Publications

Patterns of transcription factor binding and epigenome at promoters allow interpretable predictability of multiple functions of non-coding and coding genes
Omkar Chandra, Madhu Sharma, Neetesh Pandey, Indra Prakash Jha, Shreya Mishra, Say Li Kong, Vibhor Kumar
Computational and Structural Biotechnology journal, 2023, https://doi.org/10.1016/j.csbj.2023.07.014

Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis
Shreya Mishra, Neetesh Pandey, Smriti Chawla, Madhu Sharma, Omkar Chandra, Indra Prakash Jha, Debarka SenGupta, Kedar Nath Natrajan,Vibhor Kumar
Genome Research, 2023, https://doi.org/10.1101/gr.277015.122

Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs
Madhu Sharma, Indra Prakash Jha, Smriti Chawla, Neetesh Pandey, Omkar Chandra, Shreya Mishra,Vibhor Kumar
Briefings in Bioinformatics, 2022, https://doi.org/10.1093/bib/bbac241

Integrative multi-omics landscape of fluoxetine action across 27 brain regions reveals global increase in energy metabolism and region-specific chromatin remodelling.
Prabhakar S. Rayan NA, Kumar V, Aow J, Rastegar N, Lim MGL, O'Toole N, Aliwarga E, Arcego DM, Yeo HTG, Wong JY, Lee MY, Schmidt F, Haja HS, Tam WL, Zhang TY, Diorio J, Anacker C, Hen R, Parent C, Meaney MJ
Mol Psychiatry,2022, https://doi.org/10.1038/s41380-022-01725-1

Computational challenges in detection of cancer using cell-free DNA methylation
Madhu Sharma, Rohit Kumar Verma, Sunil Kumar Vibhor Kumar
Computational and Structural Biotechnology Journal,Elsevier,2021, https://doi.org/10.1016/j.csbj.2021.12.001

Improving gene network inference with graph wavelets and making insights about ageing-associated regulatory changes in lungs
Shreya Mishra, Divyanshu Srivastava,Vibhor Kumar
Briefings in bioinformatics, 2021, ​Improving gene network inference with graph wavelets and making insights about ageing-associated regulatory changes in lungs
Shreya Mishra, Divyanshu Srivastava,Vibhor Kumar
Briefings in bioinformatics, 2021, https://doi.org/10.1093/bib/bbaa360

Graph Signal Processing on protein residue networks helps in studying its biophysical properties
D Srivastava, G Bagler,Vibhor Kumar
Elsevier, Physica A ,2023,https://doi.org/10.1016/j.physa.2023.128603

UniPath: a uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles
Smriti Chawla, Sudhagar Samydurai, Say Li Kong, Zhenxun Wang, Wai Leong TAM, Debarka Sengupta, Vibhor Kumar
Nucleic Acids Research, 2020 gkaa1138, https://doi.org/10.1093/nar/gkaa1138

Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain
Neetesh Pandey, Omkar Chandra, Shreya Mishra Vibhor Kumar
Front. Genet., 08 October 2021, https://doi.org/10.3389/fgene.2021.738194

A search-engine for single-cell epigenome profiles for multi-purpose applications
Shreya Mishra, Smriti Chawla, Neetesh Pandey, Debarka SenGupta, Vibhor Kumar
bioarxiv, https://doi.org/10.1101/2021.03.24.436738

Learning the Mental Health Impact of COVID-19 in the United States With Explainable Artificial Intelligence: Observational Study
Indra Prakash Jha, Raghav Awasthi, Ajit Kumar, Vibhor Kumar, Tavpritesh Sethi
JMIR Ment Health. 2021 Apr 20;8(4):e25097. , https://doi: 10.2196/25097

FITs: forest of imputation trees for recovering true signals in single-cell open chromatin profiles
Rachesh Sharma, Neetesh Pandey, Aanchal Mongia, Shreya Mishra, Angshul Majumdar, Vibhor Kumar
NAR Genomics and Bioinformatics, 2(4) 2020, https://doi.org/10.1093/nargab/lqaa091

Local-Topology-Based Scaling for Distance Preserving Dimension Reduction Method to Improve Classification of Biomedical Data-Sets
Karaj Khosla, Indra Prakash Jha, Ajit Kumar, Vibhor Kumar
Algorithms 2020, 13(8), 192. 2020, https://doi.org/10.3390/a13080192

Improving gene-network inference with graph-wavelets and making insights about ageing associated regulatory changes in lungs
Shreya Mishra, Divyanshu Srivastava, Vibhor Kumar
Breifings in Bioinformatics.2020 (accepted) ,  https://doi.org/10.1093/bib/bbaa360

Ascorbate and Iron Are Required for the Specification and Long-Term Self-Renewal of Human Skeletal Mesenchymal Stromal Cells
Tong Ming Liu, Ege Deniz Yildirim, Pin Li, Hai Tong Fang, Vinitha Denslin, Vibhor Kumar, Yuin Han Loh, Eng Hin Lee, Simon M.Cool, Bin Tean Teh, James H.Hui, Bing Lim, Ng Shyh-Chang
Stem cell Reports, 14(2) 210-225 (2020), https://doi.org/10.1016/j.stemcr.2020.01.002

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations
Kyle M. Loh*, Lay Teng Ang*, Jingyao Zhang*, Vibhor Kumar*, Jasmin Ang, Jun Qiang Auyeong, Kian Leong Lee, Siew Hua Choo, Christina YY Lim, Massimo Nichane1,Junru Tan, Monireh Soroush Noghabi, Lisa Azzola, Elizabeth S. Ng, Jens DurruthyDurruthy, Vittorio Sebastiano, Lorenz Poellinger, Andrew G. Elefanty, Edouard G. Stanley, Qingfeng Chen, Shyam Prabhakar, Irving L. Weissman, and Bing Lim
Cell Stem Cell. doi: 10.1016/j.stem.2013.12.007, (*)equally contributing, https://doi.org/10.1016/j.stem.2013.12.007

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.
Dev Cell. doi: 10.1016/j.devcel.2012.12.011 (*) co-first author, https://doi.org/10.1016/j.devcel.2012.12.011

Uniform, optimal signal processing of mapped deep-sequencing data
Vibhor Kumar , Masafumi Muratani, Nirmala Arul Rayan, Petra Kraus, Thomas Lufkin, Huck Hui Ng & Shyam Prabhakar
Nature biotechnology. doi: https://doi.org/10.1038/nbt.2596

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. doi: 10.1016/j.cell.2016.10.031, https://doi.org/10.1016/j.cell.2016.10.031

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 & development. ​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 & development. https://doi.org/10.1101%2Fgad.195545.112

Oligomerization of hantavirus N protein: C-terminal alpha-helices interact to form a shared hydrophobic space
Pasi Kaukinen*,Vibhor Kumar*, Kirsi Tulimaki, Peter Engelhardt, Antti Vaheri, Alexander Plyusnin
Journal of virology. doi: 10.1128/JVI.78.24.13669-13677.2004 (*) co-first, https://doi.org/10.1128/jvi.78.24.13669-13677.2004

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. https://doi.org/10.1371/journal.pgen.1003852

Robust filtering and particle picking in micrograph images towards 3D reconstruction of purified proteins with cryo-electron microscopy
Vibhor Kumar , Jukka Heikkonen, Peter Engelhardt, Kimmo Kaski
Journal of Structural Biology. doi: https://doi.org/10.1016/j.jsb.2003.09.036

Minimum Description Length Denoising With Histogram Models
V. Kumar ; J. Heikkonen ; J. Rissanen ; K. Kaski
IEEE transactions on signal processing. https://doi.org/10.1109/TSP.2006.877635

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters
Vibhor Kumar , Nirmala Arul Rayan, Masafumi Muratani, Stefan Lim, Bavani Elanggovan, Lixia Xin, Tess Lu, Harshyaa Makhija, Jeremie Poschmann, Thomas Lufkin, Huck Hui Ng, Shyam Prabhakar
Genome research. https://doi.org/10.1101/gr.201038.115

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
Sumantra Chatterjee, V Sivakamasundari, Sook Peng Yap, Petra Kraus, Vibhor Kumar, Xing Xing, Siew Lan Lim, Joel Sng, Shyam Prabhakar and Thomas Lufkin
BMC Genomics. doi: https://doi.org/10.1186/1471-2164-15-1072

CellAtlasSearch: a scalable search engine for single cells
Divyanshu Srivastava, Arvind Iyer, Vibhor Kumar*, Debarka Sengupta*
Nucleic Acid Research. doi: https://doi.org/10.1093/nar/gky421 (*)co-corresponding

Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy
Ankur Sharma, Elaine Yiqun Cao, Vibhor Kumar, Xiaoqian Zhang, Hui Sun Leong, Angeline Mei Lin Wong, Neeraja Ramakrishnan, Muhammad Hakimullah, Hui Min Vivian Teo, Fui Teen Chong, Shumei Chia, Matan Thangavelu Thangavelu, Xue Lin Kwang, Ruta Gupta, Jonathan R. Clark, Giridharan Periyasamy, N. Gopalakrishna Iyer & Ramanuj DasGupta
Nature Communications. doi: https://doi.org/10.1038/s41467-018-07261-3

A Role for RE-1-Silencing Transcription Factor in Embryonic Stem Cells Cardiac Lineage Specification
Irene Aksoy, Guillaume Marcy, Jiaxuan Chen, Ushashree Divakar, Vibhor Kumar, Daniel John-Sanchez, Mehran Rahmani, Noel J. Buckley, Lawrence W. Stanton.
Stem Cells. http://dx.doi.org/ 10.1002/stem.2304

Denoising with flexible histogram models on minimum Description length principle
Vibhor Kumar , Jukka heikkonen
13th International Conference on Systems, Signals and Image Processing, IWSSIP. doi: arXiv:1601.04388

Single-cell RNA-seq unveils divergent modes of chemoresistance in squamous cell carcinoma
Ankur Sharma, Vibhor Kumar, Elaine Yiqun Cao, Hui Sun Leong, Muhammad Hakimullah, Neeraja Ramakrishnan, Xiaoqian Zhang, Fui Teen Chong, Shumei Chia, Matan Thangavelu Thangavelu, Angeline Mei Lin Wong, Xue Lin Kwang, Daniel Shao-Weng Tan, Giridharan Periyasamy, N Gopalakrishna Iyer, Ramanuj DasGupta
Mechanisms of Development. https://doi.org/10.1016/j.mod.2017.04.306

Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos
Sumantra Chatterjee, V Sivakamasundari, Petra Kraus, Sook Peng Yap, Vibhor Kumar, Shyam Prabhakar, Thomas Lufkin
Elsevier. doi: https://doi.org/10.1016/j.gdata.2015.05.031

Nucleocapsid Protein of Hantaviruses (Bunyaviridae): Structure and Functions
Alexander Plyusnin, Vibhor Kumar, Olli Vapalahti, Peter Engelhardt
Structure-Based Study Of Viral Replication. doi: https://doi.org/10.1142/9789812790859_0021

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro
Sumantra Chatterjee, Petra Kraus, V Sivakamasundari, Sook Peng Yap, Vibhor Kumar, Shyam Prabhakar, Thomas Lufkin
Genomics Data. doi: https://doi.org/10.1016/j.gdata.2016.09.002