Shyam Prabhakar

Shyam Prabhakar

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Shyam Prabhakar

Publications by authors named "Shyam Prabhakar"

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

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

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

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

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

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.

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

Massive contribution of transposable elements to mammalian regulatory sequences.

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.

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
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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.

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

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

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.

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.

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

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

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.

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.

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

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

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.

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.

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.

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
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http://dx.doi.org/10.1016/j.stem.2013.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045507PMC
February 2014

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

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.

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.

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.

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.

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

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

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.

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

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

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

Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

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.

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.

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.

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.

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

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

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.

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.

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.

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