Ewan Birney

Ewan Birney

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Ewan Birney

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The Convergence of Research and Clinical Genomics.

Authors:
Ewan Birney

Am J Hum Genet 2019 May;104(5):781-783

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507036PMC
May 2019

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

Nature 2019 02;566(7742):E1

Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

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http://www.nature.com/articles/s41586-019-0883-2
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http://dx.doi.org/10.1038/s41586-019-0883-2DOI Listing
February 2019

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

Nucleic Acids Res 2019 Jan;47(D1):D15-D22

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gky1124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323906PMC
January 2019

Integrating Genomics into Healthcare: A Global Responsibility.

Am J Hum Genet 2019 Jan;104(1):13-20

Australian Genomics Health Alliance, Melbourne VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia; Global Alliance for Genomics and Health, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2018.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323624PMC
January 2019

A call for public archives for biological image data.

Nat Methods 2018 11;15(11):849-854

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/s41592-018-0195-8DOI Listing
November 2018

PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships.

Bioinformatics 2018 09;34(17):2951-2956

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129313PMC
September 2018

A roadmap for restoring trust in Big Data.

Lancet Oncol 2018 08;19(8):1014-1015

European Alliance for Personalised Medicine, Brussels, Belgium; Gustave Roussy Cancer Campus Grand Paris, Villejuif, France.

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http://dx.doi.org/10.1016/S1470-2045(18)30425-XDOI Listing
August 2018

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

PLoS Comput Biol 2018 03 9;14(3):e1006002. Epub 2018 Mar 9.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1006002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862484PMC
March 2018

The European Bioinformatics Institute in 2017: data coordination and integration.

Nucleic Acids Res 2018 01;46(D1):D21-D29

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkx1154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753251PMC
January 2018

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

Nat Genet 2017 Apr 13;49(4):550-558. Epub 2017 Feb 13.

European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/ng.3791DOI Listing
April 2017

The Mighty Fruit Fly Moves into Outbred Genetics.

Authors:
Ewan Birney

PLoS Genet 2016 11 3;12(11):e1006388. Epub 2016 Nov 3.

European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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https://dx.plos.org/10.1371/journal.pgen.1006388
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http://dx.doi.org/10.1371/journal.pgen.1006388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094671PMC
November 2016

Ensembl regulation resources.

Database (Oxford) 2016 17;2016. Epub 2016 Feb 17.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/database/bav119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756621PMC
October 2016

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

Nature 2016 06 2;534(7605):47-54. Epub 2016 May 2.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature17676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910866PMC
June 2016

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

PLoS Genet 2016 06 23;12(6):e1006105. Epub 2016 Jun 23.

Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1006105
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http://dx.doi.org/10.1371/journal.pgen.1006105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919098PMC
June 2016

The EMBL-EBI channel.

F1000Res 2016 12;5:52. Epub 2016 Jan 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Hinxton, UK.

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http://dx.doi.org/10.12688/f1000research.7764.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743148PMC
February 2016

The European Bioinformatics Institute in 2016: Data growth and integration.

Nucleic Acids Res 2016 Jan 15;44(D1):D20-6. Epub 2015 Dec 15.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkv1352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702932PMC
January 2016

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

Authors:
Kyle J Gaulton Teresa Ferreira Yeji Lee Anne Raimondo Reedik Mägi Michael E Reschen Anubha Mahajan Adam Locke N William Rayner Neil Robertson Robert A Scott Inga Prokopenko Laura J Scott Todd Green Thomas Sparso Dorothee Thuillier Loic Yengo Harald Grallert Simone Wahl Mattias Frånberg Rona J Strawbridge Hans Kestler Himanshu Chheda Lewin Eisele Stefan Gustafsson Valgerdur Steinthorsdottir Gudmar Thorleifsson Lu Qi Lennart C Karssen Elisabeth M van Leeuwen Sara M Willems Man Li Han Chen Christian Fuchsberger Phoenix Kwan Clement Ma Michael Linderman Yingchang Lu Soren K Thomsen Jana K Rundle Nicola L Beer Martijn van de Bunt Anil Chalisey Hyun Min Kang Benjamin F Voight Gonçalo R Abecasis Peter Almgren Damiano Baldassarre Beverley Balkau Rafn Benediktsson Matthias Blüher Heiner Boeing Lori L Bonnycastle Erwin P Bottinger Noël P Burtt Jason Carey Guillaume Charpentier Peter S Chines Marilyn C Cornelis David J Couper Andrew T Crenshaw Rob M van Dam Alex S F Doney Mozhgan Dorkhan Sarah Edkins Johan G Eriksson Tonu Esko Elodie Eury João Fadista Jason Flannick Pierre Fontanillas Caroline Fox Paul W Franks Karl Gertow Christian Gieger Bruna Gigante Omri Gottesman George B Grant Niels Grarup Christopher J Groves Maija Hassinen Christian T Have Christian Herder Oddgeir L Holmen Astradur B Hreidarsson Steve E Humphries David J Hunter Anne U Jackson Anna Jonsson Marit E Jørgensen Torben Jørgensen Wen-Hong L Kao Nicola D Kerrison Leena Kinnunen Norman Klopp Augustine Kong Peter Kovacs Peter Kraft Jasmina Kravic Cordelia Langford Karin Leander Liming Liang Peter Lichtner Cecilia M Lindgren Eero Lindholm Allan Linneberg Ching-Ti Liu Stéphane Lobbens Jian'an Luan Valeriya Lyssenko Satu Männistö Olga McLeod Julia Meyer Evelin Mihailov Ghazala Mirza Thomas W Mühleisen Martina Müller-Nurasyid Carmen Navarro Markus M Nöthen Nikolay N Oskolkov Katharine R Owen Domenico Palli Sonali Pechlivanis Leena Peltonen John R B Perry Carl G P Platou Michael Roden Douglas Ruderfer Denis Rybin Yvonne T van der Schouw Bengt Sennblad Gunnar Sigurðsson Alena Stančáková Gerald Steinbach Petter Storm Konstantin Strauch Heather M Stringham Qi Sun Barbara Thorand Emmi Tikkanen Anke Tonjes Joseph Trakalo Elena Tremoli Tiinamaija Tuomi Roman Wennauer Steven Wiltshire Andrew R Wood Eleftheria Zeggini Ian Dunham Ewan Birney Lorenzo Pasquali Jorge Ferrer Ruth J F Loos Josée Dupuis Jose C Florez Eric Boerwinkle James S Pankow Cornelia van Duijn Eric Sijbrands James B Meigs Frank B Hu Unnur Thorsteinsdottir Kari Stefansson Timo A Lakka Rainer Rauramaa Michael Stumvoll Nancy L Pedersen Lars Lind Sirkka M Keinanen-Kiukaanniemi Eeva Korpi-Hyövälti Timo E Saaristo Juha Saltevo Johanna Kuusisto Markku Laakso Andres Metspalu Raimund Erbel Karl-Heinz Jöcke Susanne Moebus Samuli Ripatti Veikko Salomaa Erik Ingelsson Bernhard O Boehm Richard N Bergman Francis S Collins Karen L Mohlke Heikki Koistinen Jaakko Tuomilehto Kristian Hveem Inger Njølstad Panagiotis Deloukas Peter J Donnelly Timothy M Frayling Andrew T Hattersley Ulf de Faire Anders Hamsten Thomas Illig Annette Peters Stephane Cauchi Rob Sladek Philippe Froguel Torben Hansen Oluf Pedersen Andrew D Morris Collin N A Palmer Sekar Kathiresan Olle Melander Peter M Nilsson Leif C Groop Inês Barroso Claudia Langenberg Nicholas J Wareham Christopher A O'Callaghan Anna L Gloyn David Altshuler Michael Boehnke Tanya M Teslovich Mark I McCarthy Andrew P Morris

Nat Genet 2015 Dec 9;47(12):1415-25. Epub 2015 Nov 9.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/ng.3437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666734PMC
December 2015

Progress in Medicine: Experts Take Stock.

PLoS Med 2015 Dec 29;12(12):e1001933. Epub 2015 Dec 29.

Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1371/journal.pmed.1001933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694696PMC
December 2015

Using human genetics to make new medicines.

Nat Rev Genet 2015 10 15;16(10):561-2. Epub 2015 Sep 15.

European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1038/nrg3998DOI Listing
October 2015

Human genomics: The end of the start for population sequencing.

Nature 2015 Oct;526(7571):52-3

Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK, and at the School of Clinical Medicine, University of Cambridge, UK.

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http://dx.doi.org/10.1038/526052aDOI Listing
October 2015

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

PLoS Genet 2014 Nov 20;10(11):e1004798. Epub 2014 Nov 20.

The European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238955PMC
November 2014

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

Bioinformatics 2014 May 11;30(9):1338-9. Epub 2014 Jan 11.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998127PMC
May 2014

Integrative knowledge management to enhance pharmaceutical R&D.

Nat Rev Drug Discov 2014 Apr;13(4):239-40

IMIM and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nrd4290DOI Listing
April 2014

The Reactome pathway knowledgebase.

Nucleic Acids Res 2014 Jan 15;42(Database issue):D472-7. Epub 2013 Nov 15.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA, NYU School of Medicine, New York, NY 10016, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.

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http://dx.doi.org/10.1093/nar/gkt1102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965010PMC
January 2014

The European Bioinformatics Institute's data resources 2014.

Nucleic Acids Res 2014 Jan 23;42(Database issue):D18-25. Epub 2013 Nov 23.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkt1206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964968PMC
January 2014

Archaic humans: Four makes a party.

Nature 2014 Jan 18;505(7481):32-4. Epub 2013 Dec 18.

Departments of Genetics and Biology and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305-5120, USA.

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http://www.nature.com/articles/nature12847
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http://dx.doi.org/10.1038/nature12847DOI Listing
January 2014

Policy challenges of clinical genome sequencing.

BMJ 2013 Nov 22;347:f6845. Epub 2013 Nov 22.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1136/bmj.f6845DOI Listing
November 2013

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

Authors:
Verneri Anttila Bendik S Winsvold Padhraig Gormley Tobias Kurth Francesco Bettella George McMahon Mikko Kallela Rainer Malik Boukje de Vries Gisela Terwindt Sarah E Medland Unda Todt Wendy L McArdle Lydia Quaye Markku Koiranen M Arfan Ikram Terho Lehtimäki Anine H Stam Lannie Ligthart Juho Wedenoja Ian Dunham Benjamin M Neale Priit Palta Eija Hamalainen Markus Schürks Lynda M Rose Julie E Buring Paul M Ridker Stacy Steinberg Hreinn Stefansson Finnbogi Jakobsson Debbie A Lawlor David M Evans Susan M Ring Markus Färkkilä Ville Artto Mari A Kaunisto Tobias Freilinger Jean Schoenen Rune R Frants Nadine Pelzer Claudia M Weller Ronald Zielman Andrew C Heath Pamela A F Madden Grant W Montgomery Nicholas G Martin Guntram Borck Hartmut Göbel Axel Heinze Katja Heinze-Kuhn Frances M K Williams Anna-Liisa Hartikainen Anneli Pouta Joyce van den Ende Andre G Uitterlinden Albert Hofman Najaf Amin Jouke-Jan Hottenga Jacqueline M Vink Kauko Heikkilä Michael Alexander Bertram Muller-Myhsok Stefan Schreiber Thomas Meitinger Heinz Erich Wichmann Arpo Aromaa Johan G Eriksson Bryan Traynor Daniah Trabzuni Elizabeth Rossin Kasper Lage Suzanne B R Jacobs J Raphael Gibbs Ewan Birney Jaakko Kaprio Brenda W Penninx Dorret I Boomsma Cornelia van Duijn Olli Raitakari Marjo-Riitta Jarvelin John-Anker Zwart Lynn Cherkas David P Strachan Christian Kubisch Michel D Ferrari Arn M J M van den Maagdenberg Martin Dichgans Maija Wessman George Davey Smith Kari Stefansson Mark J Daly Dale R Nyholt Daniel Chasman Aarno Palotie

Nat Genet 2013 Aug 23;45(8):912-917. Epub 2013 Jun 23.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.2676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041123PMC
August 2013

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

Nature 2013 Feb 23;494(7435):77-80. Epub 2013 Jan 23.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1038/nature11875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672958PMC
February 2013

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

Nucleic Acids Res 2013 Jan 29;41(Database issue):D171-6. Epub 2012 Nov 29.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1093/nar/gks1221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531197PMC
January 2013

Journey to the genetic interior. Interview by Stephen S Hall.

Authors:
Ewan Birney

Sci Am 2012 Oct;307(4):80-2, 84

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October 2012

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

Genome Biol 2012 Sep 28;13(9):R49. Epub 2012 Sep 28.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

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http://dx.doi.org/10.1186/gb-2012-13-9-r49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491393PMC
September 2012

The making of ENCODE: Lessons for big-data projects.

Authors:
Ewan Birney

Nature 2012 Sep;489(7414):49-51

European Molecular Biology Laboratory's European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/489049aDOI Listing
September 2012

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

Genome Res 2012 Sep;22(9):1798-812

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1101/gr.139105.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431495PMC
September 2012

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

Hum Mutat 2012 Aug 7;33(8):1188-1191. Epub 2012 Jun 7.

Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom.

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http://dx.doi.org/10.1002/humu.22114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640174PMC
August 2012

The future of DNA sequence archiving.

Gigascience 2012 Jul 12;1(1). Epub 2012 Jul 12.

EMBL-Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom.

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https://academic.oup.com/gigascience/article-lookup/doi/10.1
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http://dx.doi.org/10.1186/2047-217X-1-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617450PMC
July 2012

Modeling gene expression using chromatin features in various cellular contexts.

Genome Biol 2012 Jun 13;13(9):R53. Epub 2012 Jun 13.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491397PMC
June 2012

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

Bioinformatics 2012 Apr 24;28(8):1086-92. Epub 2012 Feb 24.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324515PMC
April 2012

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

Cell 2012 Feb;148(3):473-86

Genome Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.cell.2012.01.030DOI Listing
February 2012

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

Genome Res 2012 Jan 16;22(1):9-24. Epub 2011 Nov 16.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1101/gr.127597.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246210PMC
January 2012

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

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

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

Genome Res 2011 May 18;21(5):734-40. Epub 2011 Jan 18.

European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1101/gr.114819.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083090PMC
May 2011

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

Authors:
Ewan Birney

Trends Genet 2011 May 16;27(5):172-6. Epub 2011 Mar 16.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S016895251100031
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http://dx.doi.org/10.1016/j.tig.2011.02.005DOI Listing
May 2011

Assemblies: the good, the bad, the ugly.

Authors:
Ewan Birney

Nat Methods 2011 Jan;8(1):59-60

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1038/nmeth0111-59DOI Listing
January 2011

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

Mol Cell Proteomics 2010 Dec 5;9(12):2642-53. Epub 2010 Aug 5.

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1074/mcp.M110.001594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101853PMC
December 2010

Allele-specific and heritable chromatin signatures in humans.

Hum Mol Genet 2010 Oct 16;19(R2):R204-9. Epub 2010 Sep 16.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/hmg/ddq404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953746PMC
October 2010

The BioPAX community standard for pathway data sharing.

Nat Biotechnol 2010 Sep 9;28(9):935-42. Epub 2010 Sep 9.

Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.1666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001121PMC
September 2010

The systematic annotation of the three main GPCR families in Reactome.

Database (Oxford) 2010 Jul 29;2010:baq018. Epub 2010 Jul 29.

European Bioinformatics Institute, Hinxton, Cambridge CB101SD, UK.

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http://dx.doi.org/10.1093/database/baq018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945921PMC
July 2010

Ensembl variation resources.

BMC Genomics 2010 May 11;11:293. Epub 2010 May 11.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2164-11-293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894800PMC
May 2010

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

BMC Bioinformatics 2010 May 11;11:238. Epub 2010 May 11.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2105-11-238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882931PMC
May 2010

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

Science 2010 Apr 18;328(5975):235-9. Epub 2010 Mar 18.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA.

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http://dx.doi.org/10.1126/science.1184655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018PMC
April 2010

International network of cancer genome projects.

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Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard 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Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010