Publications by authors named "Paul Flicek"

99Publications

Transcriptional activity and strain-specific history of mouse pseudogenes.

Nat Commun 2020 Jul 29;11(1):3695. Epub 2020 Jul 29.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

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http://dx.doi.org/10.1038/s41467-020-17157-wDOI Listing
July 2020

Progress, Challenges, and Surprises in Annotating the Human Genome.

Annu Rev Genomics Hum Genet 2020 May 18. Epub 2020 May 18.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; email:

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http://dx.doi.org/10.1146/annurev-genom-121119-083418DOI Listing
May 2020

Identification of male heterogametic sex-determining regions on the Atlantic herring Clupea harengus genome.

J Fish Biol 2020 Jul 22;97(1):190-201. Epub 2020 May 22.

Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands.

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http://dx.doi.org/10.1111/jfb.14349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115899PMC
July 2020

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project.

Wellcome Open Res 2019 30;4:50. Epub 2019 Dec 30.

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

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http://dx.doi.org/10.12688/wellcomeopenres.15126.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059836PMC
December 2019

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.

Genome Biol 2020 01 7;21(1). Epub 2020 Jan 7.

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

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http://dx.doi.org/10.1186/s13059-019-1894-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945661PMC
January 2020

Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly.

Sci Rep 2019 11 27;9(1):17716. Epub 2019 Nov 27.

Amplexa Genetics A/S, Hoyvíksvegur 51, FO-100, Tórshavn, Faroe Islands.

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http://dx.doi.org/10.1038/s41598-019-54151-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881392PMC
November 2019

Ensembl 2020.

Nucleic Acids Res 2020 01;48(D1):D682-D688

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/gkz966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145704PMC
January 2020

IPD-IMGT/HLA Database.

Nucleic Acids Res 2020 01;48(D1):D948-D955

Anthony Nolan Research Institute, London, UK.

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http://dx.doi.org/10.1093/nar/gkz950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145640PMC
January 2020

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources.

Nucleic Acids Res 2020 01;48(D1):D941-D947

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/gkz836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943028PMC
January 2020

Getting the Entire Message: Progress in Isoform Sequencing.

Front Genet 2019 16;10:709. Epub 2019 Aug 16.

Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States.

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http://dx.doi.org/10.3389/fgene.2019.00709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706457PMC
August 2019

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.

Department 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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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