Dr Vibhor Kumar                                     

Assistant Professor

Computational Biology

IIIT Delhi, Okhla, Phase III 

New Delhi-110020 
India                                                               cellatlassearch , DFilter/EFilter , MDL-histo

Current Research Topics

Generalized approach for/from computational biology problems

I view the complexity in biological data-sets as an opportunity to develop generalized methods which can be useful for other fields. Hence I am interested in developing generalised 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. 

Studying patterns in gene regulation and omic data

We study transcriptional and post-transcriptional regulation of genes during development and diseases. For such purpose we usually take help of next gen sequencing data from different assays (ChIP-seq, RNA-seq, ATAC-seq, Dnase-seq etc). Recently we have been studying epigenome profiles from invivo and invitro model of diseases such as cancer. Especially we are trying to study cancer stem cells using its epigenome profile.

In past we made a few insights which can be listed as following :

.Larger fraction of developmental enhancers are primed in stem cells. Discovery of new state of primed enhancers before being active.

. Gene specific biases which are correlated across many cell-types.

Similarly we have found several patterns in RNA-stability and cell-state specific localisation of a few markers. We are trying to integrate such novel findings such that they could be used for diagnostics and understanding of cell behaviour. 

(For all publications click here)

Selected publications :

(1) 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.

(2) 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.

(3) 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)

(4) 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. 2014 Feb 6;14(2):237-52. (*equally contributing) (#corresponding authors)

(5) 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.

 (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,  (# corresponding Authors)

(7) 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.

(8) 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)

(9) 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/)