Shyam Prabhakar, Ph.D.
Senior Group Leader, Computational and Systems Biology
Associate Director, Integrated Genomics
prabhakars@gis.a-star.edu.sg
RESEARCH FOCUS
 

Transcriptional Regulation
Disease Mechanisms, Therapeutics, Diagnostics, Omics, Algorithms, Data Analysis

The majority of genetic mutations responsible for common diseases reside within gene-regulatory sequences such as enhancers, promoters and insulators. In addition, transcriptional and epigenetic dysregulation are known to drive tumorigenesis, tumor progression and drug resistance. Thus, gene regulation lies at the heart of disease mechanisms and treatment response.

The Prabhakar Lab uses a combination of high-throughput omics assays (wet-lab) and data analytics (dry-lab) to study gene-regulatory mechanisms of human diseases. In particular, we use single-cell RNA-seq, cohort-scale histone ChIP-seq and other NGS technologies to understand autism, psychiatric drug response, lung and colon cancer, chronic myeloid leukemia, autoimmune disorders and host response to infection.

We also develop cutting-edge algorithms and pipelines for deriving biological insights from large datasets. This involves statistics, machine learning and extensive benchmarking for performance and scalability.

In addition to curiosity-driven science, we pursue inventions and discoveries that will (hopefully) make a difference in the world. For example, we are engaged in team science to discover markers of immunotherapy response and develop new imaging-based diagnostic technologies. The methods we develop have spawned research collaborations with multiple industry partners spanning biotech, IT and pharma.

Major achievements include the first single-cell transcriptomic analysis of colorectal tumors (Li, Courtois et al., Nat Genet 2017), the first study of histone acetylation changes in autism spectrum disorder (Sun, Poschmann et al., Cell 2016), the first large-scale study of variants that alter histone acetylation and contribute to disease susceptibility (del Rosario, Poschmann et al., Nat Methods 2015) and the first unified signal-processing method for peak detection in whole-genome profiling data (Kumar et al., Nat Biotechnol 2013). We have also uncovered fundamental properties of transcription factor binding to genomic DNA (Jankowski et al., Genome Res 2013) and demonstrated that H2BK20ac is a distinctive signature of enhancers and cell-type-specific promoters (Kumar, Rayan, Muratani et al., Genome Res 2016). Earlier work explored the contribution of gene regulatory elements to human origins (Prabhakar, Noonan et al., Science 2006; Prabhakar et al., Science 2008).

Centre for Big Data and Integrative Genomics (c-BIG)

Autism paper video (Straits Times)

Job Openings
Wet-lab PhD students, Postdoctoral Fellows
Computational Biology PhD students, Postdoctoral Fellows 1
Computational Biology PhD students, Postdoctoral Fellows 2
Bioinformatics Specialists

 

EDUCATION

2000 PhD, Applied Physics, Stanford University

1992 BTech, Electronics & Communications Engineering, Indian Institute of Technology, Madras

 

PROFESSIONAL APPOINTMENTS

2017- Senior Group Leader, Genome Institute of Singapore

2012- Associate Director, Integrative Genomics, Genome Institute of Singapore

2011-17 Group Leader, Genome Institute of Singapore

2007-11 Senior Research Scientist, Genome Institute of Singapore

2003-07 Postdoctoral Fellow, EM Rubin lab, Genomics Division, Lawrence Berkeley National Laboratory

2000-03 Postdoctoral Fellow, Samuel Karlin group, Dept. of Mathematics, Stanford University

 

HONORS AND AWARDS

2019 Co-leader of team that received Genome Institute of Singapore's Super Team Award (Spatial Omics)

2018 Member of team that received the Genome Institute of Singapore's Super Team Award (SG10K)

2008 First prize: poster competition at HUGO 13th Human Genome Meeting

2001 American Physical Society Award for Outstanding Doctoral Thesis Research in Beam Physics

 

COMMITTEE AND ADVISORY BOARD

2013 Grant review panel: bilateral grant call issued by BMBF (Germany) and ANR (France)

2014-2016 Grant review Panel: A*STAR Young Investigator Grants

2014-... Organizing Committee, Asian Epigenomics Meeting series

2015 Grant review panel: Agence Nationale de la Recherche (France)

2015 Grant Review Panel: Wellcome Trust

2015-... Assay Standards Working Group, International Human Epigenome Consortium

2016 Organizing committee: 15th International Conference On BioInformatics (InCOB 2016)

2016 Symposium Chair: Inaugural Symposium, centre for Big Data and Integrative Genomics (c-BIG)

2016-... International Scientific Steering Committee, International Human Epigenome Consortium (IHEC)

2017 Symposium co-Chair: Joint Singapore-EMBL Symposium on Precision Medicine

2017-... Human Frontiers Science Program Long-Term Fellowship Grant Panel

2017-... Enabling Platforms Working Group, National Precision Medicine Program, Singapore

2017-... Organizing Committee, Human Cell Atlas-Asia

2018 Organizing Committee of Single Cells: Technology to Biology (Cell Symposia)

2018 Organizing Committee: DTU-A*STAR Mini-Workshop on Precision Medicine

2018 Organizing Committee: International Human Epigenome Consortium Annual Meeting

 

EXTERNAL GRANT
 

2019-Mar1 - 2023-Feb28 (PI) IAF-PP-H18/01/a0/020: Single-Cell In Situ Spatial Omics at subcellular Resolution (SCISSOR) - Convergence and Disruption of the Molecular Diagnostics Market
2018-Jan02 - 2021-Jan01 (co-I) IAF-PP-H17/01/a0/007: National Precision Medicine Program (Phase 1A): Population Level Genomic Infrastructure
2018-Feb01 - 2021-Jan31 (PI) CDAP201703-172-76-00056: Enabling Data Analytics Technologies for Next-Generation Pathology from 3D Transcriptomics
2018-Aug01 - 2021-Jul31 (co-I) SFARI: Regulatory genomics variation in the developing human brain and autism
2017-Aug01 - 2020-Aug31 (co-I) CIRG16nov032: Single cell omics and mouse models to understand cellular heterogeneity and therapeutic resistance in chromic myeloid leukemia
2016-Aug10 - 2020-Apr30 (co-I) 1R01MH110927 Integrative Genomic Analysis of Human Brain Development and Autism
2015-Jan01 - 2019-Dec31 (PI) NRF2013-THE001-093 SynBioLogics: A Platform for Rational Design of Human Cells for Synthesis of Biologics
2015-Aug13 - 2019-Feb12 (PI) IAF111184 : Identifying new markers for characterising cell diversity in colorectal and lung cancers
2013-Sep13 - 2016-Sep12 (PI) JCO1331CFG080: Single Cell Transcriptomic Characterization of Tumour Heterogeneity and Network Analysis of Response to Targeted Therapeutics
2013-Dec01 - 2015-Nov30 (PI) IAF111118: Validation of the Chromatin Immunoprecipitation Assay Kit LysoChIP
2012-Sep26 - 2012-Dec31 (PI) IAF311010 JAIC: Multidecades Ethnic Study Pilot Phase
2012-Dec19 - 2014-Jun30 (PI) IAF111085: Optimizing Data Storage Infrastructure for Genomic Applications
2011-Aug25 - 2015-Jun30 (co-I) 1R01MH094714: Epigenetic and Transcriptional Dysregulation in Autism Spectrum Disorder
2009-Oct15 - 2012-Oct14 (PI) JCOAG03_FG02_2009: Toward a systems biology framework for estrogen signaling integrating technology, biology and computation

 

COMPLETE PUBLICATION LIST

Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease.
Ferrari Bardile C, Garcia-Miralles M, Caron NS, Rayan NA, Langley SR, Harmston N, Rondelli AM, Teo RTY, Waltl S, Anderson LM, Bae HG, Jung S, Williams A, Prabhakar S, Petretto E, Hayden MR, Pouladi MA.
Proc Natl Acad Sci USA 2019 May; 116:9622-9627.
Abstract
 
A Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response.
Lee DP, Tan WLW, Anene-Nzelu CG, Lee CJM, Li PY, Anh TD, Chan CX, Tiang Z, Ng SL, Huang X, Efthymios M, Autio MI, Jiang J, Fullwood MJ, Prabhakar S, Lieberman Aiden E, Foo RS.
Circulation 2019 Apr; 139:1937-1956.
Abstract
 
Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures.
Kong SL, Li H, Tai JA, Courtois ET, Poh HM, Lau DP, Haw YX, Iyer NG, Tan DSW, Prabhakar S, Ruff D, Hillmer AM.
Clin Chem 2019 Feb; 65:272-281.
Abstract
 
DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.
Wang X, Srivastava Y, Jankowski A, Malik V, Wei Y, Del Rosario RCH, Cojocaru V, Prabhakar S, Jauch R.
Nucleic Acids Res 2018 Jun;46:5470-5486.
Abstract
 
An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos.
Lee WJ, Chatterjee S, Yap SP, Lim SL, Xing X, Kraus P, Sun W, Hu X, Sivakamasundari V, Chan HY, Kolatkar PR, Prabhakar S, Lufkin T.
Biomed Res Int 2017; 2017:8932583.
Abstract
 
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Li H, Courtois ET, Sengupta D, Tan Y, Chen KH, Goh JJL, Kong SL, Chua C, Hon LK, Tan WS, Wong M, Choi PJ, Wee LJK, Hillmer AM, Tan IB, Robson P, Prabhakar S.
Nat Genet 2017 May; 49(5):708-18.
Abstract
 
Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness.
Heilmann-Heimbach S, Herold C, Hochfeld LM, Hillmer AM, Nyholt DR, Hecker J, Javed A, Chew EG, Pechlivanis S, Drichel D, Heng XT, Del Rosario RC, Fier HL, Paus R, Rueedi R, Galesloot TE, Moebus S, Anhalt T, Prabhakar S, Li R, Kanoni S, Papanikolaou G, Kutalik Z, Deloukas P, Philpott MP, Waeber G, Spector TD, Vollenweider P, Kiemeney LA, Dedoussis G, Richards JB, Nothnagel M, Martin NG, Becker T, Hinds DA, Nöthen MM.
Nat Commun 2017 Mar 08; 8:14694.
Abstract
 
A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus.
Kumar D, Puan KJ, Andiappan AK, Lee B, Westerlaken GH, Haase D, Melchiotti R, Li Z, Yusof N, Lum J, Koh G, Foo S, Yeong J, Alves AC, Pekkanen J, Sun LD, Irwanto A, Fairfax BP, Naranbhai V, Common JE, Tang M, Chuang CK, Jarvelin MR, Knight JC, Zhang X, Chew FT, Prabhakar S, Jianjun L, Wang Y, Zolezzi F, Poidinger M, Lane EB, Meyaard L, Rötzschke O.
Genome Med 2017 Feb 20; 9(1):18.
Abstract
 
A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development.
Sivakamasundari V, Kraus P, Sun W, Hu X, Lim SL, Prabhakar S, Lufkin T.
Biol Open 2017 Feb 15; 6(2):187-199.
Abstract
 
A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data.
Hu Y, Hase T, Li HP, Prabhakar S, Kitano H, Ng SK, Ghosh S, Wee LJ.
BMC Genomics 2016 Dec 22; 17(Suppl 13):1025.
Abstract
 
Histone Acetylome-wide Association Study of Autism Spectrum Disorder.
Sun W, Poschmann JF, del Rosario RC, Parikshak NN, Hajan HS, Kumar V, Ramaswamy R, Belgard TG, Elanggovan B, Wong CCY, Mill J, Geschwind DH, Prabhakar S.
Cell 2016 Nov; 167:1385-1397.
Abstract
 
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
Stunnenberg HG, The International Human Epigenome Consortium [including Prabhakar S], Hirst M.
Cell 2016 Nov; 167:1145-1149.
Abstract
 
Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro.
Chatterjee S, Kraus P, Sivakamasundari V, Yap SP, Kumar V, Prabhakar S, Lufkin T
Genom Data 2016 Sep 8; 10:51-3.
Abstract
 
Massive contribution of transposable elements to mammalian regulatory sequences.
Rayan NA, Del Rosario RC, Prabhakar S.
Semin Cell Dev Biol 2016 Sep; 57:51-6.
Abstract
 
Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.
Jankowski A, Tiuryn J, Prabhakar S.
Bioinformatics 2016 Aug 15; 32:2419-26.
Abstract
 
Tumor-derived circulating endothelial cell clusters in colorectal cancer.
Cima I, Kong SL, Sengupta D, Tan IB, Phyo WM, Lee D, Hu M, Iliescu C, Alexander I, Goh WL, Rahmani M, Suhaimi NA, Vo JH, Tai JA, Tan JH, Chua C, Ten R, Lim WJ, Chew MH, Hauser CA, van Dam RM, Lim WY, Prabhakar S, Lim B, Koh PK, Robson P, Ying JY, Hillmer AM, Tan MH.
Sci Transl Med 2016 Jun; 8(345):345ra89.
Abstract
 
Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters.
Kumar V, Rayan NA, Muratani M, Lim S, Elanggovan B, Lixia X, Lu T, Makhija H, Poschmann J, Lufkin T, Ng HH, Prabhakar S.
Genome Res 2016 May; 26(5):612-23.
Abstract
 
The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis.
Leow SC, Poschmann J, Too PG, Yin J, Joseph R, McFarlane C, Dogra S, Shabbir A, Ingham PW, Prabhakar S, Leow MK, Lee YS, Ng KL, Chong YS, Gluckman PD, Stünkel W.
Development 2016 Mar 15; 143(6):950-61.
Abstract
 
The PsychENCODE project.
Akbarian S, ... [79 other authors, including Prabhakar S] ..., Senthil G, Lehner T, Sklar P, Sestan N.
Nat Neurosci 2015 Nov 25; 18:1707-12.
Abstract
 
Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.
Li Y, Zhou QL, Sun W, Chandrasekharan P, Cheng HS, Ying Z, Lakshmanan M, Raju A, Tenen DG, Cheng SY, Chuang KH, Li J, Prabhakar S, Li M, Tergaonkar V.
Nat Cell Biol 2015 Oct; 17:1327-38.
Abstract
 
Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos.
Chatterjee S, Sivakamasundari V, Kraus P, Yap SP, Kumar V, Prabhakar S, Lufkin T.
Genom Data 2015 Sep; 5:103-105.
Abstract
 
ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content.
Joseph R, Poschmann J, Sukarieh R, Too PG, Julien SG, Xu F, Teh AL, Holbrook JD, Ng KL, Chong YS, Gluckman PD, Prabhakar S, Stünkel W.
Mol Endocrinol 2015 Jun; 29:909-20.
Abstract
 
SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains.
Huang YH, Jankowski A, Cheah KS, Prabhakar S, Jauch R.
Sci Rep 2015 May; 5:10398.
Abstract
 
Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms.
Del Rosario RC, Poschmann J, Rouam SL, Png E, Khor CC, Hibberd ML, Prabhakar S.
Nat Methods 2015 May; 12:458-64.
Abstract
 
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.
Chatterjee S, Sivakamasundari V, Yap SP, Kraus P, Kumar V, Xing X, Lim SL, Sng J, Prabhakar S, Lufkin T.
BMC Genomics 2014 Dec 5; 15:1072.
Abstract
 
Noncoding Origins of Anthropoid Traits and a New Null Model of Transposon Functionalization.
del Rosario RC, Rayan NA, Prabhakar S.
Genome Research 2014 Sep; 24(9):1469-84.
Abstract
 
The common marmoset genome provides insight into primate biology and evolution.
Marmoset Genome Sequencing and Analysis Consortium (including Prabhakar S).
Nat Genet 2014 Aug; 46:850-7.
Abstract
 
MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGFβ/BMP signaling.
Bhinge A, Poschmann J, Namboori SC, Tian X, Loh SJH, Traczyk A, Prabhakar S, Stanton LW.
EMBO Journal 2014 Jun 2; 33:1271-83.
Abstract
 
TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.
Jankowski A, Prabhakar S#, Tiuryn J. (#: corresponding author)
BMC Genomics 2014; 15(1):208 Epub 2014 Mar 19.
Abstract
 
Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations.
Loh KM, Ang LT, Zhang J, Kumar V, Ang J, Auyeong JQ, Lee KL, Choo SH, Lim CY, Nichane M, Tan J, Noghabi MS, Azzola L, Ng ES, Durruthy-Durruthy J, Sebastiano V, Poellinger L, Elefanty AG, Stanley EG, Chen Q, Prabhakar S, Weissman IL, Lim B.
Cell Stem Cell 2014 Feb 6; 14(2):237-52. Epub 2014 Jan 9.
Abstract
 
Genome wide analysis reveals zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.
Winata CL, Kondrychyn I, Kumar V, Srinivasan KG, Orlov Y, Ravishankar A, Prabhakar S, Stanton LW, Korzh V, Mathavan S.
PLoS Genet 2013 Oct; 9(10):e1003852 Epub 2013 Oct 31.
Abstract
 
Uniform, optimal signal processing of mapped deep-sequencing data.
Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S.
Nat Biotechnol 2013 July; 31(7):615-22.
Abstract
 
TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.
Sun W, Hu X, Lim MH, Ng CK, Choo S, Castro D, Drechsel D, Guillemot F, Kolatkar PR, Jauch R, Prabhakar S.
Nucleic Acids Res 2013 Jun 1; 41(11):5555-68.
Abstract
 
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers.
Jankowski A, Szczurek E, Jauch R, Tiuryn J, Prabhakar S.
Genome Res 2013 Aug;23(8):1307-18.
Abstract
 
Study Sequence Rules of ERα - DNA Interactions Using Dual Polarisation Interferometry and Computational Modeling.
Song HY, Sun W, Prabhakar S, Aung KM, Su X.
Anal Biochem 2013 Feb 15; 433(2):121-8.
Abstract
 
In Vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.
Ng JH, Kumar V, Muratani M, Kraus P, Yeo JC, Yaw LP, Xue K, Lufkin T, Prabhakar S#, Ng HH#. (#: corresponding author)
Dev Cell 2013 Feb 11; 24(3):324-33.
Abstract
 
Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming.
Percharde M, Lavial F, Ng JH, Kumar V, Tomaz RA, Martin N, Yeo JC, Gil J, Prabhakar S, Ng HH, Parker MG, Azuara V.
Genes Dev 2012 Oct 15; 26(20):2286-98.
Abstract
 
Deciphering the Sox-Oct partner code by quantitative cooperativity measurements.
Ng CK, Li NX, Chee S, Prabhakar S, Kolatkar PR, Jauch R.
Nucleic Acids Res 2012 Jun; 40:4933-41.
Abstract
 
MLL fusion proteins preferentially regulate a subset of wild type MLL target genes in the leukemic genome.
Wang QF, Wu G, Mi S, He F, Wu J, Dong J, Luo RT, Mattison R, Kaberlein JJ, Prabhakar S, Ji H, Thirman MJ.
Blood 2011 Jun;117:6895-905.
Abstract
 
Integrative model of genomic factors for determining binding site selection by estrogen receptor-alpha.
Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, Pan YF, Li G, Lim M, Thomsen JS, Ruan Y, Clarke ND, Prabhakar S, Cheung E, Liu ET.
Mol Syst Biol 2010 Dec 21;6:456.
Abstract
 
Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors.
BabuRajendran N, Palasingam P, Narasimhan K, Sun W, Prabhakar S, Jauch R, Kolatkar PR.
Nucleic Acids Res 2010 Jun;38(10):3477-88.
Abstract
 
Human-specific gain of function in a developmental enhancer.
Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick DR, Afzal V, Rubin EM, Noonan JP.
Science. 2008 Sep;321:1346-50.
Abstract
 
Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA.
Nature Genetics. 2008 Jan;40:158-60.
Abstract
 
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer.
Nottingham WT, Jarratt A, Burgess M, Speck CL, Cheng JF, Prabhakar S, Rubin EM, Li PS, Sloane-Stanley J, Kong-A-San J, de Bruijn MF.
Blood. 2007 Dec;110:4188-97.
Abstract
 
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.
Wang QF*, Prabhakar S*, Chanan S, Cheng JF, Rubin EM, Boffelli D (* = equal contribution).
Genome Biology 2007 Jan;8(1):R1.
Abstract
 
In vivo enhancer analysis of human conserved non-coding sequences.
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega M, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM.
Nature. 2006 Nov;444:499-502.
Abstract
 
Accelerated evolution of conserved noncoding sequences in humans.
Prabhakar S*, Noonan JP*, Pääbo S, Rubin EM (* = equal contribution).
Science. 2006 Nov;314:786.
Abstract
 
Primate-specific evolution of an LDLR enhancer.
Wang QF*, Prabhakar S*, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D (* = equal contribution).
Genome Biology. 2006 Aug;7(8):R68.
Abstract
 
Close sequence comparisons are sufficient to identify human cis-regulatory elements.
Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA.
Genome Research. 2006 Jul;16:855-63.
Abstract
 
Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.
Ahituv N*, Prabhakar S*, Poulin F, Rubin EM, Couronne O (* = equal contribution).
Human Molecular Genetics. 2005 Oct;14:3057-63.
Abstract
 
Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.
Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.
Proc. National Academy of Sciences USA. 2005 Jul;102(28):9830-5.
Abstract
 
Zambon AC, Zhang L, Minovitsky S, Kanter JR, Prabhakar S, Salomonis N, Vranizan K, Dubchak I, Conklin BR, Insel PA.
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 14;102(24):8561-6.
Abstract
 
The sequence and analysis of duplication-rich human chromosome 16.
Martin J, Han C, Gordon LA, Terry A, Prabhakar S, ... [115 authors] ..., Pennacchio LA.
Nature. 2004 Dec;432(7020):988-94.
Abstract
 
The DNA sequence and comparative analysis of human chromosome 5.
Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, ... [61 authors] ..., Rubin EM.
Nature. 2004 Sep;431(7006):268-74.
Abstract