Alvaro Rada-Iglesias

Alvaro Rada-Iglesias

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Alvaro Rada-Iglesias

Alvaro Rada-Iglesias

Publications by authors named "Alvaro Rada-Iglesias"

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Transcriptional and epigenetic control of germline competence and specification.

Curr Opin Cell Biol 2019 Jun 21;61:1-8. Epub 2019 Jun 21.

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.ceb.2019.05.006DOI Listing
June 2019

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.

Cell Stem Cell 2019 May 11;24(5):736-752.e12. Epub 2019 Apr 11.

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.03.004DOI Listing
May 2019

yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs.

Cell Stem Cell 2019 Feb 13;24(2):318-327.e8. Epub 2018 Dec 13.

Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.11.005DOI Listing
February 2019

Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations.

Hum Mol Genet 2018 12;27(23):4117-4134

Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne, Germany.

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http://dx.doi.org/10.1093/hmg/ddy304DOI Listing
December 2018

Pioneering of Enhancer Landscapes during Pluripotent State Transitions.

Cell Stem Cell 2018 08;23(2):149-151

Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Albert Einstein 22, 39011 Santander, Spain; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.07.012DOI Listing
August 2018

Forces driving the three-dimensional folding of eukaryotic genomes.

Mol Syst Biol 2018 06 1;14(6):e8214. Epub 2018 Jun 1.

Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6024091PMC
http://dx.doi.org/10.15252/msb.20188214DOI Listing
June 2018

Lineage specific transcription factors and epigenetic regulators mediate TGFβ-dependent enhancer activation.

Nucleic Acids Res 2018 04;46(7):3351-3365

Department of Molecular Genomics. Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/nar/gky093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909450PMC
April 2018

Is H3K4me1 at enhancers correlative or causative?

Nat Genet 2018 01;50(1):4-5

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.

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http://dx.doi.org/10.1038/s41588-017-0018-3DOI Listing
January 2018

Ready, Set…Poised!: Polycomb target genes are bound by poised RNA polymerase II throughout differentiation.

Mol Syst Biol 2017 10 23;13(10):950. Epub 2017 Oct 23.

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658701PMC
http://dx.doi.org/10.15252/msb.20177968DOI Listing
October 2017

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

J Vis Exp 2017 08 29(126). Epub 2017 Aug 29.

Center for Molecular Medicine Cologne (CMMC), University of Cologne; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Research Center and Systems Biology of Ageing Cologne, University of Cologne;

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http://dx.doi.org/10.3791/56186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5614393PMC
August 2017

PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation.

Cell Stem Cell 2017 05 9;20(5):689-705.e9. Epub 2017 Mar 9.

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.02.004DOI Listing
May 2017

GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps.

Hum Mol Genet 2017 02;26(4):742-752

Center for Molecular Medicine Cologne (CMMC), Robert-Koch-Str. 21, 50931 Cologne, Germany.

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http://dx.doi.org/10.1093/hmg/ddw423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409087PMC
February 2017

Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations.

Cell Rep 2016 12;17(11):3062-3076

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.11.046DOI Listing
December 2016

Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification.

Cell Stem Cell 2016 Jan;18(1):118-33

Center for Molecular Medicine Cologne, University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909150041
Publisher Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048917PMC
http://dx.doi.org/10.1016/j.stem.2015.09.010DOI Listing
January 2016

Human genetic variation within neural crest enhancers: molecular and phenotypic implications.

Philos Trans R Soc Lond B Biol Sci 2013 6;368(1620):20120360. Epub 2013 May 6.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1098/rstb.2012.0360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682725PMC
December 2013

Pioneering barren land: mitotic bookmarking by transcription factors.

Dev Cell 2013 Feb;24(4):342-4

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.devcel.2013.02.005DOI Listing
February 2013

Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest.

Cell Stem Cell 2012 Nov 13;11(5):633-48. Epub 2012 Sep 13.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.stem.2012.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751405PMC
November 2012

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.

Genome Med 2011 Jun 7;3(6):36. Epub 2011 Jun 7.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/gm252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218810PMC
June 2011

A unique chromatin signature uncovers early developmental enhancers in humans.

Nature 2011 Feb 15;470(7333):279-83. Epub 2010 Dec 15.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nature09692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445674PMC
February 2011

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates.

Nat Struct Mol Biol 2011 Feb 23;18(2):120-7. Epub 2010 Dec 23.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/nsmb.2000DOI Listing
February 2011

Integrative epigenomic and genomic analysis of malignant pheochromocytoma.

Exp Mol Med 2010 Jul;42(7):484-502

Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, SE-75185 Uppsala, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912476PMC
http://dx.doi.org/10.3858/emm.2010.42.7.050DOI Listing
July 2010

Two polypyrimidine tracts in the nitric oxide synthase 2 gene: similar regulatory sequences with different properties.

Mol Biol Rep 2010 Apr 8;37(4):2021-30. Epub 2009 Aug 8.

Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85, Uppsala, Sweden.

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http://dx.doi.org/10.1007/s11033-009-9653-9DOI Listing
April 2010

CHD7 cooperates with PBAF to control multipotent neural crest formation.

Nature 2010 Feb 3;463(7283):958-62. Epub 2010 Feb 3.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://www.nature.com/doifinder/10.1038/nature08733
Publisher Site
http://dx.doi.org/10.1038/nature08733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890258PMC
February 2010

Nucleosomes are well positioned in exons and carry characteristic histone modifications.

Genome Res 2009 Oct 17;19(10):1732-41. Epub 2009 Aug 17.

The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden.

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http://dx.doi.org/10.1101/gr.092353.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765275PMC
October 2009

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.

Nucleic Acids Res 2009 Jul 18;37(12):e85. Epub 2009 May 18.

The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden.

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http://dx.doi.org/10.1093/nar/gkp381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709586PMC
July 2009

Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation.

Epigenetics 2009 Feb 1;4(2):107-13. Epub 2009 Mar 1.

Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.4161/epi.4.2.8038DOI Listing
February 2009

Histone acetylation and methylation at sites initiating divergent polycistronic transcription in Trypanosoma cruzi.

J Biol Chem 2008 Jun 9;283(23):15884-92. Epub 2008 Apr 9.

Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.

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http://dx.doi.org/10.1074/jbc.M802081200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259629PMC
June 2008

Monte Carlo feature selection for supervised classification.

Bioinformatics 2008 Jan 28;24(1):110-7. Epub 2007 Nov 28.

Institute of Computer Science, Polish Academy of Science, Ordona 21, PL-01-237 Warsaw, Poland.

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http://dx.doi.org/10.1093/bioinformatics/btm486DOI Listing
January 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

In vitro analysis of DNA-protein interactions by proximity ligation.

Proc Natl Acad Sci U S A 2007 Feb 20;104(9):3067-72. Epub 2007 Feb 20.

Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Dag Hammarskjöldsväg 20, SE-75185 Uppsala, Sweden.

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http://dx.doi.org/10.1073/pnas.0611229104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805562PMC
February 2007

The promoter of inducible nitric oxide synthase implicated in glaucoma based on genetic analysis and nuclear factor binding.

Mol Vis 2005 Nov 4;11:950-7. Epub 2005 Nov 4.

Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden.

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November 2005

Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding.

Gene 2004 Oct;341:149-65

Department of Genetics and Pathology, Unit of Clinical Genetic, Rudbeck Laboratory, Uppsala University, Uppsala SE-75185, Sweden.

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http://dx.doi.org/10.1016/j.gene.2004.06.035DOI Listing
October 2004