S
Shyam Prabhakar
Researcher at Genome Institute of Singapore
Publications - 127
Citations - 8549
Shyam Prabhakar is an academic researcher from Genome Institute of Singapore. The author has contributed to research in topics: Gene & Enhancer. The author has an hindex of 36, co-authored 112 publications receiving 6957 citations. Previous affiliations of Shyam Prabhakar include National Institute for Medical Research & Stanford University.
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Journal ArticleDOI
In vivo enhancer analysis of human conserved non-coding sequences
Len A. Pennacchio,Len A. Pennacchio,Nadav Ahituv,Alan M. Moses,Shyam Prabhakar,Marcelo A. Nobrega,Marcelo A. Nobrega,Malak Shoukry,Simon Minovitsky,Inna Dubchak,Inna Dubchak,Amy Holt,Keith D. Lewis,Ingrid Plajzer-Frick,Jennifer A. Akiyama,Sarah De Val,Veena Afzal,Brian L. Black,Olivier Couronne,Olivier Couronne,Michael B. Eisen,Michael B. Eisen,Axel Visel,Edward M. Rubin,Edward M. Rubin +24 more
TL;DR: This study characterized the in vivo enhancer activity of a large group of non-coding elements in the human genome that are conserved in human–pufferfish, Takifugu (Fugu) rubripes, or ultraconserved in human-mouse–rat.
Journal ArticleDOI
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
Huipeng Li,Elise T. Courtois,Debarka Sengupta,Debarka Sengupta,Yuliana Tan,Kok Hao Chen,Jolene Jie Lin Goh,Say Li Kong,Clarinda Chua,Lim Kiat Hon,Wah Siew Tan,Mark T. C. Wong,Paul Jongjoon Choi,Lawrence J K Wee,Axel M. Hillmer,Iain Beehuat Tan,Iain Beehuat Tan,Paul Robson,Shyam Prabhakar +18 more
TL;DR: The results demonstrate that unbiased single-cell RNA–seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor.
Journal ArticleDOI
Accelerated Evolution of Conserved Noncoding Sequences in Humans
Shyam Prabhakar,James P. Noonan,James P. Noonan,Svante Pääbo,Edward M. Rubin,Edward M. Rubin +5 more
TL;DR: The results indicate that widespread cis-regulatory changes in human evolution may have contributed to uniquely human features of brain development and function.
Journal ArticleDOI
The PsychENCODE project
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,Jonathan Mill,Angus C. Nairn,Alexej Abyzov,Sirisha Pochareddy,Shyam Prabhakar,Sherman M. Weissman,Patrick F. Sullivan,Matthew W. State,Zhiping Weng,Mette A. Peters,Kevin P. White,Mark 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,Fabio C. P. Navarro,Nicole North,Larsson Omberg,David M. Panchision,Neelroop N. Parikshak,Jeremie Poschmann,Amanda J. Price,Michael J. 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,Chloe C. Y. Wong,Gregory A. Wray,Emily Wu,Xuming Xu,Lijing Yao,Geetha Senthil,Thomas Lehner,Pamela Sklar,Nenad Sestan +85 more
TL;DR: The PsychENCODE project aims to produce a public resource of multidimensional genomic data using tissue- and cell type–specific samples from approximately 1,000 phenotypically well-characterized, high-quality healthy and disease-affected human post-mortem brains, as well as functionally characterize disease-associated regulatory elements and variants in model systems.
Journal ArticleDOI
Human-specific gain of function in a developmental enhancer.
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,Len A. Pennacchio,Edward M. Rubin,Edward M. Rubin,James P. Noonan +14 more
TL;DR: In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque.