Shyam Prabhakar

Shyam Prabhakar

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Shyam Prabhakar

Publications by authors named "Shyam Prabhakar"

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56Publications

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Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas.

Authors:
Fumiharu Ohka Keiko Shinjo Shoichi Deguchi Yusuke Matsui Yusuke Okuno Keisuke Katsushima Miho Suzuki Akira Kato Noboru Ogiso Akane Yamamichi Kosuke Aoki Hiromichi Suzuki Shinya Sato Nirmala Arul Rayan Shyam Prabhakar Jonathan Göke Teppei Shimamura Reo Maruyama Satoru Takahashi Akio Suzumura Hiroshi Kimura Toshihiko Wakabayashi Hui Zong Atsushi Natsume Yutaka Kondo

Cancer Res 2019 Oct 20;79(19):4814-4827. Epub 2019 Aug 20.

Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.

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http://dx.doi.org/10.1158/0008-5472.CAN-19-1272DOI Listing
October 2019

Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation.

Authors:
Dilip Kumar Bernett Lee Kia Joo Puan Wendy Lee Boris San Luis Nurhashikin Yusof Anand Kumar Andiappan Ricardo Del Rosario Jeremie Poschmann Pavanish Kumar Gennaro DeLibero Amit Singhal Shyam Prabhakar Wang De Yun Michael Poidinger Olaf Rötzschke

Sci Rep 2019 Oct 23;9(1):15245. Epub 2019 Oct 23.

Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore.

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http://dx.doi.org/10.1038/s41598-019-51592-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811637PMC
October 2019

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue.

Authors:
Chloe C Y Wong Rebecca G Smith Eilis Hannon Gokul Ramaswami Neelroop N Parikshak Elham Assary Claire Troakes Jeremie Poschmann Leonard C Schalkwyk Wenjie Sun Shyam Prabhakar Daniel H Geschwind Jonathan Mill

Hum Mol Genet 2019 07;28(13):2201-2211

University of Exeter Medical School, University of Exeter, Exeter, UK.

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http://dx.doi.org/10.1093/hmg/ddz052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602383PMC
July 2019

Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease.

Authors:
Costanza Ferrari Bardile Marta Garcia-Miralles Nicholas S Caron Nirmala Arul Rayan Sarah R Langley Nathan Harmston Ana Maria Rondelli Roy Tang Yi Teo Sabine Waltl Lisa M Anderson Han-Gyu Bae Sangyong Jung Anna Williams Shyam Prabhakar Enrico Petretto Michael R Hayden Mahmoud A Pouladi

Proc Natl Acad Sci U S A 2019 May 23;116(19):9622-9627. Epub 2019 Apr 23.

Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (A*STAR), Immunos, 138648 Singapore;

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http://dx.doi.org/10.1073/pnas.1818042116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511031PMC
May 2019

Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response.

Authors:
Dominic Paul Lee Wilson Lek Wen Tan Chukwuemeka George Anene-Nzelu Chang Jie Mick Lee Peter Yiqing Li Tuan Danh Anh Luu Cheryl Xueli Chan Zenia Tiang Shi Ling Ng Xingfan Huang Motakis Efthymios Matias I Autio Jianming Jiang Melissa Jane Fullwood Shyam Prabhakar Erez Lieberman Aiden Roger Sik-Yin Foo

Circulation 2019 Apr;139(16):1937-1956

Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.118.036726DOI Listing
April 2019

Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures.

Authors:
Say Li Kong Huipeng Li Joyce A Tai Elise T Courtois Huay Mei Poh Dawn Pingxi Lau Yu Xuan Haw Narayanan Gopalakrishna Iyer Daniel Shao Weng Tan Shyam Prabhakar Dave Ruff Axel M Hillmer

Clin Chem 2019 02 6;65(2):272-281. Epub 2018 Dec 6.

Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore;

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http://dx.doi.org/10.1373/clinchem.2018.295717DOI Listing
February 2019

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.

Authors:
Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Igor Cima Min-Han Tan Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar

Nat Genet 2018 12;50(12):1754

Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1038/s41588-018-0299-1DOI Listing
December 2018

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.

Authors:
Xuecong Wang Yogesh Srivastava Aleksander Jankowski Vikas Malik Yuanjie Wei Ricardo Ch Del Rosario Vlad Cojocaru Shyam Prabhakar Ralf Jauch

Nucleic Acids Res 2018 06;46(11):5470-5486

CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.

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https://academic.oup.com/nar/article/46/11/5470/4970502
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http://dx.doi.org/10.1093/nar/gky259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009666PMC
June 2018

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos.

Authors:
Wenqing Jean Lee Sumantra Chatterjee Sook Peng Yap Siew Lan Lim Xing Xing Petra Kraus Wenjie Sun Xiaoming Hu V Sivakamasundari Hsiao Yun Chan Prasanna R Kolatkar Shyam Prabhakar Thomas Lufkin

Biomed Res Int 2017 28;2017:8932583. Epub 2017 May 28.

Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA.

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http://dx.doi.org/10.1155/2017/8932583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467288PMC
March 2018

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.

Authors:
Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Paul Jongjoon Choi Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar

Nat Genet 2017 May 20;49(5):708-718. Epub 2017 Mar 20.

Computational and Systems Biology, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1038/ng.3818DOI Listing
May 2017

Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness.

Authors:
Stefanie Heilmann-Heimbach Christine Herold Lara M Hochfeld Axel M Hillmer Dale R Nyholt Julian Hecker Asif Javed Elaine G Y Chew Sonali Pechlivanis Dmitriy Drichel Xiu Ting Heng Ricardo C-H Del Rosario Heide L Fier Ralf Paus Rico Rueedi Tessel E Galesloot Susanne Moebus Thomas Anhalt Shyam Prabhakar Rui Li Stavroula Kanoni George Papanikolaou Zoltán Kutalik Panos Deloukas Michael P Philpott Gérard Waeber Tim D Spector Peter Vollenweider Lambertus A L M Kiemeney George Dedoussis J Brent Richards Michael Nothnagel Nicholas G Martin Tim Becker David A Hinds Markus M Nöthen

Nat Commun 2017 03 8;8:14694. Epub 2017 Mar 8.

Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany.

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http://dx.doi.org/10.1038/ncomms14694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5344973PMC
March 2017

A developmental transcriptomic analysis of and in embryonic intervertebral disc development.

Authors:
V Sivakamasundari Petra Kraus Wenjie Sun Xiaoming Hu Siew Lan Lim Shyam Prabhakar Thomas Lufkin

Biol Open 2017 Feb 15;6(2):187-199. Epub 2017 Feb 15.

Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA

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http://dx.doi.org/10.1242/bio.023218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312110PMC
February 2017

A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus.

Authors:
Dilip Kumar Kia Joo Puan Anand Kumar Andiappan Bernett Lee Geertje H A Westerlaken Doreen Haase Rossella Melchiotti Zhuang Li Nurhashikin Yusof Josephine Lum Geraldine Koh Shihui Foo Joe Yeong Alexessander Couto Alves Juha Pekkanen Liang Dan Sun Astrid Irwanto Benjamin P Fairfax Vivek Naranbhai John E A Common Mark Tang Chin Keh Chuang Marjo-Riitta Jarvelin Julian C Knight Xuejun Zhang Fook Tim Chew Shyam Prabhakar Liu Jianjun De Yun Wang Francesca Zolezzi Michael Poidinger E Birgitte Lane Linde Meyaard Olaf Rötzschke

Genome Med 2017 02 20;9(1):18. Epub 2017 Feb 20.

Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove #04-06, Singapore, 138648, Republic of Singapore.

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http://dx.doi.org/10.1186/s13073-017-0404-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319034PMC
February 2017

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro.

Authors:
Sumantra Chatterjee Petra Kraus V Sivakamasundari Sook Peng Yap Vibhor Kumar Shyam Prabhakar Thomas Lufkin

Genom Data 2016 Dec 8;10:51-3. Epub 2016 Sep 8.

Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA.

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http://dx.doi.org/10.1016/j.gdata.2016.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030313PMC
December 2016

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data.

Authors:
Yongli Hu Takeshi Hase Hui Peng Li Shyam Prabhakar Hiroaki Kitano See Kiong Ng Samik Ghosh Lawrence Jin Kiat Wee

BMC Genomics 2016 12 22;17(Suppl 13):1025. Epub 2016 Dec 22.

Institute for Infocomm Research, A*STAR, 1 Fusionopolis Way, #21-01 Connexis (South Tower), Singapore, Singapore.

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http://dx.doi.org/10.1186/s12864-016-3317-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260093PMC
December 2016

Histone Acetylome-wide Association Study of Autism Spectrum Disorder.

Authors:
Wenjie Sun Jeremie Poschmann Ricardo Cruz-Herrera Del Rosario Neelroop N Parikshak Hajira Shreen Hajan Vibhor Kumar Ramalakshmi Ramasamy T Grant Belgard Bavani Elanggovan Chloe Chung Yi Wong Jonathan Mill Daniel H Geschwind Shyam Prabhakar

Cell 2016 11;167(5):1385-1397.e11

Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.10.031DOI Listing
November 2016

Massive contribution of transposable elements to mammalian regulatory sequences.

Authors:
Nirmala Arul Rayan Ricardo C H Del Rosario Shyam Prabhakar

Semin Cell Dev Biol 2016 09 10;57:51-56. Epub 2016 May 10.

Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, 60 Biopolis Street, 138672, Singapore. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10849521163012
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http://dx.doi.org/10.1016/j.semcdb.2016.05.004DOI Listing
September 2016

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.

Authors:
Aleksander Jankowski Jerzy Tiuryn Shyam Prabhakar

Bioinformatics 2016 08 19;32(16):2419-26. Epub 2016 Apr 19.

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

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btw209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978937PMC
August 2016

Tumor-derived circulating endothelial cell clusters in colorectal cancer.

Authors:
Igor Cima Say Li Kong Debarka Sengupta Iain B Tan Wai Min Phyo Daniel Lee Min Hu Ciprian Iliescu Irina Alexander Wei Lin Goh Mehran Rahmani Nur-Afidah Mohamed Suhaimi Jess H Vo Joyce A Tai Joanna H Tan Clarinda Chua Rachel Ten Wan Jun Lim Min Hoe Chew Charlotte A E Hauser Rob M van Dam Wei-Yen Lim Shyam Prabhakar Bing Lim Poh Koon Koh Paul Robson Jackie Y Ying Axel M Hillmer Min-Han Tan

Sci Transl Med 2016 06;8(345):345ra89

Institute of Bioengineering and Nanotechnology, Singapore 138669, Singapore. National Cancer Centre Singapore, Singapore 169610, Singapore. Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore. Concord Cancer Hospital, Singapore 289891, Singapore.

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http://dx.doi.org/10.1126/scitranslmed.aad7369DOI Listing
June 2016

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters.

Authors:
Vibhor Kumar Nirmala Arul Rayan Masafumi Muratani Stefan Lim Bavani Elanggovan Lixia Xin Tess Lu Harshyaa Makhija Jeremie Poschmann Thomas Lufkin Huck Hui Ng Shyam Prabhakar

Genome Res 2016 05 8;26(5):612-23. Epub 2016 Mar 8.

Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore;

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http://dx.doi.org/10.1101/gr.201038.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864461PMC
May 2016

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis.

Authors:
Shi Chi Leow Jeremie Poschmann Peh Gek Too Juan Yin Roy Joseph Craig McFarlane Shaillay Dogra Asim Shabbir Philip W Ingham Shyam Prabhakar Melvin K S Leow Yung Seng Lee Kai Lyn Ng Yap Seng Chong Peter D Gluckman Walter Stünkel

Development 2016 Mar 18;143(6):950-61. Epub 2016 Feb 18.

Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609

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http://dx.doi.org/10.1242/dev.131573DOI Listing
March 2016

The PsychENCODE project.

Authors:
Schahram Akbarian Chunyu Liu James A Knowles Flora M Vaccarino Peggy J Farnham Gregory E Crawford Andrew E Jaffe Dalila Pinto Stella Dracheva Daniel H Geschwind Jonathan Mill Angus C Nairn Alexej Abyzov Sirisha Pochareddy Shyam Prabhakar Sherman Weissman Patrick F Sullivan Matthew W State Zhiping Weng Mette A Peters Kevin P White Mark B Gerstein Anahita Amiri Chris Armoskus Allison E Ashley-Koch Taejeong Bae Andrea Beckel-Mitchener Benjamin P Berman Gerhard A Coetzee Gianfilippo Coppola Nancy Francoeur Menachem Fromer Robert Gao Kay Grennan Jennifer Herstein David H Kavanagh Nikolay A Ivanov Yan Jiang Robert R Kitchen Alexey Kozlenkov Marija Kundakovic Mingfeng Li Zhen Li Shuang Liu Lara M Mangravite Eugenio Mattei Eirene Markenscoff-Papadimitriou Fábio C P Navarro Nicole North Larsson Omberg David Panchision Neelroop Parikshak Jeremie Poschmann Amanda J Price Michael Purcaro Timothy E Reddy Panos Roussos Shannon Schreiner Soraya Scuderi Robert Sebra Mikihito Shibata Annie W Shieh Mario Skarica Wenjie Sun Vivek Swarup Amber Thomas Junko Tsuji Harm van Bakel Daifeng Wang Yongjun Wang Kai Wang Donna M Werling A Jeremy Willsey Heather Witt Hyejung Won Chloe C Y Wong Gregory A Wray Emily Y Wu Xuming Xu Lijing Yao Geetha Senthil Thomas Lehner Pamela Sklar Nenad Sestan

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.

Authors:
Yinghui Li Qi-Ling Zhou Wenjie Sun Prashant Chandrasekharan Hui Shan Cheng Zhe Ying Manikandan Lakshmanan Anandhkumar Raju Daniel G Tenen Shi-Yuan Cheng Kai-Hsiang Chuang Jun Li Shyam Prabhakar Mengfeng Li Vinay Tergaonkar

Nat Cell Biol 2015 Oct 21;17(10):1327-38. Epub 2015 Sep 21.

Institute of Molecular and Cell Biology (IMCB), A∗STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.

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http://dx.doi.org/10.1038/ncb3240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772727PMC
October 2015

Gene expression profiles of expressing FACS sorted cells from wildtype and null mouse embryos.

Authors:
Sumantra Chatterjee V Sivakamasundari Petra Kraus Sook Peng Yap Vibhor Kumar Shyam Prabhakar Thomas Lufkin

Genom Data 2015 Sep;5:103-105

Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA.

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http://dx.doi.org/10.1016/j.gdata.2015.05.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474491PMC
September 2015

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content.

Authors:
Roy Joseph Jeremie Poschmann Rami Sukarieh Peh Gek Too Sofi G Julien Feng Xu Ai Ling Teh Joanna D Holbrook Kai Lyn Ng Yap Seng Chong Peter D Gluckman Shyam Prabhakar Walter Stünkel

Mol Endocrinol 2015 Jun 27;29(6):909-20. Epub 2015 Apr 27.

Singapore Institute for Clinical Sciences (R.J., R.S., P.G.T., S.G.J., F.X., A.L.T., J.D.H., Y.S.C., P.D.G., W.S.), Agency for Science, Technology and Research, Singapore 117609; Genome Institute of Singapore (J.P., S.P.), Agency for Science, Technology and Research, Singapore 138672; Department of Obstetrics and Gynaecology (K.L.N., Y.S.C.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228; and Liggins Institute (P.D.G.), University of Auckland, Auckland 1142, New Zealand.

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http://dx.doi.org/10.1210/me.2015-1020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5414735PMC
June 2015

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms.

Authors:
Ricardo Cruz-Herrera del Rosario Jeremie Poschmann Sigrid Laure Rouam Eileen Png Chiea Chuen Khor Martin Lloyd Hibberd Shyam Prabhakar

Nat Methods 2015 May 23;12(5):458-64. Epub 2015 Mar 23.

Computational and Systems Biology Group, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1038/nmeth.3326DOI Listing
May 2015

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains.

Authors:
Yong-Heng Huang Aleksander Jankowski Kathryn S E Cheah Shyam Prabhakar Ralf Jauch

Sci Rep 2015 May 27;5:10398. Epub 2015 May 27.

Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, 190 Kai Yuan Avenue,Science Park, 510530 Guangzhou, China.

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http://dx.doi.org/10.1038/srep10398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445065PMC
May 2015

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column.

Authors:
Sumantra Chatterjee V Sivakamasundari Sook Peng Yap Petra Kraus Vibhor Kumar Xing Xing Siew Lan Lim Joel Sng Shyam Prabhakar Thomas Lufkin

BMC Genomics 2014 Dec 5;15:1072. Epub 2014 Dec 5.

Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA.

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http://dx.doi.org/10.1186/1471-2164-15-1072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302147PMC
December 2014

Noncoding origins of anthropoid traits and a new null model of transposon functionalization.

Authors:
Ricardo C H del Rosario Nirmala Arul Rayan Shyam Prabhakar

Genome Res 2014 Sep 20;24(9):1469-84. Epub 2014 Jul 20.

Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672

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http://dx.doi.org/10.1101/gr.168963.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158753PMC
September 2014

MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-β/BMP signaling.

Authors:
Akshay Bhinge Jeremie Poschmann Seema C Namboori Xianfeng Tian Sharon Jia Hui Loh Anna Traczyk Shyam Prabhakar Lawrence W Stanton

EMBO J 2014 Jun 6;33(11):1271-83. Epub 2014 May 6.

Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore City, Singapore Department of Biological Sciences, National University of Singapore, Singapore City, Singapore School of Biological Sciences Nanyang Technological University, Singapore City, Singapore

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http://dx.doi.org/10.1002/embj.201387215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198029PMC
June 2014

TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.

Authors:
Aleksander Jankowski Shyam Prabhakar Jerzy Tiuryn

BMC Genomics 2014 Mar 19;15:208. Epub 2014 Mar 19.

Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.

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http://dx.doi.org/10.1186/1471-2164-15-208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004051PMC
March 2014

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations.

Authors:
Kyle M Loh Lay Teng Ang Jingyao Zhang Vibhor Kumar Jasmin Ang Jun Qiang Auyeong Kian Leong Lee Siew Hua Choo Christina Y Y Lim Massimo Nichane Junru Tan Monireh Soroush Noghabi Lisa Azzola Elizabeth S Ng Jens Durruthy-Durruthy Vittorio Sebastiano Lorenz Poellinger Andrew G Elefanty Edouard G Stanley Qingfeng Chen Shyam Prabhakar Irving L Weissman Bing Lim

Cell Stem Cell 2014 Feb 9;14(2):237-52. Epub 2014 Jan 9.

Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/cms/attachment/2012539438/2034733303/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S193459091300556
Publisher Site
http://dx.doi.org/10.1016/j.stem.2013.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045507PMC
February 2014

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.

Authors:
Cecilia L Winata Igor Kondrychyn Vibhor Kumar Kandhadayar G Srinivasan Yuriy Orlov Ashwini Ravishankar Shyam Prabhakar Lawrence W Stanton Vladimir Korzh Sinnakaruppan Mathavan

PLoS Genet 2013 Oct 31;9(10):e1003852. Epub 2013 Oct 31.

Human Genetics, Genome Institute of Singapore, Singapore, Singapore.

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http://dx.plos.org/10.1371/journal.pgen.1003852
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http://dx.doi.org/10.1371/journal.pgen.1003852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814314PMC
October 2013

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers.

Authors:
Aleksander Jankowski Ewa Szczurek Ralf Jauch Jerzy Tiuryn Shyam Prabhakar

Genome Res 2013 Aug 3;23(8):1307-18. Epub 2013 Apr 3.

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

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http://dx.doi.org/10.1101/gr.154922.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730104PMC
August 2013

Uniform, optimal signal processing of mapped deep-sequencing data.

Authors:
Vibhor Kumar Masafumi Muratani Nirmala Arul Rayan Petra Kraus Thomas Lufkin Huck Hui Ng Shyam Prabhakar

Nat Biotechnol 2013 Jul 16;31(7):615-22. Epub 2013 Jun 16.

Computational and Systems Biology, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1038/nbt.2596DOI Listing
July 2013

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.

Authors:
Wenjie Sun Xiaoming Hu Michael H K Lim Calista K L Ng Siew Hua Choo Diogo S Castro Daniela Drechsel François Guillemot Prasanna R Kolatkar Ralf Jauch Shyam Prabhakar

Nucleic Acids Res 2013 Jun 16;41(11):5555-68. Epub 2013 Apr 16.

Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore 138672, Singapore.

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http://dx.doi.org/10.1093/nar/gkt250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675472PMC
June 2013

Study sequence rules of estrogen receptor α-DNA interactions using dual polarization interferometry and computational modeling.

Authors:
Hong Yan Song Wenjie Sun Shyam Prabhakar Khin Moh Moh Aung Xiaodi Su

Anal Biochem 2013 Feb 23;433(2):121-8. Epub 2012 Oct 23.

Institute of Materials Research and Engineering, Agency for Science, Technology, and Research (A*STAR), Singapore 117602, Singapore.

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https://linkinghub.elsevier.com/retrieve/pii/S00032697120053
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http://dx.doi.org/10.1016/j.ab.2012.10.021DOI Listing
February 2013

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.

Authors:
Jia-Hui Ng Vibhor Kumar Masafumi Muratani Petra Kraus Jia-Chi Yeo Lai-Ping Yaw Kun Xue Thomas Lufkin Shyam Prabhakar Huck-Hui Ng

Dev Cell 2013 Feb 24;24(3):324-33. Epub 2013 Jan 24.

Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672.

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https://linkinghub.elsevier.com/retrieve/pii/S15345807120058
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http://dx.doi.org/10.1016/j.devcel.2012.12.011DOI Listing
February 2013

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming.

Authors:
Michelle Percharde Fabrice Lavial Jia-Hui Ng Vibhor Kumar Rute A Tomaz Nadine Martin Jia-Chi Yeo Jesús Gil Shyam Prabhakar Huck-Hui Ng Malcolm G Parker Véronique Azuara

Genes Dev 2012 Oct 26;26(20):2286-98. Epub 2012 Sep 26.

Institute of Reproductive and Developmental Biology, Imperial College, London, United Kingdom.

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http://dx.doi.org/10.1101/gad.195545.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475801PMC
October 2012

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements.

Authors:
Calista K L Ng Noel X Li Sheena Chee Shyam Prabhakar Prasanna R Kolatkar Ralf Jauch

Nucleic Acids Res 2012 Jun 16;40(11):4933-41. Epub 2012 Feb 16.

Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gks153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367189PMC
June 2012

MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome.

Authors:
Qian-Fei Wang George Wu Shuangli Mi Fuhong He Jun Wu Jingfang Dong Roger T Luo Ryan Mattison Joseph J Kaberlein Shyam Prabhakar Hongkai Ji Michael J Thirman

Blood 2011 Jun 25;117(25):6895-905. Epub 2011 Apr 25.

Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1182/blood-2010-12-324699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3128481PMC
June 2011

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α.

Authors:
Roy Joseph Yuriy L Orlov Mikael Huss Wenjie Sun Say Li Kong Leena Ukil You Fu Pan Guoliang Li Michael Lim Jane S Thomsen Yijun Ruan Neil D Clarke Shyam Prabhakar Edwin Cheung Edison T Liu

Mol Syst Biol 2010 Dec;6:456

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

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http://msb.embopress.org/cgi/doi/10.1038/msb.2010.109
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http://dx.doi.org/10.1038/msb.2010.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018168PMC
December 2010

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors.

Authors:
Nithya BabuRajendran Paaventhan Palasingam Kamesh Narasimhan Wenjie Sun Shyam Prabhakar Ralf Jauch Prasanna R Kolatkar

Nucleic Acids Res 2010 Jun 10;38(10):3477-88. Epub 2010 Feb 10.

Laboratory of Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore.

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http://dx.doi.org/10.1093/nar/gkq046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879523PMC
June 2010

Human-specific gain of function in a developmental enhancer.

Authors:
Shyam Prabhakar Axel Visel Jennifer A Akiyama Malak Shoukry Keith D Lewis Amy Holt Ingrid Plajzer-Frick Harris Morrison David R Fitzpatrick Veena Afzal Len A Pennacchio Edward M Rubin James P Noonan

Science 2008 Sep;321(5894):1346-50

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1126/science.1159974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658639PMC
September 2008

Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

Authors:
Axel Visel Shyam Prabhakar Jennifer A Akiyama Malak Shoukry Keith D Lewis Amy Holt Ingrid Plajzer-Frick Veena Afzal Edward M Rubin Len A Pennacchio

Nat Genet 2008 Feb 6;40(2):158-60. Epub 2008 Jan 6.

Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/ng.2007.55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647775PMC
February 2008

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer.

Authors:
Wade T Nottingham Andrew Jarratt Matthew Burgess Caroline L Speck Jan-Fang Cheng Shyam Prabhakar Eddy M Rubin Pik-Shan Li Jackie Sloane-Stanley John Kong-A-San Marella F T R de Bruijn

Blood 2007 Dec 6;110(13):4188-97. Epub 2007 Sep 6.

Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1182/blood-2007-07-100883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2234795PMC
December 2007

Primate-specific evolution of an LDLR enhancer.

Authors:
Qian-fei Wang Shyam Prabhakar Qianben Wang Alan M Moses Sumita Chanan Myles Brown Michael B Eisen Jan-Fang Cheng Edward M Rubin Dario Boffelli

Genome Biol 2006 2;7(8):R68. Epub 2006 Aug 2.

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1186/gb-2006-7-8-R68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779597PMC
June 2007

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.

Authors:
Qian-fei Wang Shyam Prabhakar Sumita Chanan Jan-Fang Cheng Edward M Rubin Dario Boffelli

Genome Biol 2007 ;8(1):R1

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1186/gb-2007-8-1-r1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839124PMC
April 2007

Accelerated evolution of conserved noncoding sequences in humans.

Authors:
Shyam Prabhakar James P Noonan Svante Pääbo Edward M Rubin

Science 2006 Nov;314(5800):786

U.S. Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1126/science.1130738DOI Listing
November 2006

In vivo enhancer analysis of human conserved non-coding sequences.

Authors:
Len A Pennacchio Nadav Ahituv Alan M Moses Shyam Prabhakar Marcelo A Nobrega Malak Shoukry Simon Minovitsky Inna Dubchak Amy Holt Keith D Lewis Ingrid Plajzer-Frick Jennifer Akiyama Sarah De Val Veena Afzal Brian L Black Olivier Couronne Michael B Eisen Axel Visel Edward M Rubin

Nature 2006 Nov 5;444(7118):499-502. Epub 2006 Nov 5.

US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature05295DOI Listing
November 2006

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Authors:
Shyam Prabhakar Francis Poulin Malak Shoukry Veena Afzal Edward M Rubin Olivier Couronne Len A Pennacchio

Genome Res 2006 Jul 12;16(7):855-63. Epub 2006 Jun 12.

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.4717506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484452PMC
July 2006

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.

Authors:
Nadav Ahituv Shyam Prabhakar Francis Poulin Edward M Rubin Olivier Couronne

Hum Mol Genet 2005 Oct 9;14(20):3057-63. Epub 2005 Sep 9.

Genomics Division, Lawrence Berkeley National Laboratory, CA 94720, USA.

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http://dx.doi.org/10.1093/hmg/ddi338DOI Listing
October 2005

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.

Authors:
Jim R Hughes Jan-Fang Cheng Nicki Ventress Shyam Prabhakar Kevin Clark Eduardo Anguita Marco De Gobbi Pieter de Jong Eddy Rubin Douglas R Higgs

Proc Natl Acad Sci U S A 2005 Jul 5;102(28):9830-5. Epub 2005 Jul 5.

Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0503401102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174996PMC
July 2005

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

Authors:
Alexander C Zambon Lingzhi Zhang Simon Minovitsky Joan R Kanter Shyam Prabhakar Nathan Salomonis Karen Vranizan Inna Dubchak Bruce R Conklin Paul A Insel

Proc Natl Acad Sci U S A 2005 Jun 6;102(24):8561-6. Epub 2005 Jun 6.

Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141, USA.

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http://dx.doi.org/10.1073/pnas.0503363102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150853PMC
June 2005

The sequence and analysis of duplication-rich human chromosome 16.

Authors:
Joel Martin Cliff Han Laurie A Gordon Astrid Terry Shyam Prabhakar Xinwei She Gary Xie Uffe Hellsten Yee Man Chan Michael Altherr Olivier Couronne Andrea Aerts Eva Bajorek Stacey Black Heather Blumer Elbert Branscomb Nancy C Brown William J Bruno Judith M Buckingham David F Callen Connie S Campbell Mary L Campbell Evelyn W Campbell Chenier Caoile Jean F Challacombe Leslie A Chasteen Olga Chertkov Han C Chi Mari Christensen Lynn M Clark Judith D Cohn Mirian Denys John C Detter Mark Dickson Mira Dimitrijevic-Bussod Julio Escobar Joseph J Fawcett Dave Flowers Dea Fotopulos Tijana Glavina Maria Gomez Eidelyn Gonzales David Goodstein Lynne A Goodwin Deborah L Grady Igor Grigoriev Matthew Groza Nancy Hammon Trevor Hawkins Lauren Haydu Carl E Hildebrand Wayne Huang Sanjay Israni Jamie Jett Phillip B Jewett Kristen Kadner Heather Kimball Arthur Kobayashi Marie-Claude Krawczyk Tina Leyba Jonathan L Longmire Frederick Lopez Yunian Lou Steve Lowry Thom Ludeman Chitra F Manohar Graham A Mark Kimberly L McMurray Linda J Meincke Jenna Morgan Robert K Moyzis Mark O Mundt A Christine Munk Richard D Nandkeshwar Sam Pitluck Martin Pollard Paul Predki Beverly Parson-Quintana Lucia Ramirez Sam Rash James Retterer Darryl O Ricke Donna L Robinson Alex Rodriguez Asaf Salamov Elizabeth H Saunders Duncan Scott Timothy Shough Raymond L Stallings Malinda Stalvey Robert D Sutherland Roxanne Tapia Judith G Tesmer Nina Thayer Linda S Thompson Hope Tice David C Torney Mary Tran-Gyamfi Ming Tsai Levy E Ulanovsky Anna Ustaszewska Nu Vo P Scott White Albert L Williams Patricia L Wills Jung-Rung Wu Kevin Wu Joan Yang Pieter Dejong David Bruce Norman A Doggett Larry Deaven Jeremy Schmutz Jane Grimwood Paul Richardson Daniel S Rokhsar Evan E Eichler Paul Gilna Susan M Lucas Richard M Myers Edward M Rubin Len A Pennacchio

Nature 2004 Dec;432(7020):988-94

DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature03187DOI Listing
December 2004

The DNA sequence and comparative analysis of human chromosome 5.

Authors:
Jeremy Schmutz Joel Martin Astrid Terry Olivier Couronne Jane Grimwood Steve Lowry Laurie A Gordon Duncan Scott Gary Xie Wayne Huang Uffe Hellsten Mary Tran-Gyamfi Xinwei She Shyam Prabhakar Andrea Aerts Michael Altherr Eva Bajorek Stacey Black Elbert Branscomb Chenier Caoile Jean F Challacombe Yee Man Chan Mirian Denys John C Detter Julio Escobar Dave Flowers Dea Fotopulos Tijana Glavina Maria Gomez Eidelyn Gonzales David Goodstein Igor Grigoriev Matthew Groza Nancy Hammon Trevor Hawkins Lauren Haydu Sanjay Israni Jamie Jett Kristen Kadner Heather Kimball Arthur Kobayashi Frederick Lopez Yunian Lou Diego Martinez Catherine Medina Jenna Morgan Richard Nandkeshwar James P Noonan Sam Pitluck Martin Pollard Paul Predki James Priest Lucia Ramirez James Retterer Alex Rodriguez Stephanie Rogers Asaf Salamov Angelica Salazar Nina Thayer Hope Tice Ming Tsai Anna Ustaszewska Nu Vo Jeremy Wheeler Kevin Wu Joan Yang Mark Dickson Jan-Fang Cheng Evan E Eichler Anne Olsen Len A Pennacchio Daniel S Rokhsar Paul Richardson Susan M Lucas Richard M Myers Edward M Rubin

Nature 2004 Sep;431(7006):268-74

Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA.

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http://dx.doi.org/10.1038/nature02919DOI Listing
September 2004