Research Groups

Dinesh Gupta

Translational Bioinformatics

Group Leader

Research Interests and Description

Dinesh Gupta

International Centre for Genetic Engineering and Biotechnology
Aruna Asaf Ali Marg
110 067 New Delhi, India

E-mail: dineshicgeb.res.in

Education

All India Institute of Medical Sciences, New Delhi, India, Ph.D., 1998

Career History

Since 2004, Staff Research Scientist, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
2001-2005, Member, Scientific Working Group, Bioinformatics Initiative, TDR/WHO
2001-2005, Coordinator, WHO/TDR Regional training centre for Bioinformatics at ICGEB
2001-2005, World Health Organization Fellow, University of Pennsylvania, USA
2001, World Health Organization Fellow, Sanger Centre, UK
1998-2004, Staff Research Scientist, Malaria Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi
Since 2000, Founder and In-charge, Bioinformatics facility at the ICGEB, New Delhi, India
Since 1998, System Administrator, ICGEB, New Delhi
1998, DST fellow, All India Institute of Medical Sciences, New Delhi, India

Teaching Activity

Coordinator, WHO funded ICGEB Regional Bioinformatics Training Centre for Tropical Disease Researchers. The Centre has organized several International Bioinformatics Workshops.
Founder of Bioinformatics Course for PhD students at ICGEB New Delhi.
International Bioinformatics workshops including those organized by WHO, NAS (USA), and regional universities.

Scientific Activity

The scientific interests of his Group include the use of computational biology tools to solve research problems in the post genomic era. The Group has recently developed ProtRepeatsDB, a database of different types of protein repeats in genomes. The Group is also interested in using artificial intelligence based methods to solve bioinformatics problems such as prediction of cyclin sequences and virulence proteins. The Group has also performed large scale molecular modeling of Plasmodium falciparum proteins. Based on comparisons of the modeled proteins with host proteins, an ortholog of prokaryotic hslV, a parasite specific protease in Plasmodium falciparum (PfHslV) has been identified as a new drug target. Currently, the Group is designing inhibitors for the protein using in silico techniques. Other research interests of his laboratory include comparative genomics to identify regulatory elements like miRNAs and transcription factors in genomes.

Other Activities

Collaborative research and Computational Biology support to different research Groups at ICGEB. Setting up of high performance Linux based cluster for computational biology. In charge of maintenance of the IT infrastructure and computerization of ICGEB New Delhi operations.

Selected publications

Zeeshan M., Kaur I., Joy J., Saini E., Paul G., Kaushik A., Dabral S., Mohmmed A., Gupta D., Malhotra P. 2017. Proteomic Identification and Analysis of Arginine-Methylated Proteins of Plasmodium falciparum at Asexual Blood Stages. J Proteome Res. Jan 3. doi: 10.1021/acs.jproteome.5b01052

Kaushik, A., Shakir Ali, S., Gupta, D. 2017. Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways. Nat. Sci. Rep. 7, 40450; doi:10.1038/srep40450 (2017)

Kaur I., Zeeshan M., Saini E., et al. Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages. Sci Rep . 2016;6. doi:10.1038/srep35432. 


Kumar R., Gupta D. Identification of CYP1B1-specific candidate inhibitors using combination of in silico screening, integrated knowledge-based filtering, and molecular dynamics simulations. Chem Biol Drug Des . 2016. doi:10.1111/cbdd.12803.

Kaushik, A., Bhatia, Y., Ali, S., Gupta, D. 2015. Gene network rewiring to study melanoma stage progression and elements essential for driving melanoma. PLOS ONE. 10(11):e0142443. doi: 10.1371/journal.pone.0142443.

Kaushik, A., Saraf, S., Mukherjee, S.K., Gupta, D. 2015. miRMOD: A tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data. PeerJ. 3:e1332; DOI 10.7717/peerj.1332.

Saraf, A., Sanan-Mishra, N., Gursanscky, N.R., Carroll, B.J., Gupta, D., Mukherjee, S.K. 2015. 3' and 5' microRNA-end post-biogenesis modifications in plant transcriptomes: evidences from small RNA next generation sequencing data analysis. BBRC 467:892-9.

Jagga Z. and Gupta D. 2015. Machine learning for biomarker identification in cancer research- developments towards its clinical application. Future Medicine. 12:371-387.

Tajedin L., Anwar M., Gupta D, and Tuteja R. 2015. Comparative insight into nucleotide excision repair components of Plasmodium falciparum. DNA repair 28:60-72


Subramaniam. S., Mehrotra, M., Gupta, D. 2012. Development of target focused library against drug target of P. falciparum using SVM and molecular docking. J Cheminformatics. (Suppl 1), P48

Subramaniam, S., Mehrotra, M., Gupta, D. 2011. Support Vector Machine Based Prediction of P. falciparum Proteasome Inhibitors and Development of Focused Library by Molecular Docking. Combinatorial Chemistry & High Throughput Screening 14, 898-907

Subramaniam, S., Mehrotra, M., Gupta, D. 2011. Support Vector Machine Based Classification Model for screening Plasmodium falciparum proliferation Inhibitors and non-Inhibitors. Biomed Eng Comp Biol 3, 13–24 doi: 10.4137/BECB.S7503

Rathore S, Jain S, Sinha D, Gupta M, Asad M, Srivastava A, Narayanan, Ramasamy G, Chauhan VS, Gupta D, Mohmmed A. 2011. Disruption of a mitochondrial protease machinery in Plasmodium falciparum is an intrinsic signal for parasite cell death. Cell Death Dis. 2:e231. doi: 10.1038/cddis.2011.118

Gupta, D., Tuteja, N., 2011. Chaperones and foldases in endoplasmic reticulum stress signaling in plants. Plant Signal Behav 6, 2320

Ramana, J., Gupta D. 2010. Machine Learning Methods for Prediction of CDK-Inhibitors. PLoS ONE 5, e13357.doi:10.1371/journal.pone.0013357

Ramana, J., Gupta, D. 2010. FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like Proteins. PLoS One 5 [doi: 10.1371/journal.pone.0009695] PubMed

Ramana, J., Gupta, D. 2009. LipocalinPred: a SVM-based method for prediction of lipocalins. BMC Bioinformatics 10, 445

Ramana, J., Gupta, D. 2009. ProtVirDB: A database of protozoan virulent proteins. Bioinformatics 25, 1568-1569

Subramaniam, S., Mohmmed, A., Gupta, D. 2009. Molecular modeling studies of the interaction between plasmodium falciparum HslU and HslV subunits. J. Biomol. Struct. Dyn. 26, 473-479

Garg, A., Gupta, D. 2008. VirulentPred: A SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics 9, 62

Kalita, M.K., Nandal, U.K., Pattnaik, A., Anandhan, S., Gowthaman R., Kumar, M., Raghava, G.P.S., Gupta, D. 2008. CyclinPred: a SVM-based method for predicting cyclin protein sequences. PLOS One 3 [doi:10.1371/journal.pone.0002605] PubMed

Bahl, A., Brunk, B., Crabtree, J., Fraunholz, M., Gajria, B., Grant, G.R., Ginsburg, H., Gupta, D., Kissinger, J.C., Labo, P., Li, L., Mailman, M.D., Milgram, A.J., Pearson, D.S., Roos, D.S., Schug, J., Stoeckert, Cj. Jr., Whetzel, P. 2003. PlasmoDB : The Plasmodium genome resource. A database integrating experimental and computational data. Nucl. Acids Res. 31, 212-215

Kissinger, J.C., Brunk, B., Crabtree, J., Fraunholz, M., Gajria, B., Milgram, A.J., Pearson, D.S., Schug, J., Bahl, A., Diskin, S.J., Ginsburg, H., Grant, G.R., Gupta, D., Labo, P., Li, L., Mailman, M.D., McWeeney, S.K., Whetzel, P., Stoeckert, Cj. Jr., Roos, D.S. 2002. The Plasmodium genome database. Designing and mining a eukaryotic genomic resource. Nature 3, 490-492

Bioinformatics Web servers

http://bioinfo.icgeb.res.in/faap/ Prediction method for fungal adhesins
http://bioinfo.icgeb.res.in/protvirdb/ a database of protozoan virulent proteins
http://bioinfo.icgeb.res.in/lipocalinpred/ Prediction method for Lipocalins
http://bioinfo.icgeb.res.in/codes/model.html
Homology modelling of P. falciparum proteins.
http://bioinfo.icgeb.res.in/repeats ProtRepeatsDB database of amino acid repeats in genomes
http://bioinfo.icgeb.res.in/virulent SVM based prediction method for predicting virulent proteins.
http://bioinfo.icgeb.res.in/cyclinpred SVM based prediction method for predicting cyclin sequences.

ICGEB New Delhi

ICGEB Campus
Aruna Asaf Ali Marg
110 067 New Delhi
INDIA
Tel: +91-11-26741358/1007
Fax: +91-11-26742316
icgebicgeb.res.in

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