Shyam Prabhakar Lab



Software

Selected Publications


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2022

Integrative multi-omics landscape of fluoxetine action across 27 brain regions reveals global increase in energy metabolism and region-specific chromatin remodelling.
Nirmala Arul Rayan, Vibhor Kumar, Jonathan Aow, Naghmeh Rastegar, Michelle Gek Liang Lim, Nicholas O’Toole, Edita Aliwarga, Danusa Mar Arcego, Hui Ting Grace Yeo, Jen Yi Wong, May Yin Lee, Florian Schmidt, Hajira Shreen Haja, Wai Leong Tam, Tie-Yuan Zhang, Josie Diorio, Christoph Anacker, Rene Hen, Carine Parent, Michael J Meaney & Shyam Prabhakar.
Molecular Psychiatry 2022.09.02 Mol Psychiatry

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer.
Ignasius Joanito, Pratyaksha Wirapati, Nancy Zhao, Zahid Nawaz, Grace Yeo, Fiona Lee, Christine L. P. Eng, Dominique Camat Macalinao, Merve Kahraman, Harini Srinivasan, Vairavan Lakshmanan, Sara Verbandt, Petros Tsantoulis, Nicole Gunn, Prasanna Nori Venkatesh, Zhong Wee Poh, Rahul Nahar, Hsueh Ling Janice Oh, Jia Min Loo, Shumei Chia, Lih Feng Cheow, Elsie Cheruba, Michael Thomas Wong, Lindsay Kua, Clarinda Chua, Andy Nguyen, Justin Golovan, Anna Gan, Wan-Jun Lim, Yu Amanda Guo, Choon Kong Yap, Brenda Tay, Yourae Hong, Dawn Qingqing Chong, Aik-Yong Chok, Woong-Yang Park, Shuting Han, Mei Huan Chang, Isaac Seow-En, Cherylin Fu, Ronnie Mathew, Ee-Lin Toh, Lewis Z. Hong, Anders Jacobsen Skanderup, Ramanuj DasGupta, Chin-Ann Johnny Ong, Kiat Hon Lim, Emile K. W. Tan, Si-Lin Koo, Wei Qiang Leow, Sabine Tejpar, Shyam Prabhakar & Iain Beehuat Tan.
Nat Genet (2022). Nature Genetics

BANKSY: A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation.
Vipul Singhal, Nigel Chou, Joseph Lee, Jinyue Liu, Wan Kee Chock, Li Lin, Yun-Ching Chang, Erica Teo, Hwee Kuan Lee, Kok Hao Chen, Shyam Prabhakar.
bioRxiv 2022.04.14.488259. bioRxiv

Histone acetylome-wide associations in immune cells from individuals with active Mycobacterium tuberculosis infection.
Del Rosario RCH, Poschmann J, Lim C, Cheng CY, Kumar P, Riou C, Ong ST, Gerges S, Hajan HS, Kumar D, Marzuki M, Lu X, Lee A, Wijaya GC, Rayan NA, Zhuang Z, Du Bruyn E, Chee CBE, Lee B, Lum J, Zolezzi F, Poidinger M, Rotzschke O, Khor CC, Wilkinson RJ, Wang YT, Chandy GK, De Libero G, Singhal A, Prabhakar S.
Nat Microbiol. 2022 Feb;7(2):312-326. Pubmed

2021

DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data.
Ranjan B, Sun W, Park J, Mishra K, Schmidt F, Xie R, Alipour F, Singhal V, Joanito I, Honardoost MA, Yong JMY, Koh ET, Leong KP, Rayan NA, Lim MGL, Prabhakar S.
Nat Commun. 2021 Oct 6;12(1):5849. Pubmed

RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.
Schmidt F, Ranjan B, Lin QXX, Krishnan V, Joanito I, Honardoost MA, Nawaz Z, Venkatesh PN, Tan J, Rayan NA, Ong ST, Prabhakar S.
Nucleic Acids Res. 2021 Sep 7;49(15):8505-8519. Pubmed

2020

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer.
Lee HO, Hong Y, Etlioglu HE, Cho YB, Pomella V, Van den Bosch B, Vanhecke J, Verbandt S, Hong H, Min JW, Kim N, Eum HH, Qian J, Boeckx B, Lambrechts D, Tsantoulis P, De Hertogh G, Chung W, Lee T, An M, Shin HT, Joung JG, Jung MH, Ko G, Wirapati P, Kim SH, Kim HC, Yun SH, Tan IBH, Ranjan B, Lee WY, Kim TY, Choi JK, Kim YJ, Prabhakar S, Tejpar S, Park WY.
Nat Genet. 2020 Jun;52(6):594-603. Pubmed

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development.
Utz SG, See P, Mildenberger W, Thion MS, Silvin A, Lutz M, Ingelfinger F, Rayan NA, Lelios I, Buttgereit A, Asano K, Prabhakar S, Garel S, Becher B, Ginhoux F, Greter M.
Cell. 2020 Apr 30;181(3):557-573.e18. Pubmed

2019

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore.
Wu D, Dou J, Chai X, Bellis C, Wilm A, Shih CC, Soon WWJ, Bertin N, Lin CB, Khor CC, DeGiorgio M, Cheng S, Bao L, Karnani N, Hwang WYK, Davila S, Tan P, Shabbir A, Moh A, Tan EK, Foo JN, Goh LL, Leong KP, Foo RSY, Lam CSP, Richards AM, Cheng CY, Aung T, Wong TY, Ng HH; SG10K Consortium, Liu J, Wang C.
Cell. 2019 Oct 17;179(3):736-749.e15. Pubmed

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, Luu TDA, 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 16;139(16):1937-1956. Pubmed

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(2):272-281. Pubmed

2018

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 RC, Cojocaru V, Prabhakar S, Jauch R.
Nucleic Acids Res. 2018 Jun 20;46(11):5470-5486. Pubmed

2017

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):708-718. Pubmed

2016

Histone Acetylome-wide Association Study of Autism Spectrum Disorder.
Sun W, Poschmann J, Cruz-Herrera Del Rosario R, Parikshak NN, Hajan HS, Kumar V, Ramasamy R, Belgard TG, Elanggovan B, Wong CCY, Mill J, Geschwind DH, Prabhakar S.
Cell. 2016 Nov 17;167(5):1385-1397.e11. Pubmed

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(16):2419-26. Pubmed

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, Xin L, Lu T, Makhija H, Poschmann J, Lufkin T, Ng HH, Prabhakar S.
Genome Res. 2016 May;26(5):612-23. Pubmed

2015

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(10):1327-38. Pubmed

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(5):458-64. Pubmed

2014

Noncoding origins of anthropoid traits and a new null model of transposon functionalization.
del Rosario RC, Rayan NA, Prabhakar S.
Genome Res. 2014 Sep;24(9):1469-84. Pubmed

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. Pubmed

2013

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. Pubmed

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 Jul;31(7):615-22. Pubmed

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.
Sun W, Hu X, Lim MH, Ng CK, Choo SH, Castro DS, Drechsel D, Guillemot F, Kolatkar PR, Jauch R, Prabhakar S.
Nucleic Acids Res. 2013 Jun;41(11):5555-68. Pubmed