Skip to content

Home Search Authors Pakistan News Saved

SciRah

SciRah does not host or store research papers. Results come live from free, official scholarly APIs, and every paper links back to its original source.

Data sources

OpenAlex
Semantic Scholar
Crossref
CORE
arXiv
PubMed

Privacy policy Terms of service

Shyam Prabhakar · SciRah

Researcher profile · Semantic Scholar

Shyam Prabhakar

Share profile

Shyam Prabhakar — researcher profile on SciRah

h-index: 46
Works: 105
Citations: 10K

Most-cited papers

In vivo enhancer analysis of human conserved non-coding sequences
L. Pennacchio, N. Ahituv, Alan M. Moses, Shyam Prabhakar +15 more
2006Nature1,226 citations Open access
Semantic Scholar
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
Hui-Peng Li, E. Courtois, Debarka Sengupta, Yuliana Tan +13 more
2017Nature Genetics982 citations
Semantic Scholar
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer
Hae-Ock Lee, Yourae Hong, H. Etlioglu, Y. Cho +33 more
2020Nature Genetics740 citations
Semantic Scholar
Accelerated Evolution of Conserved Noncoding Sequences in Humans
Shyam Prabhakar, James P. Noonan, S. Pääbo, E. Rubin
2006Science475 citations
Semantic Scholar
The PsychENCODE project
S. Akbarian, Chunyu Liu, J. Knowles, F. Vaccarino +80 more
2015Nature Neuroscience418 citations Open access
Semantic Scholar
Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development.
Sebastian G. Utz, Peter See, Wiebke Mildenberger, M. S. Thion +12 more
2020Cell381 citations Open access
Semantic Scholar
Ultraconservation identifies a small subset of extremely constrained developmental enhancers
A. Visel, Shyam Prabhakar, J. Akiyama, Malak I. Shoukry +6 more
2008Nature Genetics342 citations Open access
Semantic Scholar
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
Ignasius Joanito, P. Wirapati, Nancy Q. Zhao, Zahid Nawaz +49 more
2022Nature Genetics339 citations Open access
Semantic Scholar
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer.
Wade T. Nottingham, A. Jarratt, M. Burgess, Caroline L. Speck +7 more
2007Blood280 citations Open access
Semantic Scholar
Histone Acetylome-wide Association Study of Autism Spectrum Disorder.
Wen-Jie Sun, Jeremie Poschmann, Ricardo Cruz-Herrera Del Rosario, Neelroop N. Parikshak +9 more
2016Cell279 citations Open access
Semantic Scholar
Response to Comment on "Human-Specific Gain of Function in a Developmental Enhancer"
Shyam Prabhakar, A. Visel, J. Akiyama, Malak I. Shoukry +9 more
2009Science257 citations
Semantic Scholar
The Common Marmoset Genome Provides Insight into Primate Biology and Evolution
Kim C Wesley C Jeffrey Devin Donna M Elaine R George M Worley Warren Rogers Locke Muzny Mardis Weinstock, K. Worley, W. Warren, Jeffrey Rogers +108 more
2014Nature Genetics242 citations Open access
Semantic Scholar
Close sequence comparisons are sufficient to identify human cis-regulatory elements.
Shyam Prabhakar, F. Poulin, Malak I. Shoukry, Veena Afzal +3 more
2005Genome Research202 citations Open access
Semantic Scholar
Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation
Yinghui Li, Qi-Ling Zhou, Wen-Jie Sun, P. Chandrasekharan +11 more
2015Nature Cell Biology193 citations Open access
Semantic Scholar
Uniform, optimal signal processing of mapped deep-sequencing data
Vibhor Kumar, M. Muratani, N. Rayan, P. Kraus +3 more
2013Nature Biotechnology173 citations Open access
Semantic Scholar
Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing
S. K. Leung, A. Jeffries, I. Castanho, B. Jordan +16 more
2021Cell Reports157 citations Open access
Semantic Scholar
MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome.
Qian-Fei Wang, George Wu, Shuangli Mi, F. He +8 more
2011Blood134 citations Open access
Semantic Scholar
In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.
Jia-Hui Ng, Vibhor Kumar, M. Muratani, P. Kraus +6 more
2013Developmental Cell126 citations Open access
Semantic Scholar
Supplementary information for Integrative model of genomic factors for determining binding site selection by estrogen receptor α
R. Joseph, Y. Orlov, Mikael Huss, Wen-Jie Sun +11 more
2010123 citations
Semantic Scholar
Tumor-derived circulating endothelial cell clusters in colorectal cancer
I. Cima, Say-Li Kong, Debarka Sengupta, I. Tan +25 more
2016Science Translational Medicine117 citations
Semantic Scholar
Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism
G. Ramaswami, H. Won, Michael Jeffrey Gandal, J. Haney +6 more
2019Nature Communications104 citations Open access
Semantic Scholar
Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming.
Michelle Percharde, F. Lavial, Jia-Hui Ng, Vibhor Kumar +8 more
2012Genes & Development101 citations Open access
Semantic Scholar
Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease
Costanza Ferrari Bardile, M. Garcia-Miralles, N. Caron, N. Rayan +13 more
2019Proceedings of the National Academy of Sciences of the United States of America100 citations Open access
Semantic Scholar
Deciphering the Sox-Oct partner code by quantitative cooperativity measurements
C. Ng, N. Li, Sheena Chee, Shyam Prabhakar +2 more
2012Nucleic Acids Research95 citations Open access
Semantic Scholar
Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.
N. Ahituv, Shyam Prabhakar, F. Poulin, E. Rubin +1 more
2005Human Molecular Genetics92 citations Open access
Semantic Scholar
SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains
Yong-Heng Huang, A. Jankowski, K. Cheah, Shyam Prabhakar +1 more
2015Scientific Reports87 citations Open access
Semantic Scholar
Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue
C. Wong, Rebecca G. Smith, E. Hannon, G. Ramaswami +9 more
2019Human Molecular Genetics79 citations Open access
Semantic Scholar
Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness
S. Heilmann-Heimbach, C. Herold, L. Hochfeld, A. M. Hillmer +32 more
2017Nature Communications79 citations Open access
Semantic Scholar
The Singapore National Precision Medicine Strategy
Eleanor Wong, N. Bertin, M. Hebrard, Roberto Tirado-Magallanes +86 more
2023Nature Genetics76 citations
Semantic Scholar
Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods
Drew R. Neavin, A. Senabouth, Himanshi Arora, J. Lee +8 more
2022bioRxiv73 citations Open access
Semantic Scholar
Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-β effectors
N. Baburajendran, P. Palasingam, K. Narasimhan, Wen-Jie Sun +3 more
2010Nucleic Acids Research71 citations Open access
Semantic Scholar
DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data
B. Ranjan, Wenjie Sun, Jinyu Park, Kunal Mishra +12 more
2021Nature Communications70 citations Open access
Semantic Scholar
Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype
W. Tan, C. Anene-Nzelu, Eleanor Wong, Chang Jie Mick Lee +26 more
2020Circulation Research67 citations Open access
Semantic Scholar
A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development
V. Sivakamasundari, P. Kraus, Wen-Jie Sun, Xiaoming Hu +3 more
2016Biology Open65 citations Open access
Semantic Scholar
MiR‐135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF‐β/BMP signaling
A. Bhinge, Jeremie Poschmann, Seema C. Namboori, Xian-Feng Tian +4 more
2014EMBO Journal64 citations Open access
Semantic Scholar
Single-nucleotide variant calling in single-cell sequencing data with Monopogen
Jin-Zhuang Dou, Yu-Kun Tan, K. Kock, Jun Wang +14 more
2023Nature Biotechnology61 citations Open access
Semantic Scholar
ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content.
R. Joseph, Jeremie Poschmann, R. Sukarieh, Peh Gek Too +9 more
2015Molecular Endocrinology58 citations Open access
Semantic Scholar
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
Qian-Fei Wang, Shyam Prabhakar, Sumita Chanan, Jan-Fang Cheng +2 more
2006Genome Biology55 citations Open access
Semantic Scholar
Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms
R. C. del Rosario, Jeremie Poschmann, S. Rouam, E. Png +3 more
2015Nature Methods54 citations
Semantic Scholar
Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress–Gene Response
D. Lee, W. Tan, C. Anene-Nzelu, Chang Jie Mick Lee +13 more
2019Circulation50 citations Open access
Semantic Scholar
The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis
S. Leow, Jeremie Poschmann, Peh Gek Too, Juan Yin +12 more
2016Development50 citations Open access
Semantic Scholar
Publisher Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
Hui-Peng Li, E. Courtois, Debarka Sengupta, Yuliana Tan +13 more
2022Nature Genetics46 citations Open access
Semantic Scholar
Fast, scalable and accurate differential expression analysis for single cells
Debarka Sengupta, N. Rayan, M. Lim, B. Lim +1 more
2016bioRxiv44 citations Open access
Semantic Scholar
A Single-cell Atlas Identifies Pretreatment Features of Primary Imatinib Resistance in Chronic Myeloid Leukemia.
V. Krishnan, Florian Schmidt, Zahid Nawaz, P. Venkatesh +18 more
2022Blood43 citations Open access
Semantic Scholar
Histone acetylome-wide association study of tuberculosis
R. C. del Rosario, Jeremie Poschmann, Pavanish Kumar, Catherine Y. Cheng +20 more
2019bioRxiv42 citations Open access
Semantic Scholar
A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data
Yongli Hu, T. Hase, Hui-Peng Li, Shyam Prabhakar +4 more
2016BMC Genomics42 citations Open access
Semantic Scholar
Genome Wide Analysis Reveals Zic3 Interaction with Distal Regulatory Elements of Stage Specific Developmental Genes in Zebrafish
C. Winata, I. Kondrychyn, Vibhor Kumar, K. Srinivasan +6 more
2013PLoS Genetics41 citations Open access
Semantic Scholar
Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters
Vibhor Kumar, N. Rayan, M. Muratani, Stefan Lim +8 more
2016Genome Research36 citations Open access
Semantic Scholar
Noncoding origins of anthropoid traits and a new null model of transposon functionalization
R. C. del Rosario, N. Rayan, Shyam Prabhakar
2014Genome Research36 citations Open access
Semantic Scholar
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers
A. Jankowski, E. Szczurek, R. Jauch, J. Tiuryn +1 more
2013Genome Research35 citations Open access
Semantic Scholar

Frequent co-authors

Invite them to SciRah by sharing their profile.

Jeremie Poschmann×9
Invite
Jeremie Poschmann — researcher profile on SciRah
N. Rayan×9
Invite
N. Rayan — researcher profile on SciRah
E. Rubin×8
Invite
E. Rubin — researcher profile on SciRah
Wen-Jie Sun×8
Vibhor Kumar×6
Invite
Vibhor Kumar — researcher profile on SciRah

Invite

J. Mill — researcher profile on SciRah

R. C. del Rosario×5

Invite

R. C. del Rosario — researcher profile on SciRah

L. Pennacchio×4

Invite

L. Pennacchio — researcher profile on SciRah

Malak I. Shoukry×4

Invite

Malak I. Shoukry — researcher profile on SciRah

Invite

Veena Afzal — researcher profile on SciRah

Debarka Sengupta×4

Invite

Debarka Sengupta — researcher profile on SciRah

Invite

Say-Li Kong — researcher profile on SciRah