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