Lukas Chavez

Lukas Chavez

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Lukas Chavez

Lukas Chavez

Publications by authors named "Lukas Chavez"

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An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays.

F1000Res 2018 5;7. Epub 2018 Dec 5.

Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.12688/f1000research.16338.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498745PMC
September 2019

InTAD: chromosome conformation guided analysis of enhancer target genes.

BMC Bioinformatics 2019 Jan 31;20(1):60. Epub 2019 Jan 31.

Department of Medicine, Division of Medical Genetics, University of California San Diego (UCSD), San Diego, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-019-2655-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357397PMC
January 2019

Extensive Molecular and Clinical Heterogeneity in Patients With Histologically Diagnosed CNS-PNET Treated as a Single Entity: A Report From the Children's Oncology Group Randomized ACNS0332 Trial.

J Clin Oncol 2018 Oct 17:JCO2017764720. Epub 2018 Oct 17.

Eugene I. Hwang and Roger J. Packer, Children's National Medical Center, Washington, DC; Marcel Kool, Lukas Chavez, Sebastian Brabetz, David T.W. Jones, and Stefan M. Pfister, German Cancer Research Center; David Capper, Andreas von Deimling, and Stefan M. Pfister, University Hospital Heidelberg; Stefan M. Pfister, National Center for Tumor Diseases, Heidelberg; David Capper, Charité Medical University, Berlin, Germany; Peter C. Burger, Johns Hopkins University, Baltimore, MD; Chris Williams-Hughes, Children's Oncology Group, Littleton, CO; Catherine Billups, Yimei Li, and Amar Gajjar, St Jude Children's Research Hospital, Memphis, TN; Linda Heier, Weill Cornell Medical College, New York, NY; Alok Jaju, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Jeff Michalski, Washington University School of Medicine, St. Louis, MO; Sarah Leary and James M. Olson, Seattle Children's Hospital and Research Institute; Sarah Leary and James M. Olson, Fred Hutchinson Cancer Research Center, Seattle, WA; Tianni Zhou, California State University, Long Beach, Long Beach, CA; Maryam Fouladi, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; and Ian F. Pollack, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA.

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http://dx.doi.org/10.1200/JCO.2017.76.4720DOI Listing
October 2018

Author Correction: The landscape of genomic alterations across childhood cancers.

Nature 2018 07;559(7714):E10

Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41586-018-0167-2DOI Listing
July 2018

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

Lancet Oncol 2018 06 9;19(6):785-798. Epub 2018 May 9.

Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center at the NCT Heidelberg, Heidelberg, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S14702045183024
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http://dx.doi.org/10.1016/S1470-2045(18)30242-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984248PMC
June 2018

The landscape of genomic alterations across childhood cancers.

Nature 2018 03 28;555(7696):321-327. Epub 2018 Feb 28.

Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature25480DOI Listing
March 2018

DNA methylation-based classification of central nervous system tumours.

Authors:
David Capper David T W Jones Martin Sill Volker Hovestadt Daniel Schrimpf Dominik Sturm Christian Koelsche Felix Sahm Lukas Chavez David E Reuss Annekathrin Kratz Annika K Wefers Kristin Huang Kristian W Pajtler Leonille Schweizer Damian Stichel Adriana Olar Nils W Engel Kerstin Lindenberg Patrick N Harter Anne K Braczynski Karl H Plate Hildegard Dohmen Boyan K Garvalov Roland Coras Annett Hölsken Ekkehard Hewer Melanie Bewerunge-Hudler Matthias Schick Roger Fischer Rudi Beschorner Jens Schittenhelm Ori Staszewski Khalida Wani Pascale Varlet Melanie Pages Petra Temming Dietmar Lohmann Florian Selt Hendrik Witt Till Milde Olaf Witt Eleonora Aronica Felice Giangaspero Elisabeth Rushing Wolfram Scheurlen Christoph Geisenberger Fausto J Rodriguez Albert Becker Matthias Preusser Christine Haberler Rolf Bjerkvig Jane Cryan Michael Farrell Martina Deckert Jürgen Hench Stephan Frank Jonathan Serrano Kasthuri Kannan Aristotelis Tsirigos Wolfgang Brück Silvia Hofer Stefanie Brehmer Marcel Seiz-Rosenhagen Daniel Hänggi Volkmar Hans Stephanie Rozsnoki Jordan R Hansford Patricia Kohlhof Bjarne W Kristensen Matt Lechner Beatriz Lopes Christian Mawrin Ralf Ketter Andreas Kulozik Ziad Khatib Frank Heppner Arend Koch Anne Jouvet Catherine Keohane Helmut Mühleisen Wolf Mueller Ute Pohl Marco Prinz Axel Benner Marc Zapatka Nicholas G Gottardo Pablo Hernáiz Driever Christof M Kramm Hermann L Müller Stefan Rutkowski Katja von Hoff Michael C Frühwald Astrid Gnekow Gudrun Fleischhack Stephan Tippelt Gabriele Calaminus Camelia-Maria Monoranu Arie Perry Chris Jones Thomas S Jacques Bernhard Radlwimmer Marco Gessi Torsten Pietsch Johannes Schramm Gabriele Schackert Manfred Westphal Guido Reifenberger Pieter Wesseling Michael Weller Vincent Peter Collins Ingmar Blümcke Martin Bendszus Jürgen Debus Annie Huang Nada Jabado Paul A Northcott Werner Paulus Amar Gajjar Giles W Robinson Michael D Taylor Zane Jaunmuktane Marina Ryzhova Michael Platten Andreas Unterberg Wolfgang Wick Matthias A Karajannis Michel Mittelbronn Till Acker Christian Hartmann Kenneth Aldape Ulrich Schüller Rolf Buslei Peter Lichter Marcel Kool Christel Herold-Mende David W Ellison Martin Hasselblatt Matija Snuderl Sebastian Brandner Andrey Korshunov Andreas von Deimling Stefan M Pfister

Nature 2018 03 14;555(7697):469-474. Epub 2018 Mar 14.

Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature26000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093218PMC
March 2018

Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma.

Dev Cell 2018 03 15;44(6):709-724.e6. Epub 2018 Mar 15.

Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), Hamburg 20251, Germany; Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2018.02.012DOI Listing
March 2018

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.

Nature 2018 01 20;553(7686):101-105. Epub 2017 Dec 20.

Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.

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http://dx.doi.org/10.1038/nature25169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993422PMC
January 2018

Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming.

Genes Dev 2018 01 9;32(2):96-111. Epub 2018 Feb 9.

Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.

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http://dx.doi.org/10.1101/gad.309583.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5830932PMC
January 2018

DNA-methylation profiling discloses significant advantages over NanoString method for molecular classification of medulloblastoma.

Acta Neuropathol 2017 Dec 13;134(6):965-967. Epub 2017 Oct 13.

German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

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http://dx.doi.org/10.1007/s00401-017-1776-9DOI Listing
December 2017

Telomerase activation in posterior fossa group A ependymomas is associated with dismal prognosis and chromosome 1q gain.

Neuro Oncol 2017 Sep;19(9):1183-1194

Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Austria; Comprehensive Cancer Center, Medical University of Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Austria; Neuromed Campus, Kepler University Hospital, Linz, Austria; Institute of Neurology, Medical University of Vienna, Austria; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neuropathology, University Hospital Heidelberg, Germany; Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neurosurgery, Medical University of Vienna, Austria; Department of Radiotherapy, Medical University of Vienna, Austria.

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http://dx.doi.org/10.1093/neuonc/nox027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570194PMC
September 2017

The whole-genome landscape of medulloblastoma subtypes.

Nature 2017 07;547(7663):311-317

Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature22973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905700PMC
July 2017

Genetic confirmation that ependymoma can arise as part of multiple endocrine neoplasia type 1 (MEN1) syndrome.

Acta Neuropathol 2017 04 25;133(4):661-663. Epub 2017 Feb 25.

Division of Neuropathology, Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA.

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http://dx.doi.org/10.1007/s00401-017-1689-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391795PMC
April 2017

TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells.

Nat Immunol 2017 01 21;18(1):45-53. Epub 2016 Nov 21.

Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.

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http://dx.doi.org/10.1038/ni.3630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376256PMC
January 2017

Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data.

Methods Mol Biol 2016 ;1418:191-208

German Cancer Research Center, In Neuenheimer Feld 580, 69120, Heidelberg, Germany.

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http://dx.doi.org/10.1007/978-1-4939-3578-9_10DOI Listing
December 2016

Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling.

Proc Natl Acad Sci U S A 2016 12 5;113(51):E8267-E8276. Epub 2016 Dec 5.

Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1617802113
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http://dx.doi.org/10.1073/pnas.1617802113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187696PMC
December 2016

Dynamic Changes in Chromatin Accessibility Occur in CD8 T Cells Responding to Viral Infection.

Immunity 2016 12 6;45(6):1327-1340. Epub 2016 Dec 6.

Division of Signaling and Gene Expression, La Jolla Institute, 9420 Athena Circle, San Diego, CA 92037, USA.

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http://dx.doi.org/10.1016/j.immuni.2016.10.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5214519PMC
December 2016

Evidence of H3 K27M mutations in posterior fossa ependymomas.

Acta Neuropathol 2016 10 18;132(4):635-7. Epub 2016 Aug 18.

Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

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http://dx.doi.org/10.1007/s00401-016-1608-3DOI Listing
October 2016

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.

Genome Biol 2016 Mar 14;17:49. Epub 2016 Mar 14.

Department of Computer Science, Aalto University School of Science, Aalto, FI-00076, Finland.

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http://dx.doi.org/10.1186/s13059-016-0911-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792102PMC
March 2016

Acute loss of TET function results in aggressive myeloid cancer in mice.

Nat Commun 2015 Nov 26;6:10071. Epub 2015 Nov 26.

Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/ncomms10071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674670PMC
November 2015

Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis.

Proc Natl Acad Sci U S A 2015 Aug 21;112(31):E4236-45. Epub 2015 Jul 21.

Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037; Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093; Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037

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http://dx.doi.org/10.1073/pnas.1510510112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534209PMC
August 2015

The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine.

Nat Cell Biol 2015 May 27;17(5):545-57. Epub 2015 Apr 27.

1] The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02114, USA [2] The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1038/ncb3147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593707PMC
May 2015

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Proc Natl Acad Sci U S A 2014 Dec 18;111(48):E5149-58. Epub 2014 Nov 18.

Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093

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http://www.pnas.org/lookup/doi/10.1073/pnas.1419513111
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http://dx.doi.org/10.1073/pnas.1419513111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260599PMC
December 2014

Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility.

Nat Immunol 2014 Aug 6;15(8):777-88. Epub 2014 Jul 6.

1] La Jolla Institute for Allergy & Immunology, La Jolla, California, USA. [2] Clinical and Experimental Sciences, Southampton National Institute for Health Research Respiratory Biomedical Research Unit, University of Southampton, Faculty of Medicine, Southampton, UK. [3] University of California San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1038/ni.2937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140783PMC
August 2014

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.

Bioinformatics 2014 Jan 13;30(2):284-6. Epub 2013 Nov 13.

Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, Department of Rheumatology and Clinical Immunology, Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany and Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892689PMC
January 2014

Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells.

Proc Natl Acad Sci U S A 2014 Jan 13;111(4):1361-6. Epub 2014 Jan 13.

Divisions of Signalling and Gene Expression and Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037.

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http://dx.doi.org/10.1073/pnas.1322921111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910590PMC
January 2014

Comparative molecular portraits of human unfertilized oocytes and primordial germ cells at 10 weeks of gestation.

Int J Dev Biol 2012 ;56(10-12):789-97

Department of Vertebrate Genomics, Molecular Embryology and Aging Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin, Germany.

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http://dx.doi.org/10.1387/ijdb.120230jaDOI Listing
August 2013

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.

Nature 2013 May 7;497(7447):122-6. Epub 2013 Apr 7.

Division of Signaling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature12052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643997PMC
May 2013

Comparative analysis of human embryonic stem cell and induced pluripotent stem cell-derived hepatocyte-like cells reveals current drawbacks and possible strategies for improved differentiation.

Stem Cells Dev 2011 Jul 24;20(7):1259-75. Epub 2011 Jan 24.

Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1089/scd.2010.0361DOI Listing
July 2011

Molecular characterization of cultured adult human liver progenitor cells.

Tissue Eng Part C Methods 2010 Oct;16(5):821-34

Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1089/ten.TEC.2009.0578DOI Listing
October 2010

A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells.

PLoS One 2010 May 21;5(5):e10709. Epub 2010 May 21.

Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010709PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873957PMC
May 2010