Go to our lab website : ReggenLab


Dr Vibhor Kumar                                     

Assistant Professor

Computational Biology

IIIT Delhi, Okhla, Phase III 

New Delhi-110020 

adjunct : Genome Institute of Singapore.

lab in India : ReggenLab

Current Research Topics

1. Developing computational methods using Generalized approach 

We view the complexity in biological data-sets as an opportunity to develop generalized methods which can be useful for other fields also. Hence we are interested in developing generalized methods for bioinformatics projects involving signal processing, NP-complete, classification and feature-selection problems which could have wide application in other fields also. For example epigenome analysis has now become a signal processing problem. Similarly genome assembly involves a lot of steps which could be NP-complete. Analysis of single cell expression involves feature selection and classification. Currently we are developing computational methods for, analysing single cell data-sets, network inference and new applications of Graph signal processing. 

2. Studying patterns in gene regulation and omic data for fundamental discoveries and translational applications

We study transcriptional and post-transcriptional regulation of genes during development and diseases. For such purpose we  try to use computational approach which are novel and robust. For this purpose, we process multiple kinds of data-set from different experimental protocols and technologies, such as next gen sequencing data from different assays (HiC, ChIP-seq, RNA-seq, ATAC-seq, Dnase-seq etc) , high throughput screening and microarray. More details are as such

  Utility of single cell genomics for clinical decisions and Translational research 

  We are trying to develop new analysis techniques for single expression and epigenome profiles and trying to extend application of single cell genomics beyond classical applications of finding heterogeneity and rare cells. We are analysing single cell genomic profiles with new perspectives so that it could help in development of novel diagnostic techniques and prediction of response to environment. One such application which can help doctors in finding matching cells for taking clinical decisions is the first single cell expression search engine (http://cellatlassearch.com/) made by us.

 Cancer epigenome

Drug response of cancer is often dependent on underlying mutations and epigenome. epigenomeWith our collaborators we have recently shown that drug response of cancer cells is primed by  and targeting epigentics modifiers can help in reducing plasticity of cancer cells (Ankur et al, Nature communications). Now we are making new extended observations with chromatin interaction profiles of cancer cells. We are trying to figure out how insights from chromatin interactions can help in cancer therapeutics.   

 Identifying molecular markers for research and diagnosis

We published first comprehensive study on H2BK20ac (1 out 35 histone acetylations) and showed it's uniqueness in detecting cell state specific promoter activity and enhancers (Kumar et al., Genome Research). We are exploring its applications in diagnostics. 

With a grant on cell free DNA analysis, we are trying to find new markers for early cancer detection and developing new methods for reducing error in prediction of diseases using cfDNA.  

(For all publications click here)

google scholar

Awards/Grants :

1) young investigator grant  by, BMRC, Agency for Science and Technology, Singapore, 2015

2) Genomic technology development, 2018, DBT, India

Selected publications :

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

(2) Vibhor Kumar, Masafumi Muratani, Nirmala Arul Rayan, Petra Kraus, Thomas Lufkin, Huck Hui Ng and Shyam Prabhakar, Uniform, optimal signal processing of mapped deep-sequencing data, Nature biotechnology, 2013.

(3) Vibhor Kumar, Nirmala Arul Rayan, Masafumi Muratani, Stefan Lim, Bavani Elanggovan, XIN Lixia, Tess Lu, Harshyaa Makhija, Jeremie Poschmann, Thomas Lufkin, Huck Hui Ng# & Shyam Prabhakar#, Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters. Genome Research, 2016.

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

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

(6) Divyanshu Srivastava, Arvind Iyer, Vibhor Kumar #, Debarka Sengupta#, CellAtlasSearch: a scalable search engine for single cells, Nucleic Acids  Researchhttps://doi.org/10.1093/nar/gky421, 2018  (# corresponding Authors)

(7) Kyle M. Loh*, Lay Teng Ang*, Jingyao Zhang*, Vibhor Kumar*, Jasmin Ang, Jun Qiang Auyeong, Kian , Leong Lee, Massimo Nichane, Lorenz Poellinger, Qingfeng Chen, Shyam Prabhakar, Irving L. Weissman & Bing Lim. Efficient Endoderm Induction from Human Pluripotent Stem Cells by Logically Directing Signals Controlling Lineage Bifurcations. Cell Stem cell ,14(2):237-52. 2014. (*equal contributing)

(8) Vibhor Kumar, Sarah Butcher, Kati Öörni, Peter Engelhardt, Jukka Heikkonen, et al. Three-Dimensional cryoEM Reconstruction of Native LDL Particles to 16Å Resolution at Physiological Body Temperature. PloS ONE 6(5): e18841. 2011.

 (9) Jia-Hui Ng*, Vibhor Kumar*, Masafumi Muratani*, Petra Kraus, Jia-Chi Yeo, Lai-Ping Yaw, Kun Xue, Thomas Lufkin, Shyam Prabhakars#, Huck-Hui Ng#, In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures. Dev Cell. 2013 Feb 11;24(3):324-33.. (* equal contributor)

(10) Vibhor Kumar, Jukka Heikkonen, Jorma Rissanen and Kimmo Kaski, Minimum description length denoising with histogram models, IEEE transaction on signal Processing, 54(8): 2922-2928, 2006.

(11) Pasi Kaukinen*, Vibhor Kumar*, Kirsi Tulimäki, Peter Engelhardt, Antti Vaheri, and Alexander Plyusnin, Oligomerization of Hantavirus N protein: C-terminal α-helices interact to form a shared hydrophobic space, Journal of Virology, 78(24): 13669-13677, 2004. (* equal contributor)

(12) Vibhor Kumar, Jukka Heikkonen, Peter Engelhardt and Kimmo Kaski, Robust filtering and particle picking in micrograph images towards 3D reconstruction of purified proteins with cryo-electron microscopy. Journal of Structural Biology, 145(1-2):41-51, 2004.

News and Blogs for previous publications

1. Formal mathematics underpins new approach that standardizes analysis of genome information (Phys.org)

2. Novel Study On Histones Provides Better Understanding Of Gene Regulation

3. Scientists succeed in manipulating stem cells into liver and pancreas precursor (Phys.org) cells

4. A*STAR develops novel method to map epigenome 

5. First structure of LDL at Human body temperature(http://www.healthcentral.com/cholesterol/c/434851/138202/temperature/)