Javier Herrero

Javier Herrero

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Javier Herrero

Publications by authors named "Javier Herrero"

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Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology.

Nat Commun 2019 07 2;10(1):2908. Epub 2019 Jul 2.

Research Department of Cancer Biology, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.

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http://dx.doi.org/10.1038/s41467-019-10725-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606583PMC
July 2019

Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability.

Bioinformatics 2019 Feb 6. Epub 2019 Feb 6.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz082DOI Listing
February 2019

Aequatus: an open-source homology browser.

Gigascience 2018 11 1;7(11). Epub 2018 Nov 1.

Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.

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http://dx.doi.org/10.1093/gigascience/giy128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251984PMC
November 2018

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

Cell 2018 04 12;173(3):595-610.e11. Epub 2018 Apr 12.

Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.03.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938372PMC
April 2018

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

Authors:
Christopher Abbosh Nicolai J Birkbak Gareth A Wilson Mariam Jamal-Hanjani Tudor Constantin Raheleh Salari John Le Quesne David A Moore Selvaraju Veeriah Rachel Rosenthal Teresa Marafioti Eser Kirkizlar Thomas B K Watkins Nicholas McGranahan Sophia Ward Luke Martinson Joan Riley Francesco Fraioli Maise Al Bakir Eva Grönroos Francisco Zambrana Raymondo Endozo Wenya Linda Bi Fiona M Fennessy Nicole Sponer Diana Johnson Joanne Laycock Seema Shafi Justyna Czyzewska-Khan Andrew Rowan Tim Chambers Nik Matthews Samra Turajlic Crispin Hiley Siow Ming Lee Martin D Forster Tanya Ahmad Mary Falzon Elaine Borg David Lawrence Martin Hayward Shyam Kolvekar Nikolaos Panagiotopoulos Sam M Janes Ricky Thakrar Asia Ahmed Fiona Blackhall Yvonne Summers Dina Hafez Ashwini Naik Apratim Ganguly Stephanie Kareht Rajesh Shah Leena Joseph Anne Marie Quinn Phil A Crosbie Babu Naidu Gary Middleton Gerald Langman Simon Trotter Marianne Nicolson Hardy Remmen Keith Kerr Mahendran Chetty Lesley Gomersall Dean A Fennell Apostolos Nakas Sridhar Rathinam Girija Anand Sajid Khan Peter Russell Veni Ezhil Babikir Ismail Melanie Irvin-Sellers Vineet Prakash Jason F Lester Malgorzata Kornaszewska Richard Attanoos Haydn Adams Helen Davies Dahmane Oukrif Ayse U Akarca John A Hartley Helen L Lowe Sara Lock Natasha Iles Harriet Bell Yenting Ngai Greg Elgar Zoltan Szallasi Roland F Schwarz Javier Herrero Aengus Stewart Sergio A Quezada Karl S Peggs Peter Van Loo Caroline Dive C Jimmy Lin Matthew Rabinowitz Hugo J W L Aerts Allan Hackshaw Jacqui A Shaw Bernhard G Zimmermann Charles Swanton

Nature 2018 02 20;554(7691):264. Epub 2017 Dec 20.

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http://dx.doi.org/10.1038/nature25161DOI Listing
February 2018

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution.

Cell 2017 Nov 26;171(6):1259-1271.e11. Epub 2017 Oct 26.

Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5720478PMC
November 2017

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs.

PLoS Pathog 2017 Aug 24;13(8):e1006524. Epub 2017 Aug 24.

UCL Cancer Institute, Research Department of Cancer Biology, Paul O'Gorman Building, University College London, London, England, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1006524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570218PMC
August 2017

Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection.

BMC Bioinformatics 2017 Jul 25;18(1):354. Epub 2017 Jul 25.

UCL Cancer Institute, University College London, London, UK.

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http://dx.doi.org/10.1186/s12859-017-1753-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526259PMC
July 2017

Tracking the Evolution of Non-Small-Cell Lung Cancer.

N Engl J Med 2017 06 26;376(22):2109-2121. Epub 2017 Apr 26.

From the Cancer Research UK Lung Cancer Centre of Excellence (M.J.-H., G.A.W., N. McGranahan, N.J.B., S.V., S.S., D.H.J., R.R., S.-M.L., M.D.F., C.A., S.M.J., C.D., C.S.), London and Manchester, Good Clinical Laboratory Practice Facility, University College London (UCL) Experimental Cancer Medicine Centre (H.L.L., J.A.H.), Bill Lyons Informatics Centre (J.H.), and Cancer Immunology Unit (S.A.Q.), UCL Cancer Institute, the Translational Cancer Therapeutics Laboratory (G.A.W., N. McGranahan, N.J.B., T.B.K.W., A.R., T.C., S. Turajlic, H.X., C.T.H., C.S.), Department of Bioinformatics and Biostatistics (R.M., M.S., S.H., M.E., A.S.), Advanced Sequencing Facility (N. Matthews), and Cancer Genomics Laboratory (S.D., P.V.L.), Francis Crick Institute, the Renal and Skin Units, Royal Marsden Hospital (S. Turajlic), the Departments of Medical Oncology (M.J.-H., S.-M.L., M.D.F., T.A., C.A., C.S.), Pathology (M.F., E.B., T.M.), Cardiothoracic Surgery (D.L., M.H., S. Kolvekar, N.P.), Respiratory Medicine (S.M.J., R.T.), and Radiology (A.A.), UCL Hospitals, Lungs for Living, UCL Respiratory, UCL (S.M.J.), the Department of Radiotherapy, North Middlesex University Hospital (G.A.), the Department of Respiratory Medicine, Royal Free Hospital (S. Khan), and UCL Cancer Research UK and Cancer Trials Centre (N.I., H.B., Y.N., A.H.), London, Cancer Studies, University of Leicester (D.A.M., D.A.F., J.A.S., J.L.Q.), the Department of Thoracic Surgery, Glenfield Hospital (A.N., S.R.), and the Medical Research Center Toxicology Unit (J.L.Q.), Leicester, the Institute of Cancer Studies, University of Manchester (F.B.), the Christie Hospital (F.B., Y.S.), the Departments of Cardiothoracic Surgery (R.S.) and Pathology (L.J., A.M.Q.) and the North West Lung Centre (P.A.C.), University Hospital of South Manchester, and Cancer Research UK Manchester Institute (C.D.), Manchester, the Departments of Thoracic Surgery (B.N.) and Cellular Pathology (G.L., S. Trotter), Birmingham Heartlands Hospital, Molecular Pathology Diagnostic Services, Queen Elizabeth Hospital (P.T., B.O.), and Institute of Immunology and Immunotherapy, University of Birmingham (G.M.), Birmingham, the Departments of Medical Oncology (M.N.), Cardiothoracic Surgery (H.R.), Pathology (K.K.), Respiratory Medicine (M.C.), and Radiology (L.G.), Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen, the Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Barnet (S. Khan), the Department of Respiratory Medicine, Princess Alexandra Hospital, Harlow (P.R.), the Department of Clinical Oncology, St. Luke's Cancer Centre, Guildford (V.E.), the Departments of Pathology (B.I.), Respiratory Medicine (M.I.-S.), and Radiology (V.P.), Ashford and St. Peters' Hospitals, Surrey, the Department of Clinical Oncology, Velindre Hospital (J.F.L.), the Departments of Radiology (H.A.) and Respiratory Medicine (H.D.), University Hospital Llandough, the Departments of Pathology (R.A.) and Cardiothoracic Surgery (M.K.), University Hospital of Wales, and Cardiff University (R.A.), Cardiff, and Wellcome Trust Sanger Institute, Hinxton, and Big Data Institute, University of Oxford, Oxford (S.D.) - all in the United Kingdom; the Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby (Z.S.); the Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston (Z.S.); MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary (Z.S.); Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin (R.F.S.); and the Department of Human Genetics, University of Leuven, Leuven, Belgium (P.V.L.).

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http://dx.doi.org/10.1056/NEJMoa1616288DOI Listing
June 2017

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

Authors:
Christopher Abbosh Nicolai J Birkbak Gareth A Wilson Mariam Jamal-Hanjani Tudor Constantin Raheleh Salari John Le Quesne David A Moore Selvaraju Veeriah Rachel Rosenthal Teresa Marafioti Eser Kirkizlar Thomas B K Watkins Nicholas McGranahan Sophia Ward Luke Martinson Joan Riley Francesco Fraioli Maise Al Bakir Eva Grönroos Francisco Zambrana Raymondo Endozo Wenya Linda Bi Fiona M Fennessy Nicole Sponer Diana Johnson Joanne Laycock Seema Shafi Justyna Czyzewska-Khan Andrew Rowan Tim Chambers Nik Matthews Samra Turajlic Crispin Hiley Siow Ming Lee Martin D Forster Tanya Ahmad Mary Falzon Elaine Borg David Lawrence Martin Hayward Shyam Kolvekar Nikolaos Panagiotopoulos Sam M Janes Ricky Thakrar Asia Ahmed Fiona Blackhall Yvonne Summers Dina Hafez Ashwini Naik Apratim Ganguly Stephanie Kareht Rajesh Shah Leena Joseph Anne Marie Quinn Phil A Crosbie Babu Naidu Gary Middleton Gerald Langman Simon Trotter Marianne Nicolson Hardy Remmen Keith Kerr Mahendran Chetty Lesley Gomersall Dean A Fennell Apostolos Nakas Sridhar Rathinam Girija Anand Sajid Khan Peter Russell Veni Ezhil Babikir Ismail Melanie Irvin-Sellers Vineet Prakash Jason F Lester Malgorzata Kornaszewska Richard Attanoos Haydn Adams Helen Davies Dahmane Oukrif Ayse U Akarca John A Hartley Helen L Lowe Sara Lock Natasha Iles Harriet Bell Yenting Ngai Greg Elgar Zoltan Szallasi Roland F Schwarz Javier Herrero Aengus Stewart Sergio A Quezada Karl S Peggs Peter Van Loo Caroline Dive C Jimmy Lin Matthew Rabinowitz Hugo J W L Aerts Allan Hackshaw Jacqui A Shaw Bernhard G Zimmermann Charles Swanton

Nature 2017 04;545(7655):446-451

Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK.

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http://dx.doi.org/10.1038/nature22364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812436PMC
April 2017

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening.

BMC Genomics 2016 11 14;17(1):917. Epub 2016 Nov 14.

Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.

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http://dx.doi.org/10.1186/s12864-016-3268-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109649PMC
November 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

Saturation analysis for whole-genome bisulfite sequencing data.

Nat Biotechnol 2016 07 27;34(7):691-693. Epub 2016 Jun 27.

Medical Genomics, UCL Cancer Institute, University College London, London, UK.

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http://dx.doi.org/10.1038/nbt.3524DOI Listing
July 2016

DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.

Genome Biol 2016 Feb 22;17:31. Epub 2016 Feb 22.

UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Paul O'Gorman Building, Huntley Street, London, WC1E 6DD, UK.

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http://dx.doi.org/10.1186/s13059-016-0893-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762164PMC
February 2016

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Syst Biol 2015 Sep 1;64(5):778-91. Epub 2015 Jun 1.

University College London, Gower St, London WC1E 6BT, UK; and European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK;

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http://dx.doi.org/10.1093/sysbio/syv033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538881PMC
September 2015

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

BMC Genomics 2015 Feb 14;16:87. Epub 2015 Feb 14.

Department of Mathematics and Computer Science, Emory University, Atlanta, GA, 30322, USA.

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http://www.biomedcentral.com/1471-2164/16/87
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http://dx.doi.org/10.1186/s12864-015-1245-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333152PMC
February 2015

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
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

A time to look back: analysis of morphokinetic characteristics of human embryo development.

Fertil Steril 2013 Dec 29;100(6):1602-9.e1-4. Epub 2013 Sep 29.

Instituto Valenciano de Infertilidad, Universidad de Valencia, Valencia, Spain.

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http://dx.doi.org/10.1016/j.fertnstert.2013.08.033DOI Listing
December 2013

The zebrafish reference genome sequence and its relationship to the human genome.

Authors:
Kerstin Howe Matthew D Clark Carlos F Torroja James Torrance Camille Berthelot Matthieu Muffato John E Collins Sean Humphray Karen McLaren Lucy Matthews Stuart McLaren Ian Sealy Mario Caccamo Carol Churcher Carol Scott Jeffrey C Barrett Romke Koch Gerd-Jörg Rauch Simon White William Chow Britt Kilian Leonor T Quintais José A Guerra-Assunção Yi Zhou Yong Gu Jennifer Yen Jan-Hinnerk Vogel Tina Eyre Seth Redmond Ruby Banerjee Jianxiang Chi Beiyuan Fu Elizabeth Langley Sean F Maguire Gavin K Laird David Lloyd Emma Kenyon Sarah Donaldson Harminder Sehra Jeff Almeida-King Jane Loveland Stephen Trevanion Matt Jones Mike Quail Dave Willey Adrienne Hunt John Burton Sarah Sims Kirsten McLay Bob Plumb Joy Davis Chris Clee Karen Oliver Richard Clark Clare Riddle David Elliot David Eliott Glen Threadgold Glenn Harden Darren Ware Sharmin Begum Beverley Mortimore Beverly Mortimer Giselle Kerry Paul Heath Benjamin Phillimore Alan Tracey Nicole Corby Matthew Dunn Christopher Johnson Jonathan Wood Susan Clark Sarah Pelan Guy Griffiths Michelle Smith Rebecca Glithero Philip Howden Nicholas Barker Christine Lloyd Christopher Stevens Joanna Harley Karen Holt Georgios Panagiotidis Jamieson Lovell Helen Beasley Carl Henderson Daria Gordon Katherine Auger Deborah Wright Joanna Collins Claire Raisen Lauren Dyer Kenric Leung Lauren Robertson Kirsty Ambridge Daniel Leongamornlert Sarah McGuire Ruth Gilderthorp Coline Griffiths Deepa Manthravadi Sarah Nichol Gary Barker Siobhan Whitehead Michael Kay Jacqueline Brown Clare Murnane Emma Gray Matthew Humphries Neil Sycamore Darren Barker David Saunders Justene Wallis Anne Babbage Sian Hammond Maryam Mashreghi-Mohammadi Lucy Barr Sancha Martin Paul Wray Andrew Ellington Nicholas Matthews Matthew Ellwood Rebecca Woodmansey Graham Clark James D Cooper James Cooper Anthony Tromans Darren Grafham Carl Skuce Richard Pandian Robert Andrews Elliot Harrison Andrew Kimberley Jane Garnett Nigel Fosker Rebekah Hall Patrick Garner Daniel Kelly Christine Bird Sophie Palmer Ines Gehring Andrea Berger Christopher M Dooley Zübeyde Ersan-Ürün Cigdem Eser Horst Geiger Maria Geisler Lena Karotki Anette Kirn Judith Konantz Martina Konantz Martina Oberländer Silke Rudolph-Geiger Mathias Teucke Christa Lanz Günter Raddatz Kazutoyo Osoegawa Baoli Zhu Amanda Rapp Sara Widaa Cordelia Langford Fengtang Yang Stephan C Schuster Nigel P Carter Jennifer Harrow Zemin Ning Javier Herrero Steve M J Searle Anton Enright Robert Geisler Ronald H A Plasterk Charles Lee Monte Westerfield Pieter J de Jong Leonard I Zon John H Postlethwait Christiane Nüsslein-Volhard Tim J P Hubbard Hugues Roest Crollius Jane Rogers Derek L Stemple

Nature 2013 Apr 17;496(7446):498-503. Epub 2013 Apr 17.

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

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http://dx.doi.org/10.1038/nature12111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703927PMC
April 2013

Selection of high potential embryos using time-lapse imaging: the era of morphokinetics.

Fertil Steril 2013 Mar 6;99(4):1030-4. Epub 2013 Feb 6.

Instituto Valenciano de Infertilidad, Universidad de Valencia, Valencia, Spain.

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http://dx.doi.org/10.1016/j.fertnstert.2013.01.089DOI Listing
March 2013

Limited implantation success of direct-cleaved human zygotes: a time-lapse study.

Fertil Steril 2012 Dec 25;98(6):1458-63. Epub 2012 Aug 25.

Instituto Valenciano de Infertilidad Valencia, Universidad de Valencia, Valencia, Spain.

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http://dx.doi.org/10.1016/j.fertnstert.2012.07.1135DOI Listing
December 2012

The subcutaneous adipose tissue reservoir of functionally active stem cells is reduced in obese patients.

FASEB J 2012 Oct 6;26(10):4327-36. Epub 2012 Jul 6.

Cardiovascular Research Center (CSIC-ICCC), Hospital de la Santa Creu i Sant Pau, Av. S. Antoni M. Claret 167, 08025 Barcelona, Spain.

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http://dx.doi.org/10.1096/fj.12-207217DOI Listing
October 2012

Time-dependent O2 consumption patterns determined optimal time ranges for selecting viable human embryos.

Fertil Steril 2012 Oct 24;98(4):849-57.e1-3. Epub 2012 Jul 24.

Instituto Valenciano de Infertilidad, Universidad de Valencia, Valencia, Spain.

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http://dx.doi.org/10.1016/j.fertnstert.2012.06.040DOI Listing
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

A patient-specific FE-based methodology to simulate prosthesis insertion during an augmentation mammoplasty.

Med Eng Phys 2011 Nov 25;33(9):1094-102. Epub 2011 May 25.

Department of Continuum Mechanics and Theory of Structures, Universitat Politècnica de València, Camino de Vera, Valencia, Spain.

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http://dx.doi.org/10.1016/j.medengphy.2011.04.014DOI Listing
November 2011

The use of morphokinetics as a predictor of embryo implantation.

Hum Reprod 2011 Oct 9;26(10):2658-71. Epub 2011 Aug 9.

Instituto Valenciano de Infertilidad, Universidad de Valencia, Plaza de la Policía Local, 3, Valencia 46015, Spain.

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http://dx.doi.org/10.1093/humrep/der256DOI Listing
October 2011

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

Oxygen consumption is a quality marker for human oocyte competence conditioned by ovarian stimulation regimens.

Fertil Steril 2011 Sep 23;96(3):618-623.e2. Epub 2011 Jul 23.

Instituto Valenciano de Infertilidad, Universidad de Valencia, Valencia, Spain.

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https://linkinghub.elsevier.com/retrieve/pii/S00150282110103
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http://dx.doi.org/10.1016/j.fertnstert.2011.06.059DOI Listing
September 2011

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

Authors:
Marilyn B Renfree Anthony T Papenfuss Janine E Deakin James Lindsay Thomas Heider Katherine Belov Willem Rens Paul D Waters Elizabeth A Pharo Geoff Shaw Emily S W Wong Christophe M Lefèvre Kevin R Nicholas Yoko Kuroki Matthew J Wakefield Kyall R Zenger Chenwei Wang Malcolm Ferguson-Smith Frank W Nicholas Danielle Hickford Hongshi Yu Kirsty R Short Hannah V Siddle Stephen R Frankenberg Keng Yih Chew Brandon R Menzies Jessica M Stringer Shunsuke Suzuki Timothy A Hore Margaret L Delbridge Hardip R Patel Amir Mohammadi Nanette Y Schneider Yanqiu Hu William O'Hara Shafagh Al Nadaf Chen Wu Zhi-Ping Feng Benjamin G Cocks Jianghui Wang Paul Flicek Stephen M J Searle Susan Fairley Kathryn Beal Javier Herrero Dawn M Carone Yutaka Suzuki Sumio Sugano Atsushi Toyoda Yoshiyuki Sakaki Shinji Kondo Yuichiro Nishida Shoji Tatsumoto Ion Mandiou Arthur Hsu Kaighin A McColl Benjamin Lansdell George Weinstock Elizabeth Kuczek Annette McGrath Peter Wilson Artem Men Mehlika Hazar-Rethinam Allison Hall John Davis David Wood Sarah Williams Yogi Sundaravadanam Donna M Muzny Shalini N Jhangiani Lora R Lewis Margaret B Morgan Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Lynne Nazareth Andrew Cree Gerald Fowler Christie L Kovar Huyen H Dinh Vandita Joshi Chyn Jing Fremiet Lara Rebecca Thornton Lei Chen Jixin Deng Yue Liu Joshua Y Shen Xing-Zhi Song Janette Edson Carmen Troon Daniel Thomas Amber Stephens Lankesha Yapa Tanya Levchenko Richard A Gibbs Desmond W Cooper Terence P Speed Asao Fujiyama Jennifer A M Graves Rachel J O'Neill Andrew J Pask Susan M Forrest Kim C Worley

Genome Biol 2011 Aug 29;12(8):R81. Epub 2011 Aug 29.

The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia.

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http://dx.doi.org/10.1186/gb-2011-12-8-r81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277949PMC
August 2011

Distally based dorsal nasal flap in nasal ala reconstruction: anatomic study and clinical experience.

Dermatol Surg 2011 Jun 4;37(6):825-34. Epub 2011 Apr 4.

Department of Plastic Surgery, Centro Medico TEKNON, Barcelona, Spain.

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http://dx.doi.org/10.1111/j.1524-4725.2011.01942.xDOI Listing
June 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

[Management of the surgical pathology of the parotid gland: A review of 54 cases].

Acta Otorrinolaringol Esp 2010 May-Jun;61(3):189-95. Epub 2010 Jan 25.

Servicio de Otorrinolaringología, Complejo Asistencial de Avila, Avila, España.

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http://dx.doi.org/10.1016/j.otorri.2009.11.006DOI Listing
August 2010

An approach to inferring transcriptional regulation among genes from large-scale expression data.

Comp Funct Genomics 2003 ;4(1):148-54

Unidad de Bioinformática, Centro Nacional de Investigaciones Oncológicas (CNIO). Melchor Fernández Almagro 3, Madrid 28029, Spain.

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http://dx.doi.org/10.1002/cfg.237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447383PMC
June 2010

eHive: an artificial intelligence workflow system for genomic analysis.

BMC Bioinformatics 2010 May 11;11:240. Epub 2010 May 11.

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

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http://dx.doi.org/10.1186/1471-2105-11-240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885371PMC
May 2010

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

Bioinformatics 2009 Feb 4;25(3):295-301. Epub 2008 Dec 4.

Department of Engineering, University of California, Santa Cruz CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn630DOI Listing
February 2009

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

Genome Res 2008 Nov 10;18(11):1814-28. Epub 2008 Oct 10.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.076554.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577869PMC
November 2008

Genome-wide nucleotide-level mammalian ancestor reconstruction.

Genome Res 2008 Nov 10;18(11):1829-43. Epub 2008 Oct 10.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.076521.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577868PMC
November 2008

[Is universal newborn hearing screening more efficient with auditory evoked potentials compared to otoacoustic emissions?].

Acta Otorrinolaringol Esp 2008 Apr;59(4):170-5

Servicio de Otorrinolaringología, Complejo Asistencial de Avila, Avila, España.

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April 2008

Next station in microarray data analysis: GEPAS.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W486-91

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, E46013, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkl197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538867PMC
July 2006

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W616-20

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO) Melchor Fernández Almagro 3, 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gki500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160260PMC
July 2005

New challenges in gene expression data analysis and the extended GEPAS.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W485-91

Bioinformatics Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro, 3, E-28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkh421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441559PMC
July 2004

GEPAS: A web-based resource for microarray gene expression data analysis.

Nucleic Acids Res 2003 Jul;31(13):3461-7

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas, c/Melchor Fernández Almagro 3, 28029, Madrid, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168997PMC
http://dx.doi.org/10.1093/nar/gkg591DOI Listing
July 2003

Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns.

J Proteome Res 2002 Sep-Oct;1(5):467-70

Bioinformatics Unit, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.

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May 2003

Comparing bacterial genomes through conservation profiles.

Genome Res 2003 May 14;13(5):991-8. Epub 2003 Apr 14.

EMBL Outstation-The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1101/gr.678303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430882PMC
May 2003