Andreas Gnirke

Andreas Gnirke

UNVERIFIED PROFILE

Are you Andreas Gnirke?   Register this Author

Register author
Andreas Gnirke

Andreas Gnirke

Publications by authors named "Andreas Gnirke"

Are you Andreas Gnirke?   Register this Author

78Publications

4195Reads

40Profile Views

Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology.

Cell Stem Cell 2018 04 15;22(4):559-574.e9. Epub 2018 Mar 15.

The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2018.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535433PMC
April 2018

Targeted bisulfite sequencing of the dynamic DNA methylome.

Epigenetics Chromatin 2016 3;9:55. Epub 2016 Dec 3.

Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ; Harvard Stem Cell Institute, Cambridge, MA 02138 USA ; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13072-016-0105-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135789PMC
January 2018

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Nature 2017 06 24;546(7658):401-405. Epub 2017 May 24.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature22400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536180PMC
June 2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Nature 2017 04 12;544(7650):309-315. Epub 2017 Apr 12.

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature22040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712493PMC
April 2017

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.

Proc Natl Acad Sci U S A 2015 Nov 23;112(47):E6456-65. Epub 2015 Oct 23.

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030; Broad Institute of MIT and Harvard, Cambridge, MA 02139;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1518552112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664323PMC
November 2015

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Cell 2015 Aug;162(4):738-50

FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://www.cell.com/cell/pdf/S0092-8674(15)00897-1.pdf
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S009286741500897
Publisher Site
http://dx.doi.org/10.1016/j.cell.2015.07.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537774PMC
August 2015

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Cell 2015 Jun;161(7):1516-26

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2015.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503805PMC
June 2015

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.

Nat Genet 2015 May 30;47(5):469-78. Epub 2015 Mar 30.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.3258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414868PMC
May 2015

Transcription factor binding dynamics during human ES cell differentiation.

Nature 2015 Feb;518(7539):344-9

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature14233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499331PMC
February 2015

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Cancer Cell 2014 Dec;26(6):813-825

Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccell.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302418PMC
December 2014

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes.

Nucleic Acids Res 2014 Aug 9;42(14):e112. Epub 2014 Jun 9.

Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132701PMC
August 2014

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.

Cell Rep 2013 Jun 20;3(6):2179-90. Epub 2013 Jun 20.

Center for Integrative Genomics, University of Lausanne, Génopode, CH-1015, Lausanne, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2013.05.031DOI Listing
June 2013

The African coelacanth genome provides insights into tetrapod evolution.

Nature 2013 Apr;496(7445):311-6

Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature12027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110PMC
April 2013

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Genome Res 2012 Jun 30;22(6):1128-38. Epub 2012 Mar 30.

Radboud University, Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, 6500 HB Nijmegen, The Netherlands.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.133728.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371717PMC
June 2012

A unique regulatory phase of DNA methylation in the early mammalian embryo.

Nature 2012 Mar 28;484(7394):339-44. Epub 2012 Mar 28.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature10960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331945PMC
March 2012

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.

Genome Biol 2011 21;12(2):R18. Epub 2011 Feb 21.

Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

View Article

Download full-text PDF

Source
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
Publisher Site
http://dx.doi.org/10.1186/gb-2011-12-2-r18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188800PMC
February 2012

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Nat Methods 2010 Sep 15;7(9):709-15. Epub 2010 Aug 15.

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.1491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005310PMC
September 2010

Hi-C: a method to study the three-dimensional architecture of genomes.

J Vis Exp 2010 May 6(39). Epub 2010 May 6.

Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3791/1869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149993PMC
May 2010

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Genome Biol 2009 16;10(10):R115. Epub 2009 Oct 16.

Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2009-10-10-r115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784330PMC
January 2010

High-throughput bisulfite sequencing in mammalian genomes.

Methods 2009 Jul 12;48(3):226-32. Epub 2009 May 12.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2009.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864123PMC
July 2009

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon.

Proc Natl Acad Sci U S A 2008 Jul 11;105(29):10085-9. Epub 2008 Jul 11.

United States Department of Agriculture, Grain Marketing and Production Research Center, Agricultural Research Service, Manhattan, KS 66502, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0800444105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481321PMC
July 2008

The genome of the model beetle and pest Tribolium castaneum.

Authors:
Stephen Richards Richard A Gibbs George M Weinstock Susan J Brown Robin Denell Richard W Beeman Richard Gibbs Richard W Beeman Susan J Brown Gregor Bucher Markus Friedrich Cornelis J P Grimmelikhuijzen Martin Klingler Marce Lorenzen Stephen Richards Siegfried Roth Reinhard Schröder Diethard Tautz Evgeny M Zdobnov Donna Muzny Richard A Gibbs George M Weinstock Tony Attaway Stephanie Bell Christian J Buhay Mimi N Chandrabose Dean Chavez Kerstin P Clerk-Blankenburg Andrew Cree Marvin Dao Clay Davis Joseph Chacko Huyen Dinh Shannon Dugan-Rocha Gerald Fowler Toni T Garner Jeffrey Garnes Andreas Gnirke Alica Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan LaRonda Jackson Christie Kovar Andrea Kowis Sandra Lee Lora R Lewis Jon Margolis Margaret Morgan Lynne V Nazareth Ngoc Nguyen Geoffrey Okwuonu David Parker Stephen Richards San-Juana Ruiz Jireh Santibanez Joël Savard Steven E Scherer Brian Schneider Erica Sodergren Diethard Tautz Selina Vattahil Donna Villasana Courtney S White Rita Wright Yoonseong Park Richard W Beeman Jeff Lord Brenda Oppert Marce Lorenzen Susan Brown Liangjiang Wang Joël Savard Diethard Tautz Stephen Richards George Weinstock Richard A Gibbs Yue Liu Kim Worley George Weinstock Christine G Elsik Justin T Reese Eran Elhaik Giddy Landan Dan Graur Peter Arensburger Peter Atkinson Richard W Beeman Jim Beidler Susan J Brown Jeffery P Demuth Douglas W Drury Yu-Zhou Du Haruhiko Fujiwara Marce Lorenzen Vincenza Maselli Mizuko Osanai Yoonseong Park Hugh M Robertson Zhijian Tu Jian-jun Wang Suzhi Wang Stephen Richards Henry Song Lan Zhang Erica Sodergren Doreen Werner Mario Stanke Burkhard Morgenstern Victor Solovyev Peter Kosarev Garth Brown Hsiu-Chuan Chen Olga Ermolaeva Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Donna Maglott Kim Pruitt Victor Sapojnikov Alexandre Souvorov Aaron J Mackey Robert M Waterhouse Stefan Wyder Evgeny M Zdobnov Evgeny M Zdobnov Stefan Wyder Evgenia V Kriventseva Tatsuhiko Kadowaki Peer Bork Manuel Aranda Riyue Bao Anke Beermann Nicola Berns Renata Bolognesi François Bonneton Daniel Bopp Susan J Brown Gregor Bucher Thomas Butts Arnaud Chaumot Robin E Denell David E K Ferrier Markus Friedrich Cassondra M Gordon Marek Jindra Martin Klingler Que Lan H Michael G Lattorff Vincent Laudet Cornelia von Levetsow Zhenyi Liu Rebekka Lutz Jeremy A Lynch Rodrigo Nunes da Fonseca Nico Posnien Rolf Reuter Siegfried Roth Joël Savard Johannes B Schinko Christian Schmitt Michael Schoppmeier Reinhard Schröder Teresa D Shippy Franck Simonnet Henrique Marques-Souza Diethard Tautz Yoshinori Tomoyasu Jochen Trauner Maurijn Van der Zee Michel Vervoort Nadine Wittkopp Ernst A Wimmer Xiaoyun Yang Andrew K Jones David B Sattelle Paul R Ebert David Nelson Jeffrey G Scott Richard W Beeman Subbaratnam Muthukrishnan Karl J Kramer Yasuyuki Arakane Richard W Beeman Qingsong Zhu David Hogenkamp Radhika Dixit Brenda Oppert Haobo Jiang Zhen Zou Jeremy Marshall Elena Elpidina Konstantin Vinokurov Cris Oppert Zhen Zou Jay Evans Zhiqiang Lu Picheng Zhao Niranji Sumathipala Boran Altincicek Andreas Vilcinskas Michael Williams Dan Hultmark Charles Hetru Haobo Jiang Cornelis J P Grimmelikhuijzen Frank Hauser Giuseppe Cazzamali Michael Williamson Yoonseong Park Bin Li Yoshiaki Tanaka Reinhard Predel Susanne Neupert Joachim Schachtner Peter Verleyen Florian Raible Peer Bork Markus Friedrich Kimberly K O Walden Hugh M Robertson Sergio Angeli Sylvain Forêt Gregor Bucher Stefan Schuetz Ryszard Maleszka Ernst A Wimmer Richard W Beeman Marce Lorenzen Yoshinori Tomoyasu Sherry C Miller Daniela Grossmann Gregor Bucher

Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature06784DOI Listing
April 2008

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.

Proc Natl Acad Sci U S A 2007 Apr 18;104(17):7145-50. Epub 2007 Apr 18.

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0701811104
Publisher Site
http://dx.doi.org/10.1073/pnas.0701811104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852749PMC
April 2007

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.

Nature 2006 Nov;444(7115):97-101

Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, D-35043 Marburg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature05248DOI Listing
November 2006

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.

Nucleic Acids Res 2005 13;33(18):5868-77. Epub 2005 Oct 13.

Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gki901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1258174PMC
October 2005