Paul Flicek

Paul Flicek

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Paul Flicek

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Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

Commun Biol 2019 7;2:97. Epub 2019 Mar 7.

27Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA 95817 USA.

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http://dx.doi.org/10.1038/s42003-019-0349-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405960PMC
March 2019

Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine?

Genome Biol Evol 2019 01 1;11(1):220-231. Epub 2019 Jan 1.

British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evy262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336007PMC
January 2019

CTCF maintains regulatory homeostasis of cancer pathways.

Genome Biol 2018 08 7;19(1):106. Epub 2018 Aug 7.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1484-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081938PMC
August 2018

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.

Nat Ecol Evol 2018 Jan 27;2(1):152-163. Epub 2017 Nov 27.

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

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http://dx.doi.org/10.1038/s41559-017-0377-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733139PMC
January 2018

Identification of genetic elements in metabolism by high-throughput mouse phenotyping.

Nat Commun 2018 01 18;9(1):288. Epub 2018 Jan 18.

German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.

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http://dx.doi.org/10.1038/s41467-017-01995-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773596PMC
January 2018

Ensembl variation resources.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://fdslive.oup.com/www.oup.com/pdf/production_in_progres
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http://dx.doi.org/10.1093/database/bay119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310513PMC
January 2018

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.

BMC Genomics 2017 12 22;18(1):986. Epub 2017 Dec 22.

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

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http://dx.doi.org/10.1186/s12864-017-4351-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741965PMC
December 2017

Corrigendum: High-throughput discovery of novel developmental phenotypes.

Nature 2017 11 8;551(7680):398. Epub 2017 Nov 8.

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http://dx.doi.org/10.1038/nature24643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849394PMC
November 2017

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

Nat Commun 2017 10 23;8(1):1092. Epub 2017 Oct 23.

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

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http://dx.doi.org/10.1038/s41467-017-01037-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653656PMC
October 2017

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

Gigascience 2017 07;6(7):1-8

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

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http://dx.doi.org/10.1093/gigascience/gix038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522380PMC
July 2017

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

Nucleic Acids Res 2017 01 15;45(D1):D854-D859. Epub 2016 Sep 15.

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

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http://dx.doi.org/10.1093/nar/gkw829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210610PMC
January 2017

The human-induced pluripotent stem cell initiative-data resources for cellular genetics.

Nucleic Acids Res 2017 01 12;45(D1):D691-D697. Epub 2016 Oct 12.

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/gkw928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210631PMC
January 2017

Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.

Cell Rep 2016 11;17(8):2101-2111

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.10.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889099PMC
November 2016

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Cell 2016 11;167(5):1398-1414.e24

Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674163144
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http://dx.doi.org/10.1016/j.cell.2016.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119954PMC
November 2016

The BLUEPRINT Data Analysis Portal.

Cell Syst 2016 11 15;3(5):491-495.e5. Epub 2016 Nov 15.

Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Spanish Bioinformatics Institute INB-ISCIII ES-ELIXIR, Madrid 28029, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.10.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919098PMC
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

Ensembl comparative genomics resources.

Database (Oxford) 2016 20;2016. Epub 2016 Feb 20.

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

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http://dx.doi.org/10.1093/database/bav096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110PMC
October 2016

ncRNA orthologies in the vertebrate lineage.

Database (Oxford) 2016 15;2016. Epub 2016 Mar 15.

European Molecular Biology Laboratory, European Bioinformatics Institute UCL Cancer Institute, University College London, London WC1E 6BT, UK.

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http://dx.doi.org/10.1093/database/bav127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792531PMC
October 2016

The Evolutionary Fates of a Large Segmental Duplication in Mouse.

Genetics 2016 Sep 2;204(1):267-85. Epub 2016 Jul 2.

Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599

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http://dx.doi.org/10.1534/genetics.116.191007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012392PMC
September 2016

High-throughput discovery of novel developmental phenotypes.

Nature 2016 09 14;537(7621):508-514. Epub 2016 Sep 14.

The Jackson Laboratory, Bar Harbor, Maine 04609, USA.

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http://dx.doi.org/10.1038/nature19356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295821PMC
September 2016

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

J Hered 2016 07 26;107(4):295-308. Epub 2016 Feb 26.

From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves).

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http://dx.doi.org/10.1093/jhered/esw010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888434PMC
July 2016

The Ensembl Variant Effect Predictor.

Genome Biol 2016 06 6;17(1):122. Epub 2016 Jun 6.

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

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http://dx.doi.org/10.1186/s13059-016-0974-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893825PMC
June 2016

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.

Genome Biol 2016 06 27;17(1):139. Epub 2016 Jun 27.

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

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http://dx.doi.org/10.1186/s13059-016-0996-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922064PMC
June 2016

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

PLoS One 2015 4;10(9):e0137367. Epub 2015 Sep 4.

University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560434PMC
May 2016

Divergence in gene expression within and between two closely related flycatcher species.

Mol Ecol 2016 05 2;25(9):2015-28. Epub 2016 Apr 2.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.13596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879514PMC
May 2016

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.

Genome Res 2015 Apr 12;25(4):504-13. Epub 2015 Feb 12.

Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom;

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http://dx.doi.org/10.1101/gr.184986.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381522PMC
April 2015

The ensembl regulatory build.

Genome Biol 2015 Mar 24;16:56. Epub 2015 Mar 24.

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

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http://dx.doi.org/10.1186/s13059-015-0621-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407537PMC
March 2015

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.

Genome Res 2015 Feb 13;25(2):167-78. Epub 2014 Nov 13.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom

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http://genome.cshlp.org/content/early/2014/12/30/gr.177840.1
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http://genome.cshlp.org/lookup/doi/10.1101/gr.177840.114
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http://dx.doi.org/10.1101/gr.177840.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315291PMC
February 2015

The Ensembl REST API: Ensembl Data for Any Language.

Bioinformatics 2015 Jan 17;31(1):143-5. Epub 2014 Sep 17.

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

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http://dx.doi.org/10.1093/bioinformatics/btu613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271150PMC
January 2015

The IPD and IMGT/HLA database: allele variant databases.

Nucleic Acids Res 2015 Jan 20;43(Database issue):D423-31. Epub 2014 Nov 20.

Anthony Nolan Research Institute, Hampstead, London, NW3 2QG, UK UCL Cancer Institute, University College London, Hampstead, London, NW3 2QG, UK

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http://dx.doi.org/10.1093/nar/gku1161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383959PMC
January 2015

Enhancer evolution across 20 mammalian species.

Cell 2015 Jan;160(3):554-66

University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313353PMC
January 2015

Computational approaches to interpreting genomic sequence variation.

Genome Med 2014 22;6(10):87. Epub 2014 Oct 22.

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

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http://dx.doi.org/10.1186/s13073-014-0087-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254438PMC
December 2014

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014