Dr Vibhor Kumar                                     

Assistant Professor

Computational Biology

IIIT Delhi, Okhla, Phase III 

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

Current Research Topics

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. 

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  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. Some of our recent works has been,

First single cell search engine (www.cellatlassearch.com)

Study of epigenome and single cell expression of oral cancer stem cells.

First comprehensive study on H2BK20ac, one out 35 known histone acetylations.

 In past we have shown that :

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

Currently we are studying patterns in single cell epigenome and chromatin interaction pattern of cancer stem cells.

(For all publications click here)

google scholar

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 ,14(2):237-52. 2014. (*equal contributing)

(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, 2018  (# 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/)