Publications by authors named "Yijun Ruan"

100Publications

A supervised learning framework for chromatin loop detection in genome-wide contact maps.

Nat Commun 2020 07 9;11(1):3428. Epub 2020 Jul 9.

Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.

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http://dx.doi.org/10.1038/s41467-020-17239-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7347923PMC
July 2020

LATS kinase-mediated CTCF phosphorylation and selective loss of genomic binding.

Sci Adv 2020 02 19;6(8):eaaw4651. Epub 2020 Feb 19.

Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA.

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http://dx.doi.org/10.1126/sciadv.aaw4651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7030924PMC
February 2020

pyBedGraph: a python package for fast operations on 1D genomic signal tracks.

Bioinformatics 2020 05;36(10):3234-3235

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214040PMC
May 2020

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms.

Genome Biol 2019 11 25;20(1):251. Epub 2019 Nov 25.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

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http://dx.doi.org/10.1186/s13059-019-1868-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876102PMC
November 2019

Methods for comparative ChIA-PET and Hi-C data analysis.

Methods 2020 01 16;170:69-74. Epub 2019 Oct 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.09.019DOI Listing
January 2020

The 5th International 3D Genomics Workshop 2018: conference report.

Epigenomics 2019 09 1;11(12):1353-1357. Epub 2019 Oct 1.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China.

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http://dx.doi.org/10.2217/epi-2019-0185DOI Listing
September 2019

Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function.

Cell Rep 2019 01;26(3):788-801.e6

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.12.083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389269PMC
January 2019

Identification of Pharmacokinetic Markers for Guanxin Danshen Drop Pills in Rats by Combination of Pharmacokinetics, Systems Pharmacology, and Pharmacodynamic Assays.

Front Pharmacol 2018 21;9:1493. Epub 2018 Dec 21.

Department of Traditional Chinese Medicine Resource and Bee Products, Bee Science College, Fujian Agriculture and Forestry University, Fuzhou, China.

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https://www.frontiersin.org/article/10.3389/fphar.2018.01493
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http://dx.doi.org/10.3389/fphar.2018.01493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6308302PMC
December 2018

Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues.

Cold Spring Harb Protoc 2018 08 1;2018(8). Epub 2018 Aug 1.

Function and Mechanism of Action of Thyroid Hormone Receptor Group, UMR 7221 CNRS and Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France;

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http://dx.doi.org/10.1101/pdb.prot104620DOI Listing
August 2018

Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues.

Cold Spring Harb Protoc 2018 08 1;2018(8). Epub 2018 Aug 1.

Function and Mechanism of Action of Thyroid Hormone Receptor Group, UMR 7221 CNRS and Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France;

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http://dx.doi.org/10.1101/pdb.prot097725DOI Listing
August 2018

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture.

Nat Genet 2018 05 26;50(5):754-763. Epub 2018 Apr 26.

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.

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http://dx.doi.org/10.1038/s41588-018-0111-2DOI Listing
May 2018

STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the gene locus.

Proc Natl Acad Sci U S A 2017 11 24;114(46):12111-12119. Epub 2017 Oct 24.

Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20892;

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http://dx.doi.org/10.1073/pnas.1714019114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699083PMC
November 2017

Evolutionarily Conserved Principles Predict 3D Chromatin Organization.

Mol Cell 2017 Sep 17;67(5):837-852.e7. Epub 2017 Aug 17.

Department of Biology, Emory University, 1510 Clifton Road Northeast, Atlanta, GA 30322, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765173054
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http://dx.doi.org/10.1016/j.molcel.2017.07.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591081PMC
September 2017

ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis.

Sci Adv 2017 Jan 20;3(1):e1601602. Epub 2017 Jan 20.

Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.

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http://dx.doi.org/10.1126/sciadv.1601602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5249256PMC
January 2017

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

PLoS Comput Biol 2016 06 23;12(6):e1004809. Epub 2016 Jun 23.

The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919057PMC
June 2016

3D-GNOME: an integrated web service for structural modeling of the 3D genome.

Nucleic Acids Res 2016 07 16;44(W1):W288-93. Epub 2016 May 16.

Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland Center for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland

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http://dx.doi.org/10.1093/nar/gkw437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987952PMC
July 2016

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.

Cell 2015 Dec 10;163(7):1611-27. Epub 2015 Dec 10.

The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA; National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)01504-4.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501504
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http://dx.doi.org/10.1016/j.cell.2015.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734140PMC
December 2015

Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module.

Mol Endocrinol 2015 Jun 13;29(6):856-72. Epub 2015 Apr 13.

Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.

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http://dx.doi.org/10.1210/me.2014-1349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447637PMC
June 2015

Super-enhancers delineate disease-associated regulatory nodes in T cells.

Nature 2015 Apr 16;520(7548):558-62. Epub 2015 Feb 16.

Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1038/nature14154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409450PMC
April 2015

Transcriptional profiles of bovine in vivo pre-implantation development.

BMC Genomics 2014 Sep 4;15:756. Epub 2014 Sep 4.

Center for Regenerative Biology, Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA.

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http://dx.doi.org/10.1186/1471-2164-15-756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162962PMC
September 2014

Dissecting the chromatin interactome of microRNA genes.

Nucleic Acids Res 2014 Mar 18;42(5):3028-43. Epub 2013 Dec 18.

Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK.

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http://dx.doi.org/10.1093/nar/gkt1294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950692PMC
March 2014

Targeted inactivation and identification of targets of the Gli2a transcription factor in the zebrafish.

Biol Open 2013 9;2(11):1203-13. Epub 2013 Sep 9.

Institute of Molecular and Cell Biology , 61 Biopolis Drive , Singapore 138673 ; Present address: High Throughput Molecular Drug Discovery Center, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China.

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http://dx.doi.org/10.1242/bio.20136262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828767PMC
November 2013

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

Nature 2013 Dec 10;504(7479):306-310. Epub 2013 Nov 10.

Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature12716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954713PMC
December 2013

Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells.

Phys Rev E Stat Nonlin Soft Matter Phys 2012 Aug 21;86(2 Pt 1):021918. Epub 2012 Aug 21.

Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.

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http://dx.doi.org/10.1103/PhysRevE.86.021918DOI Listing
August 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET).

Methods Mol Biol 2012 ;809:535-62

Genome Institute of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1007/978-1-61779-376-9_35DOI Listing
March 2012

Genome-sequencing anniversary. Presenting the human genome: now in 3D!

Authors:
Yijun Ruan

Science 2011 Feb;331(6020):1025-6

Genome Institute of Singapore, Singapore, Republic of Singapore.

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http://dx.doi.org/10.1126/science.1203602DOI Listing
February 2011

Determination of transcription factor binding.

Nat Genet 2011 Jan;43(1):11-2

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http://www.nature.com/articles/ng0111-11
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http://dx.doi.org/10.1038/ng0111-11DOI Listing
January 2011

Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome.

Proc Natl Acad Sci U S A 2010 Oct 4;107(42):18161-6. Epub 2010 Oct 4.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1073/pnas.1005595107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964235PMC
October 2010

Multiplex parallel pair-end-ditag sequencing approaches in system biology.

Wiley Interdiscip Rev Syst Biol Med 2010 Mar-Apr;2(2):224-234

Genome Technology & Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672.

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http://dx.doi.org/10.1002/wsbm.40DOI Listing
February 2011

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

Chromatin interaction analysis using paired-end tag sequencing.

Curr Protoc Mol Biol 2010 Jan;Chapter 21:Unit 21.15.1-25

Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.

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http://dx.doi.org/10.1002/0471142727.mb2115s89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924956PMC
January 2010

Metagenomic analysis of viruses in reclaimed water.

Environ Microbiol 2009 Nov 25;11(11):2806-20. Epub 2009 Jun 25.

College of Marine Science, University of South Florida, St. Petersburg, Florida, USA.

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http://dx.doi.org/10.1111/j.1462-2920.2009.01964.xDOI Listing
November 2009

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.

Genome Res 2009 Apr;19(4):521-32

Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.

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http://dx.doi.org/10.1101/gr.074906.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807531PMC
April 2009

ChIP-based methods for the identification of long-range chromatin interactions.

J Cell Biochem 2009 May;107(1):30-9

Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.

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http://dx.doi.org/10.1002/jcb.22116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748757PMC
May 2009

Evolution of the mammalian transcription factor binding repertoire via transposable elements.

Genome Res 2008 Nov 5;18(11):1752-62. Epub 2008 Aug 5.

Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore.

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http://dx.doi.org/10.1101/gr.080663.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577865PMC
November 2008

Tackling the epigenome in the pluripotent stem cells.

J Genet Genomics 2008 Jul;35(7):403-12

Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore.

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http://dx.doi.org/10.1016/S1673-8527(08)60058-2DOI Listing
July 2008

Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments.

Genome Inform 2007 ;19:83-94

Genome Institute of Singapore, Biopolis street, 60, 138672 Singapore.

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July 2008

The use of multiple displacement amplification to amplify complex DNA libraries.

Nucleic Acids Res 2008 Mar 19;36(5):e32. Epub 2008 Feb 19.

Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore.

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http://dx.doi.org/10.1093/nar/gkn074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275127PMC
March 2008

Paired-end diTagging for transcriptome and genome analysis.

Curr Protoc Mol Biol 2007 Jul;Chapter 21:Unit 21.12

Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1002/0471142727.mb2112s79DOI Listing
July 2007