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

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

3. 3' and 5' microRNA-end post-biogenesis modifications in plant transcriptomes: evidences from small RNA next generation sequencing data analysis. Saraf A, Sanan-Mishra N, Gursanscky NR, Carroll BJ, Gupta D, Mukherjee SK. 2015 BBRC accepted for publication.

4. Machine learning for biomarker identification in cancer research- developments towards its clinical application. 2015. Jagga Z. and Gupta D. Future Medicine. 2015. 12(4), 371-387.

5. Comparative insight into nucleotide excision repair components of Plasmodium falciparum. Tajedin L., Anwar M., Gupta D, and Tuteja R. 2015. DNA repair 28: 60-72. doi: 10.1016/j.dnarep.2015.02.009

6. Genome wide in silico analysis of Plasmodium falciparum phosphatome. 2014. Pandey R, Mohmmed A, Pierrot C, Khalife, J, Malhotra P and Gupta D. BMC Genomics. 15:1024

7. Gene disruption reveals a dispensable role for Plasmepsin VII in the Plasmodium berghei life cycle. Mastan B.S., Kumari A., Gupta D., Mishra S., Kumar K.A. Mol Biochem Parasitol. 2014 Jun 2. pii: S0166-6851(14)00070-X. doi: 10.1016/j.molbiopara.2014.05.004.

8. Supervised learning classification models for prediction of plant virus encoded RNA silencing suppressors. Jagga Z, Gupta D. PLoS One. 2014 May 14;9(5):e97446. doi: 10.1371/journal.pone.0097446.

9. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Andrew P. Jackson, Thomas D. Otto, Alistair Darby, Abhinay Ramaprasad, Dong Xia, Ignacio Eduardo Echaide, Marisa Farber, Sunayna Gahlot, John Gamble, Dinesh Gupta, Yask Gupta, Louise Jackson, Laurence Malandrin, Tareq B. Malas, Ehab Moussa, Mridul Nair, Adam J. Reid, Mandy Sanders, Jyotsna Sharma, Alan Tracey, Mike A. Quail, William Weir, Jonathan Wastling, Neil Hall, Peter Willadsen, Klaus Lingelbach, Brian Shiels, Andy Tait, Matt Berriman, David R. Allred, Arnab Pain. Nuc. Acid Res. 2014 42(11):7113-31. doi: 10.1093/nar/gku322.

10. Classification models for clear cell renal carcinoma stage progression, based on tumor RNAseq expression trained supervised machine learning algorithms. Jagga Z, Gupta D. Proceedings from the Great Lakes Bioinformatics Conference 2014. BMC Proceedings. October 2014, 8:S2.

11. Bacillus thuringiensis Toxin, Cry1C interacts with 128HLHFHLP134 region of Aminopeptidase N of Agricultural Pest, Spodoptera litura. Kaur R, Sharma A., Gupta D., Kalita M., Bhatnagar R. K. Process Biochemistry. 2014 49(4): 688-696 http://dx.doi.org/10.1016/j.procbio.2014.01.008

12. GFF-Ex: a genome feature extraction package. Rastogi A, Gupta D. 2014. BMC Research Notes. 7:315

13. In silico characterization and molecular dynamics simulation of Pfcyc-1, a cyclin homolog of Plasmodium falciparum. Kaushik A, Subramaniam S, Gupta D. J Biomol Struct Dyn. 2013. 32(10):1624-33. DOI:10.1080/07391102.2013.831378

14. Protein folding grand challenge: hydrophobic vs. hydrophilic forces. Kaushik A, Gupta D. J Biomol Struct Dyn. 2013. 31(9):1008-10 [Epub ahead of print] PubMed PMID: 23390926.

15. Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons. Joshi PK, Gupta D, Nandal UK, Khan Y, Mukherjee SK, Sanan-Mishra N. Genomics. 2012 Jun;99(6):370-5. doi: 10.1016/j.ygeno.2012.04.002. Epub 2012 Apr 21. PubMed PMID: 22546559.

16. Identifying bacterial virulent proteins by fusing a set of classifiers based on variants of Chou’s pseudo amino acid composition and on evolutionary information. Nanni, L., Lumini, A., Gupta, D., Garg, A., IEEE/ACM Trans. Comput. Biology Bioinform. 9(2):467-475, 2012

17. Molecular cloning and characterization of chikungunya virus genes from Indian isolate of 2006 outbreak. Gupta S., Dudha N., Appaiahgari M.B., Bharati K., Gupta D., Gupta Y., Kumar K., Gabrani R., Sharma S.K., Gupta A., Chaudhary V.K., Vrati S. J. Pharm Res. 2012,5(7), 3860-3863.

18. Development of target focused library against drug target of P. falciparum using SVM and molecular docking. Subramaniam. S., Mehrotra, M., Gupta, D. Journal of Cheminformatics. 2012 (Suppl 1)48.

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

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

21. Chaperones and foldases in endoplasmic reticulum stress signaling in plants. Gupta, D; Tuteja, N Plant Signal Behav. 6(2):232-6. Plant Signal Behav 6, 2320, 2011

22. Disruption of a mitochondrial protease machinery in Plasmodium falciparum is an intrinsic signal for parasite cell death. Rathore S, Jain S, Sinha D, Gupta M, Asad M, Srivastava A, Narayanan, Ramasamy G, Chauhan VS, Gupta D, Mohmmed A. Cell Death Dis. Nov 24;2:e231. doi: 10.1038/cddis.2011.118. 2011

23. Thermo and pH stable ATP-independent chaperone activity of heat-inducible Hsp70 from Pennisetum glaucum. Rao JLUM; Reddy PS; Mishra RN; Gupta D; Sahal D; Tuteja N; Sopory SK; Reddy MK. Plant Signal Behav 5, 110 2010.

24. Machine Learning methods for prediction of CDK-inhibitors., Ramana, J., Gupta, D., PLOS One: 3;5(10):e13357., 2010

25. A cyanobacterial serine protease of Plasmodium falciparum is targeted to the apicoplast and plays an important role in its growth and development. Rathore,S. Sinha, D. Asad, M., Böttcher, T., Afreen, F., Chauhan, V. S., Gupta, D., Sieber, S. & Mohmmed A., Molecular Microbiology, 77(4): 873-890. , 2010

26. FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like Proteins. , Ramana, J., Gupta, D., PLoS One, 5(3): e9695., 2010

27. ProtVirDB: A database of protozoan virulent proteins. , Ramana, J., Gupta, D., Bioinformatics, 25(12), 1568-1569., 2009

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

29. A systematic classification of plasmodium falciparum P-loop NTPases: Structural and functional correlation., Gangwar, D., Kalita, M. K., Gupta, D., Chauhan, V. S., Mohmmed, A, Malaria Journal, 8(1):69, 2009

30. Molecular modeling studies of the interaction between Plasmodium falciparum HslU and HslV subunits., Subramaniam, S., Mohmmed, A, Gupta, D., J. Biomol. Struc. Dyn., 26(4):473, 2008

31. Virtual high throughput screening (vHTS) – A perspective., Subramaniam, S., Mehrotra, M, Gupta, D., Bioinformation, 3(1): 14, 2008

32. CyclinPred: a SVM-based method for predicting cyclin protein sequences. , Kalita, M.K., Nandal, U.K., Pattnaik, A., Sivalingam, A., Ramasamy, G., Kumar, M., Raghava, G.P., Gupta, D. , PLoS ONE, 3(7):e2605, 2008

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

34. Characterization and localization of Plasmodium falciparum homolog of prokaryotic ClpQ/HslV protease. , Ramasamy, G., Gupta, D., Mohmmed, A., Chauhan, V.S., Mol. Biochem. Parasitol. 152, 139-148, 2007

35. ProtRepeatsDB database of amino acid repeats in genome., Kalita, M.K., Ramasamy, G., Duraisamy, S., Chauhan, V.S., Gupta, D. , BMC Bioinformatics 7, 336

36. A database for Plasmodium falciparum protein models., Gowthaman, R., Duraisamy, S., Kalita, M.K., Gupta, D. , Bioinformation 1, 50, 2005

37. A Distribution of proline-rich (PxxP) motifs in distinct proteomes: functional and therapeutic implications for malaria and tuberculosis, Ravi Chandra, B., Gowthaman, R., Raj Akhouri, R., Gupta, D., Sharma, A., Protein Eng. Des. Sel. 17(2): 175-182., 2004

38. Bioinformatic analysis of the SARS virus X1 protein shows it to be a calcium-binding protein., Singh, A. N., Gupta, D., Jameel S., Current Sci. 86 (6):842-844., 2004

39. PlasmoDB: The Plasmodium genome resource. A database integrating experimental and computational data. , 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. , Nucl. Acids Res. 31, 212-215., 2003

40. The Plasmodium genome database. Designing and mining a eukaryotic genomic resource. 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. , Nature 3, 490-492., 2002

41. PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). , Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, Labo P, Li L, McWeeney SK, Milgram AJ, Roos DS, Schug J, Stoeckert CJ Jr. , Nucl. Acids Res. 30, 87-90., 2002

42. The 3’ end of hepatitis E virus (HEV) genome binds specifically to the viral RNA-dependent RNA polymerase (RdRp)., Agarwal S, Gupta D, Panda SK , Virology 282(1):87-101., 2001

43. The ORF3 protein of hepatitis E virus binds to Src homology 3 (SH3) domains and activates MAP kinase., Korkaya H, Jameel S, Gupta D, Tyagi S, Kumar R, Zafrullah M, Mazumdar M, Lal SK, Xiaofang L, Sehgal D, Das SR, Sahal D. , J. Biol. Chem. 276(45):42389-400., 2001

44. Molecular characterization of the Rep protein of the blackgram isolate of Indian mungbean yellow mosaic virus., Pant V, Gupta D, Choudhury NR, Malathi VG, Varma A, Mukherjee SK. J. Gen. Virol. 82(10):2559-67, 2001

45. Cloning, sequencing, and expression of the Hepatitis E virus (HEV) nonstructural open reading frame 1 (ORF1)., Ansari IH, Nanda SK, Durgapal H, Agrawal S, Mohanty SK, Gupta D, Jameel S, Panda SK , J. Med. Virol. 60:275-283., 2000

46. Theoretical study of conformational flexibility of tuftsin in vacuum and in aqueous environment. , Kothekar V, Ashish, Gupta D, Kishore R , Indian J. Biochem. Biophys. 36 14-28, 1999

47. Conformational flexibility of voltage gated dihydropyridine sensitive calcium channel Molecular Dynamics., Kothekar V, Gupta D , Indian J. Biochem. Biophys. 35(5):273-283 , 1998

48. Molecular Dynamics Simulation of the interaction of nifedipine and its meta and para NO2 analogs with hydrated dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer., Gupta D, Kothekar V, J. Mol. Struc. (Theochem) 431 17-31, 1998

49. Conformation of nifedipine in hydrated 1,2-di-myristoyl-sn-glycero-3-phosphorylcholine bilayer molecular dynamics Simulation., Gupta D, Kothekar V , J. Biosci. 22 177-192, 1997

50. 500 Picosecond Molecular Dynamics simulation of amphiphilic polypeptide Ac(LKKL)4NHEt with 1,2 di-mysristoyl -sn-glycero-3-phosphorylcholine (DMPC) molecules. , Gupta D, Kothekar V , Ind. J. Biochem. Biophys. 34 501-511., 1997

51. Molecular dynamics simulation of alamethacin fragments in aqueous and membranous environment., Kothekar V, Mahajan K, Raha K, Gupta D, J. Biomol. Struct. Dyn. 14 303-316., 1996

52. 200 Picosecond molecular dynamics simulation of interaction of nifedipine with 1-2 dimyristoyl phosphatidylcholine membrane. , Kothekar V, Gupta D, Indian J. Biochem. and Biophys 31 24-30, 1994

53. Molecular Mechanics Simulation of Ligand Induced Structural Changes in Biological Membrane., Kothekar V, Gupta D , Int. J. Toxicol. Occup. Environ. Hlth. 1(3) 1-82) , 1992.

Patents:
Use of small peptides corresponding to protein-protein interface residues of Plasmodium falciparum ClpQ protease (PfClpQ) and ClpY ATPase (PfClpY) or small drug like molecules designed based upon these peptides that interfere with interaction of PfClpQ and PfClpY, as anti-malarial drugs. Inventors: Sumit Rathore, Dipto Sinha, Virander S. Chauhan, D. Gupta and A. Mohmmed