Research Groups

Mammalian Biology: Structural and Computational Biology

Staff Research Scientist

Research Interests and Description
Group Members
Group Leader

Dinesh Gupta

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

E-mail: dinesh@icgeb.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

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.