific article

The Human Cell Atlas

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

scientific article (publication date: 2001)

The International Human Genome Project

scientific article published on 14 July 2021

The Mighty Fruit Fly Moves into Outbred Genetics

scientific article

The Pfam protein families database

scientific article (publication date: 2002)

The Pfam protein families database.

scientific article

The Reactome pathway knowledgebase

scientific article from 2014

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

scientific article

The consequence of natural selection on genetic variation in the mouse

scientific article published on 18 February 2010

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates

scientific article published on 2 December 2005

The end of the start for population sequencing

scientific article published in Nature

The future of DNA sequence archiving

scientific article

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

scientific article

The genomic basis of adaptive evolution in threespine sticklebacks

scientific article

The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis

The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis.

scientific article published on 26 June 2018

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The landscape of histone modifications across 1% of the human genome in five human cell lines

scientific article

The making of ENCODE: Lessons for big-data projects

scientific article

The systematic annotation of the three main GPCR families in Reactome

scientific article

The topography of mutational processes in breast cancer genomes

scientific article published on 02 May 2016

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

scientific article

TranscriptSNPView: a genome-wide catalog of mouse coding variation

scientific article published on August 2006

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

scientific article published on 8 December 2004

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

scientific article published on 24 June 2007

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

scientific article

Unrestricted free access works and must continue

scientific article published in Nature

Update of the Anopheles gambiae PEST genome assembly

scientific article published on January 2007

Using GeneWise in the Drosophila annotation experiment

scientific article published in April 2000

Using human genetics to make new medicines

scientific article published on 15 September 2015

VectorBase: a data resource for invertebrate vector genomics

scientific article

VectorBase: a home for invertebrate vectors of human pathogens

scientific article

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

scientific article

Visualising the Epigenome

What everybody should know about the rat genome and its online resources

scientific article (publication date: May 2008)

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

scientific article

htsget: a protocol for securely streaming genomic data

article

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