Department Details

Bioinformatics Centre

1)    Gawade, P., Gunjal, G., Sharma, A., Ghosh, P. (2020). Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis. Genomics, 112 (2), 1264-1272. ISSN(print/online): 0888-7543/1089-8646, URL/DOI:
2)    Trivedi, J., Ghosh, P., Mitra, D. (2020). N-p-Tosyl-L-phenylalanine chloromethyl ketone (TPCK) inhibits HIV-1 by suppressing the activity of viral protease. Biochemical and Biophysical Research Communications, 527 (1), 167-172. ISSN(print/online): 0006-291X, URL/DOI:
4)    Joshi, S.R., Jagtap, S., Basu, B., Deobagkar, D.D., Ghosh, P. (2020). Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1. PloS One, 15 (6), e0234721. ISSN(print/online): 1932-6203, URL/DOI:
5)    Kumari, J., Bendre, A.D., Bhosale, S., Vinnakota, R., Burada, A.P., Ravelli, R., Peters, P.J., Joshi, M., Kumar, J. (2020). Structural dynamics of the GluK3-kainate receptor neurotransmitter binding domains revealed by cryo-EM. International Journal of Biological Macromolecules, 149, 1051-1058. ISSN(print/online): 0141-8130/1879-0003, URL/DOI:
6)    Sawant, P.M., Atre, N., Kulkarni, A., Gopalkrishna, V. (2020). Detection and molecular characterization of porcine enterovirus G15 and teschovirus from India. Pathogens and Disease, 78 (5), ISSN(print/online): 2049-632X, URL/DOI:
7)    Ghodke, P., Khandagale, K., Thangasamy, A., Kulkarni, A., Narwade, N., Shirsat, D., Randive, P., Roylawar, P., Singh, I., Gawande, S.J., Mahajan, V. (2020). Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress. PloS One, 15 (8), e0237457. ISSN(print/online): 1932-6203, URL/DOI:
8)    Vaidya, S., Kasibhatla, S., Bhattad, D., Ramtirthkar, M., Kale, M., Raut, C., Kulkarni-Kale, U. (2020). Characterization of diversity of measles viruses in India: Genomic sequencing and comparative genomics studies. Journal of Infection, 80 (3), 301-309. ISSN(print/online): 0163-4453/1532-2742, URL/DOI:
9)    Mane, A., Patil, L., Limaye, S., Nirmalkar, A., Kulkarni‐Kale, U. (2020). Characterization of major capsid protein (L1) variants of Human papillomavirus type 16 by cervical neoplastic status in Indian women: Phylogenetic and functional analysis. Journal of Medical Virology, ISSN(print/online): 0146-6615/1096-9071, URL/DOI:
10)    Kasibhatla, S.M., Kinikar, M., Limaye, S., Kale, M.M., Kulkarni‐Kale, U. (2020). Understanding evolution of SARS‐CoV‐2: a perspective from analysis of genetic diversity of RdRp gene. Journal of Medical Virology, ISSN(print/online): 0146-6615/1096-9071, URL/DOI:
11)    Meshram, R.J., Bagul, K.T., Aouti, S.U., Shirsath, A.M., Duggal, H., Gacche, R.N. (2020). Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major. Molecular Diversity, ISSN(print/online): 1381-1991/1573-501X, URL/DOI:
12)    Routaray, C., Bhor, R., Bai, S., Kadam, N.S., Jagtap, S., Doshi, P.J., Sundar, S., Sawant, S., Kulkarni, M.J., Pai, K. (2020). SWATH-MS based quantitative proteomics analysis to evaluate the antileishmanial effect of Commiphora wightii “Guggul” and Amphotericin B on a clinical isolate of Leishmania donovani. Journal of Proteomics, 223, 103800. ISSN(print/online): 1874-3919/1876-7737, URL/DOI:
13)    De Majumdar, S., Sikri, K., Ghosh, P., Jaisinghani, N., Nandi, M., Gandotra, S., Mande, S., Tyagi, J.S. (2019). Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis. BMC Genomics, 20 (1), 129. Google Scholar Citations: 1, WoS Citations: 1, ISSN(print/online): 1471-2164, URL/DOI:
14)    Panwar, H.S., Ojha, H., Ghosh, P., Barage, S.H., Raut, S., Sahu, A. (2019). Molecular engineering of an efficient four-domain DAF-MCP chimera reveals the presence of functional modularity in RCA proteins. Proceedings of the National Academy of Sciences of the United States of America, 116 (20), 9953-9958. ISSN(print/online): 1091-6490, URL/DOI:
15)    Ojha, H., Ghosh, P., Panwar, H.S., Shende, R., Gondane, A., Mande, S.C., Sahu, A. (2019). Spatially conserved motifs in complement control protein domains determine functionality in regulators of complement activation-family proteins. Communications Biology, 2 (1), 290. ISSN(print/online): 2399-3642, URL/DOI:
16)    Nikte, S., Gahankari, A., Mulla, J., Sengupta, D., Joshi, M., Tamhane, V. (2019). In vitro and in silico studies on membrane interactions of diverse Capsicum annuum flower γ-thionin peptides. Proteins: Structure, Function and Bioinformatics, ISSN(print/online): 0887-3585/1097-0134, URL/DOI:
17)    Narwade, N., Patel, S., Alam, A., Chattopadhyay, S., Mittal, S., Kulkarni, A. (2019). Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise. Nucleic Acids Research, 47 (14), 7247-7261. ISSN(print/online): 0305-1048/1362-4962, URL/DOI:
18)    Meshram, R.J., Bagul, K.T., Pawnikar, S.P., Barage, S.H., Kolte, B.S., Gacche, R.N. (2019). Known compounds and new lessons: structural and electronic basis of flavonoid-based bioactivities. Journal of Biomolecular Structure and Dynamics, 1-29. ISSN(print/online): 0739-1102/1538-0254, URL/DOI:
19)    Meshram, R.J., Goundge, M.B., Kolte, B.S. and Gacche, R.N. (2019). An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitology International, 69, 59-70. ISSN(print/online): 1383-5769/1873-0329, URL/DOI:
21)    Ambhore, A.N., Kamble, S.S., Kadam, S.N., Kamble, R.D., Hebade, M.J., Hese, S.V., Gaikwad, M.V., Meshram, R.J., Gacche, R.N., Dawane, B.S. (2019). Design, synthesis and in silico study of pyridine based 1, 3, 4-oxadiazole embedded hydrazinecarbothioamide derivatives as potent anti-tubercular agent. Computational Biology and Chemistry, 80, 54-65. ISSN(print/online): 1476-9271/1476-928X, URL/DOI:
22)    Kolte, B.S., Londhe, S.R., Bagul, K.T., Pawnikar, S.P., Goundge, M.B., Gacche, R.N., Meshram, R.J. (2019). FlavoDb: a web-based chemical repository of flavonoid compounds. 3 Biotech, 9 (11), 431. ISSN(print/online): 2190-572X/2190-5738, URL/DOI:
23)    Tembe, S., Ghosh, P., Sukhi, S. (2018). Influence of methylation on the bacterial efflux pump-inducing property of triclosan. Journal of Hospital Infection, 98 (2), 172-174. Google Scholar Citations: 1, ISSN(print/online): 0195-6701, URL/DOI:
24)    Gawade, P., Ghosh, P. (2018). Genomics driven approach for identification of novel therapeutic targets in Salmonella enterica. Gene, 668, 211-220. ISSN(print/online): 0378-1119/1879-0038, URL/DOI:
25)    Kharche, S., Joshi, M., Sengupta, D., Chattopadhyay, A. (2018). Membrane-induced organization and dynamics of the N-terminal domain of chemokine receptor CXCR1: insights from atomistic simulations. Chemistry and Physics of Lipids, 210, 142-148. WoS Citations: 1, ISSN(print/online): 0009-3084/1873-2941, URL/DOI:
26)    Palrecha, S., Lakade, D., Kulkarni, A., Pal, J.K., Joshi, M. (2018). Computational insights into the interaction of small molecule inhibitors with HRI kinase domain. Journal of Biomolecular Structure and Dynamics, 37 (7), 1715-1723. ISSN(print/online): 0739-1102/1538-0254, URL/DOI:
27)    Barage, S.H., Deobagkar, D.D., Baladhye, V.B. (2018). Characterization of structural and functional role of selenocysteine in selenoprotein H and its impact on DNA binding. Amino Acids, 50 (5), 593-607. Google Scholar Citations: 1, WoS Citations: 1, ISSN(print/online): 0939-4451/1438-2199, URL/DOI:
28)    Lomate, P.R., Dewangan, V., Mahajan, N., Kumar, Y., Kulkarni, A., Wang, L., Saxsena, S., Gupta, V.S., Giri, A.P. (2018). Integrated transcriptomic and proteomic analyses suggest the participation of endogenous protease inhibitors in the regulation of protease gene expression in Helicoverpa armigera. Molecular and Cellular Proteomics, 17 (7), 1324-1336. ISSN(print/online): 1535-9476/1535-9484, URL/DOI:
29)    Hussain, K., Mungikar, K., Kulkarni, A., Kamble, A. (2018). Identification, characterization and expression analysis of pigeonpea miRNAs in response to Fusarium wilt. Gene, 653, 57-64. Google Scholar Citations: 2, WoS Citations: 1, ISSN(print/online): 0378-1119/1879-0038, URL/DOI:
30)    Byukusenge, M., Nissly, R.H., Kasibhatla, S.M., Li, L., Russell, R., Springer, H., Barry, R., Van Saun, R., Wolfgang, D., Hovingh, E., Kulkarni-Kale, U., Kuchipudi, S.V. (2018). Complete Genome Sequences of Four Bovine Coronavirus Isolates from Pennsylvania. Genome Announcements, 6 (22), e00467-18. WoS Citations: 2, ISSN(print/online): 2169-8287, URL/DOI:
31)    Kolte, B.S., Londhe, S.R., Solanki, B.R., Gacche, R.N., Meshram, R.J. (2018). FilTer BaSe: A web accessible chemical database for small compound libraries. Journal of Molecular Graphics and Modelling, 80, 95-103. ISSN(print/online): 1093-3263, URL/DOI:
32)    Augustine, T., Chaudhary, P., Gupta, K., Islam, S., Ghosh, P., Santra, M.K., Mitra, D. (2017). Cyclin F/FBXO1 interacts with HIV-1 viral infectivity factor (Vif) and restricts progeny virion infectivity by ubiquitination and proteasomal degradation of vif protein through SCFcyclin F E3 ligase machinery. Journal of Biological Chemistry, 292 (13), 5349-5363. Google Scholar Citations: 2, WoS Citations: 2, ISSN(print/online): 0021-9258/1083-351X, URL/DOI:
33)    Sengupta, D., Sonar, K., Joshi, M. (2017). Characterizing clinically relevant natural variants of GPCRs using computational approaches. Methods in Cell Biology, 142, 187-204. ISSN(print/online): 0091-679X, URL/DOI:
34)    Meshram, R.J., Baladhye, V.B., Gacche, R.N., Karale, B.K., Gaikar, R.B. (2017). Pharmacophore mapping approach for drug target identification: A chemical synthesis and in silico study on novel thiadiazole compounds. Journal of Clinical and Diagnostic Research, 11 (5), KF01-KF08. Google Scholar Citations: 1, WoS Citations: 1, ISSN(print/online): 2249-782X/0973-709X, URL/DOI:
35)    Barage, S., Kulkarni, A., Pal, J.K., Joshi, M. (2017). Unravelling the structural interactions between PKR kinase domain and its small molecule inhibitors using computational approaches. Journal of Molecular Graphics and Modelling, 75, 322-329. Google Scholar Citations: 1, ISSN(print/online): 1093-3263, URL/DOI:
36)    Waman, V.P., Kale, M.M., Kulkarni-Kale, U. (2017). Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study. Infection, Genetics and Evolution, 49, 234-240. Google Scholar Citations: 7, WoS Citations: 3, ISSN(print/online): 1567-1348/1567-7257, URL/DOI:
37)    Parulekar, N.N., Kolekar, P., Jenkins, A., Kleiven, S., Utkilen, H., Johansen, A., Sawant, S., Kulkarni-Kale, U., Kale, M., Sæbø, M. (2017). Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis. PloS One, 12 (3), e0173408. Google Scholar Citations: 17, WoS Citations: 11, ISSN(print/online): 1932-6203, URL/DOI:
38)    Kadam, K., Karbhal, R., Jayaraman, V.K., Sawant, S., Kulkarni-Kale, U. (2017). AllerBase: a comprehensive allergen knowledgebase. Database: The Journal of Biological Databases and Curation, 2017, 1-12. ISSN(print/online): 1758-0463, URL/DOI:
39)    Saxena, S. (2016). Grid Computing for Big Data Mining and KDD. CSI Communicatoins, 39 (8), 16-17. ISSN(print/online): 0970-647X.
40)    Panwar, H.S., Ojha, H., Ghosh, P., Raut, S., Sahu, A. (2016). Domain swapping reveals functional modularity present in the decay-accelerating factor (CD55). Immunobiology, 10 (221), 1181-1182. ISSN(print/online): 0171-2985/1878-3279, URL/DOI:
41)    Joshi, M., Rajpathak, S.N., Narwade, S.C., Deobagkar, D. (2016). Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1. Chemical Biology and Drug Design, 88 (1), 5-16. Google Scholar Citations: 8, WoS Citations: 6, ISSN(print/online): 1747-0277/1747-0285, URL/DOI:
42)    Tandale, A., Joshi, M., Sengupta, D. (2016). Structural insights and functional implications of inter-individual variability in beta(2)-adrenergic receptor. Scientific Reports, 6, 24379. Google Scholar Citations: 7, WoS Citations: 5, ISSN(print/online): 2045-2322, URL/DOI:
43)    Agrawal, S., Kulabhusan, P.K., Joshi, M., Bodas, D., Paknikar, K.M. (2016). A high affinity phage-displayed peptide as a recognition probe for the detection of Salmonella Typhimurium. Journal of Biotechnology, 231, 40-45. Google Scholar Citations: 3, WoS Citations: 3, ISSN(print/online): 0168-1656/1873-4863, URL/DOI:
44)    Baladhye, V.B., Fawade, M.M. (2016). Affinity based proteomic profiling of yeast in response to phenobaritone. Research Journal of Pharmaceutical, Biological and Chemical Sciences, 7 (5), 94-104. ISSN(print/online): 0975-8585.
45)    Mathai, J., Mittal, S.P., Alam, A., Ranade, P., Mogare, D., Patel, S., Saxena, S., Ghorai, S., Kulkarni, A.P., Chattopadhyay, S. (2016). SMAR1 binds to T (C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster. Scientific Reports, 6, ISSN(print/online): 2045-2322, URL/DOI:
46)    Kulkarni, A.P., Mittal, S.P. (2016). Sequence data mining in search of hookworm (Necator americanus) microRNAs. Gene, 590 (2), 317-323. Google Scholar Citations: 1, WoS Citations: 1, ISSN(print/online): 0378-1119/1879-0038, URL/DOI:
47)    Kolekar, P.S., Waman, V.P., Kale, M.M., Kulkarni-Kale, U. (2016). RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach. PloS One, 11 (2), e0149350. Google Scholar Citations: 2, ISSN(print/online): 1932-6203, URL/DOI:
48)    Waman, V.P., Kasibhatla, S.M., Kale, M.M., Kulkarni-Kale, U. (2016). Population genomics of dengue virus serotype 4: insights into genetic structure and evolution. Archives of Virology, 161 (8), 2133-2148. Google Scholar Citations: 9, WoS Citations: 5, ISSN(print/online): 0304-8608/1432-8798, URL/DOI:
49)    Kolekar, P., Pataskar, A., Kulkarni-Kale, U., Pal, J., Kulkarni, A. (2016). IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES). Scientific Reports, 6, 27436. Google Scholar Citations: 14, WoS Citations: 12, ISSN(print/online): 2045-2322, URL/DOI:
50)    Mane, A., Vidhate, P., Kusro, C., Waman, V., Saxena, V., Kulkarni‐Kale, U., Risbud, A. (2016). Molecular mechanisms associated with Fluconazole resistance in clinical Candida albicans isolates from India. Mycoses, 59 (2), 93-100. Google Scholar Citations: 25, WoS Citations: 7, ISSN(print/online): 1439-0507, URL/DOI:
51)    Waman, V.P., Kolekar, P., Ramtirthkar, M.R., Kale, M.M., Kulkarni-Kale, U. (2016). Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes. PeerJ, 4 (8), e2326. Google Scholar Citations: 10, WoS Citations: 4, ISSN(print/online): 2167-8359, URL/DOI:
52)    Karbhal, R., Sawant, S., Kulkarni-Kale, U. (2016). Erratum to: BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Mining, 9 (1), ISSN(print/online): 1756-0381, URL/DOI:
53)    Sandhu, V., Lothe, I.B., Labori, K.J., Skrede, M.L., Hamfjord, J., Dalsgaard, A.M., Buanes, T., Dube, G., Kale, M.M., Sawant, S., Kulkarni-Kale, U. (2016). Differential expression of miRNAs in pancreatobiliary type of periampullary adenocarcinoma and its associated stroma. Molecular Oncology, 10 (2), 303-316. Google Scholar Citations: 7, WoS Citations: 4, ISSN(print/online): 1574-7891/1878-0261, URL/DOI:
54)    Gaikwad, P.S., Panicker, L., Mohole, M., Sawant, S., Mukhopadhyaya, R., Nath, B.B. (2016). Differential sensitivity of Chironomus and human hemoglobin to gamma radiation. Biochemical and Biophysical Research Communications, 476 (4), 371-378. Google Scholar Citations: 2, ISSN(print/online): 0006-291X, URL/DOI:
55)    Gautam, A.K., Panse, Y., Ghosh, P., Reza, M.J., Mullick, J., Sahu, A. (2015). Mutational analysis of Kaposica reveals that bridging of MG2 and CUB domains of target protein is crucial for the cofactor activity of RCA proteins. Proceedings of the National Academy of Sciences of the United States of America, 112 (41), 12794-12799. Google Scholar Citations: 6, WoS Citations: 6, ISSN(print/online): 1091-6490, URL/DOI:
56)    Karbhal, R., Sawant, S., Kulkarni-Kale, U. (2015). BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Mining, 8 (1), 1. Google Scholar Citations: 2, WoS Citations: 2, ISSN(print/online): 1756-0381, URL/DOI:
57)    Banerjee, A., Benjamin, R., Balakrishnan, K., Ghosh, P., Banerjee, S. (2014). Human protein Staufen-2 promotes HIV-1 proliferation by positively regulating RNA export activity of viral protein Rev. Retrovirology, 11 (1), 1. Google Scholar Citations: 10, WoS Citations: 5, ISSN(print/online): 1742-4690, URL/DOI:
58)    Shahane, G., Parsania, C., Sengupta, D., Joshi, M. (2014). Molecular insights into the dynamics of pharmacogenetically important N-terminal variants of the human β2-adrenergic receptor. PLoS Computational Biology, 10 (12), e1004006. Google Scholar Citations: 12, WoS Citations: 9, ISSN(print/online): 1553-7358/1553-734X, URL/DOI:
59)    Kumbhar, V., Kharche, S., Charla, S., Baladhye, V.B., Kulkarni, A.P., Joshi, M. (2014). Unraveling the function of novel yeast proteins. Journal of Proteins and Proteomics, 5 (3), 112. ISSN(print/online): 0975-8151.
60)    Mittal, S.P., Kulkarni, A.P., Mathai, J., Chattopadhyay, S., Pal, J.K. (2014). Dose-dependent differential response of mammalian cells to cytoplasmic stress is mediated through the heme-regulated eIF2α kinase. International Journal of Biochemistry and Cell Biology, 54, 186-197. Google Scholar Citations: 6, WoS Citations: 5, ISSN(print/online): 1357-2725/1878-5875, URL/DOI:
61)    Waman, V.P., Kolekar, P.S., Kale, M.M., Kulkarni-Kale, U. (2014). Population Structure and Evolution of Rhinoviruses. PloS One, 9 (2), e88981. Google Scholar Citations: 26, WoS Citations: 13, ISSN(print/online): 1932-6203, URL/DOI:
62)    Kolekar, P., Hake, N., Kale, M., Kulkarni-Kale, U. (2014). WNV Typer: A server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution. Journal of Virological Methods, 198, 41-55. Google Scholar Citations: 3, WoS Citations: 2, ISSN(print/online): 0166-0934/1879-0984, URL/DOI:
63)    Joshi, M., Kulkarni, A., Pal, J.K. (2013). Small molecule modulators of eukaryotic initiation factor 2α kinases, the key regulators of protein synthesis. Biochimie, 95 (11), 1980-1990. Google Scholar Citations: 28, WoS Citations: 19, ISSN(print/online): 0300-9084/1638-6183, URL/DOI:
64)    Mittal, S.P., Mathai, J., Kulkarni, A.P., Pal, J.K., Chattopadhyay, S. (2013). miR-320a regulates erythroid differentiation through MAR binding protein SMAR1. International Journal of Biochemistry and Cell Biology, 45 (11), 2519-2529. Google Scholar Citations: 11, WoS Citations: 9, ISSN(print/online): 1357-2725/1878-5875, URL/DOI:
65)    Banerji, A., Navare, C. (2013). Fractal nature of protein surface roughness: a note on quantification of change of surface roughness in active sites, before and after binding. Journal of Molecular Recognition, 26 (5), 201-214. Google Scholar Citations: 8, WoS Citations: 6, ISSN(print/online): 0952-3499/1099-1352, URL/DOI:
66)    Banerji, A. (2013). An attempt to construct a (general) mathematical framework to model biological “context-dependence”. Systems and Synthetic Biology, 7 (4), 221-227. Google Scholar Citations: 4, ISSN(print/online): 1872-5325/1872-5333, URL/DOI:
67)    Yadav, A., Jayaraman, V.K., Kale, M., Kulkarni-Kale, U. (2013). Phylogenetic Clustering of Protein Sequences Using Recurrence Quantification Analysis. Advanced Science Letters, 19 (5), 1336-1339. ISSN(print/online): 1936-6612/1936-7317, URL/DOI:
68)    Balakrishnan, L., Soman, S., Patil, Y.B., Advani, J., Thomas, J.K., Desai, D.V., Kulkarni-Kale, U., Harsha, H.C., Prasad, T.K., Raju, R., Pandey, A. (2013). IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Communication and Adhesion, 20 (3-4), 81-86. Google Scholar Citations: 5, WoS Citations: 4, ISSN(print/online): 1541-9061/1543-5180, URL/DOI:
69)    Ponnusamy, S., Zinjarde, S., Bhargava, S., Kulkarni-Kale, U., Sawant, S., Ravikumar, A. (2013). Deciphering the inactivation of human pancreatic α-amylase, an antidiabetic target, by bisdemethoxycurcumin, a small molecule inhibitor, isolated from Curcuma longa. Natural Products Journal, 3 (1), 15-25. Google Scholar Citations: 5, ISSN(print/online): 2210-3155 /2210-3163 , URL/DOI:
70)    Kolhi, S., Kolaskar, A.S. (2013). Metabolic Network Analysis: Current Status and Way Forward. Current Bioinformatics, 8 (3), 285-292. ISSN(print/online): 1574-8936/2212-392X, URL/DOI:
71)    Saxena, S. (2012). Using Pig on Hadoop for data analysis in Bioinformatics. International Journal of Advanced Research in Computer Science, 3 (7), 240-245. ISSN(print/online): 0976-5697, URL/DOI:
72)    Mallipeddi, P.L., Joshi, M.S., Briggs, J.M. (2012). Pharmacophore-based virtual screening to aid in the identification of unknown protein function. Chemical Biology and Drug Design, 80 (6), 828-842. Google Scholar Citations: 9, WoS Citations: 7, ISSN(print/online): 1747-0277/1747-0285, URL/DOI:
73)    Banerji, A., Magarkar, A. (2012). How happy is your web browsing? A model to quantify satisfaction of an Internet user searching for desired information. Physica A: Statistical Mechanics and its Applications, 391 (17), 4215-4224. Google Scholar Citations: 2, WoS Citations: 2, ISSN(print/online): 0378-4371/1873-2119, URL/DOI:
74)    Kulkarni-Kale, U., Waman, V., Raskar, S., Mehta, S., Saxena, S. (2012). Genome to Vaccinome: Role of Bioinformatics, Immunoinformatics & Comparative Genomics. Current Bioinformatics, 7 (4), 454-466. Google Scholar Citations: 2, ISSN(print/online): 1574-8936/2212-392X, URL/DOI:
75)    Kolekar, P., Kale, M., Kulkarni-Kale, U. (2012). Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Molecular Phylogenetics and Evolution, 65 (2), 510-522. Google Scholar Citations: 36, WoS Citations: 20, ISSN(print/online): 1055-7903/1095-9513, URL/DOI:
76)    Radhakrishnan, A., Raju, R., Tuladhar, N., Subbannayya, T., Thomas, J.K., Goel, R., Telikicherla, D., Palapetta, S.M., Rahiman, B.A., Venkatesh, D.D., Urmila, K.-K., Harsha, H.C., Mathur, P.P., Prasad, T.S.K., Pandey, A., Shemanko, C., Chatterjee, A. (2012). A pathway map of prolactin signaling. Journal of Cell Communication and Signaling, 6 (3), 169-173. Google Scholar Citations: 22, WoS Citations: 18, ISSN(print/online): 1873-9601/1873-961X, URL/DOI:
77)    Wagholikar, K.B., Sundararajan, V., Deshpande, A.W. (2012). Modeling Paradigms for Medical Diagnostic Decision Support: A Survey and Future Directions. Journal of Medical Systems, 36 (5), 3029-3049. Google Scholar Citations: 71, WoS Citations: 38, ISSN(print/online): 0148-5598/1573-689X, URL/DOI:
78)    Kolhi, S., Kolaskar, A.S. (2012). Categorization of metabolome in bacterial systems. Bioinformation, 8 (7), 309-315. Google Scholar Citations: 1, ISSN(print/online): 0973-8894/0973-2063, URL/DOI:
79)    Banerji, A., Ghosh, I. (2011). Fractal symmetry of protein interior: what have we learned?. Cellular and Molecular Life Sciences, 68 (16), 2711-2737. Google Scholar Citations: 40, WoS Citations: 24, ISSN(print/online): 1420-682X/1420-9071, URL/DOI:
80)    Singh, P.P., Banerji, A. (2011). Case for an RNA–prion world: a hypothesis based on conformational diversity. Journal of Biological Physics, 37 (2), 185-188. Google Scholar Citations: 4, WoS Citations: 1, ISSN(print/online): 0092-0606/1573-0689, URL/DOI:
81)    Banerji, A., Ghosh, I. (2011). Mathematical criteria to observe mesoscopic emergence of protein biochemical properties. Journal of Mathematical Chemistry, 49 (3), 643-665. Google Scholar Citations: 8, WoS Citations: 3, ISSN(print/online): 0259-9791/1572-8897, URL/DOI:
82)    Kolaskar, A.S., Kolhi, S. (2011). Pune University Metabolic Pathway Engineering (PuMPE) Resource. Journal of Emerging Trends in Computing and Information Sciences, 2 (7), 325-331. Google Scholar Citations: 2, ISSN(print/online): 2079-8407/2218-6301, URL/DOI:

Publications Before 2011

83)    Kulkarni, A.P., Mittal, S.P., Devasagayam, T.P.A., Pal, J.K. (2010). Hsp90 mediates activation of the heme regulated eIF-2 kinase during oxidative stress. Indian Journal of Biochemistry and Biophysics, 47 (2), 67-74. Google Scholar Citations: 10, WoS Citations: 8, ISSN(print/online): 0301-1208/0975-0959, URL/DOI:
84)    Dey, S., Jejurikar, S., Bhattacharya, S.K., Banerji, A., Adhi, K.P., Dharmadhikari, C.V. (2010). Electrical characterization of zinc oxide/aluminum nitride thin film precursor field effect transistor structures: A conducting atomic force microscopy and density functional theoretical study. Journal of Applied Physics, 108 (9), 94510-94519. Google Scholar Citations: 1, ISSN(print/online): 0021-8979/1089-7550, URL/DOI:
85)    Kulkarni-Kale, U., Sawant, S., Chavan, V. (2010). Bioinformatics education in India. Briefings in Bioinformatics, 11 (6), 616-625. Google Scholar Citations: 13, WoS Citations: 7, ISSN(print/online): 1467-5463/1477-4054, URL/DOI:
86)    Joshi, M., Ebalunode, J.O., Briggs, J.M. (2009). Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates. Proteins: Structure, Function and Bioinformatics, 75 (2), 323-335. Google Scholar Citations: 10, WoS Citations: 9, ISSN(print/online): 0887-3585/1097-0134, URL/DOI:
87)    Kulkarni, A.P., Mittal, S.P., Devasagayam, T.P., Pal, J.K. (2009). Oxidative stress perturbs cell proliferation in human K562 cells by modulating protein synthesis and cell cycle. Free Radical Research, 43 (11), 1090-1100. Google Scholar Citations: 15, WoS Citations: 10, ISSN(print/online): 1071-5762/1029-2470, URL/DOI:
88)    Kulkarni, A.P., Pal, J.K., Devasagayam, T.P.A. (2008). Radiation and free radical exposure and regulation of protein synthesis by the heme-regulated eukaryotic initiation factor 2a kinase. BARC Newsletter, 297, 80-87. Google Scholar Citations: 3, ISSN(print/online): 0976-2108, URL/DOI:
89)    Hosseini, A., Hosseini, A., Ranade, S.H., Ghosh, I., Khandekar, P. (2008). Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes: Full Length Research Paper. DNA Sequence, 19 (3), 167-176. Google Scholar Citations: 3, WoS Citations: 3, ISSN(print/online): 1042-5179/1029-2365, URL/DOI:
90)    Lad, R.K., Desai, N.G., Christian, R.A., Deshpande, A.W. (2008). Fuzzy modeling for environmental pollution potential ranking of industries. Environmental Progress, 27 (1), 84-90. Google Scholar Citations: 5, WoS Citations: 5, ISSN(print/online): 0278-4491/1547-5921, URL/DOI:
91)    Wagholikar, K.B., Deshpande, A.W. (2008). Fuzzy relation based modeling for medical diagnostic decision support: Case studies. International Journal of Knowledge- Based and Intelligent Engineering Systems, 12 (5-6), 319-326. Google Scholar Citations: 15, WoS Citations: 13, ISSN(print/online): 1327-2314/1875-8827, URL/DOI:
92)    Kulkarni-Kale, U., Ojha, J., Manjari, G.S., Deobagkar, D.D., Mallya, A.D., Dhere, R.M., Kapre, S.V. (2007). Mapping antigenic diversity and strain specificity of mumps virus: a bioinformatics approach. Virology, 359 (2), 436-446. Google Scholar Citations: 35, WoS Citations: 23, ISSN(print/online): 0042-6822/1096-0341, URL/DOI:
93)    Ghate, A.D., Bhagwat, B.U., Bhosle, S.G., Gadepalli, S.M., Kulkarni-Kale, U.D. (2007). Characterization of antibody-binding sites on proteins: development of a knowledgebase and its applications in improving epitope prediction. Protein and Peptide Letters, 14 (6), 531-535. Google Scholar Citations: 16, WoS Citations: 10, ISSN(print/online): 0929-8665 /1875-5305 , URL/DOI:
94)    Kumar, A., Ghosh, I. (2007). Mapping Selectivity and Specificity of Active Site of Plasmepsins from Plasmodium falciparum Using Molecular Interaction Field Approach. Protein and Peptide Letters, 14 (6), 569-574. Google Scholar Citations: 6, WoS Citations: 6, ISSN(print/online): 0929-8665 /1875-5305 , URL/DOI:
95)    Gaur, R.K. (2007). Helicase: Mystery of progression. Molecular Biology Reports, 34 (3), 161-164. Google Scholar Citations: 6, ISSN(print/online): 0301-4851/1573-4978 , URL/DOI:
96)    Greenbaum, J.A., Andersen, P.H., Blythe, M., Bui, H.H., Cachau, R.E., Crowe, J., Davies, M., Kolaskar, A.S., Lund, O., Morrison, S., Mumey, B. (2007). Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. Journal of Molecular Recognition, 20 (2), 75-82. Google Scholar Citations: 205, WoS Citations: 128, ISSN(print/online): 0952-3499/1099-1352, URL/DOI:
97)    Kulkarni-Kale, U., Bhosle, S.G., Manjari, G.S., Joshi, M., Bansode, S., Kolaskar, A.S. (2006). Curation of viral genomes: challenges, applications and the way forward. BMC Bioinformatics, 7 (5), 1-21. Google Scholar Citations: 9, WoS Citations: 5, ISSN(print/online): 1471-2105, URL/DOI:
98)    Baladhye, V.B., Kamble, S.P., Fawade, M.M. (2006). Phenobarbitone Induced Changes in Yeast Mitochondrial Proteome. Journal of Bioinfolet, 3 (2), 123-125.
99)    Salokhe, S., Sarkar, A., Kulkarni, A., Mukherjee, S., Pal, J.K. (2006). Flufenoxuron, an acylurea insect growth regulator, alters development of Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) by modulating levels of chitin, soluble protein content, and HSP70 and p34cdc2 in the larval tissues. Pesticide Biochemistry and Physiology, 85 (2), 84-90. Google Scholar Citations: 19, WoS Citations: 10, ISSN(print/online): 0048-3575/1095-9939, URL/DOI:
100)    Singh, V.K., Ghosh, I. (2006). Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. Theoretical Biology and Medical Modelling, 3 (1), 27. Google Scholar Citations: 65, WoS Citations: 34, ISSN(print/online): 1742-4682, URL/DOI:
101)    Ghosh, I. (2006). Target based high throughput screening and lead designing in pharmaceutical drug industry. Indian Journal of Chemistry -Section A, 45 (1), 163-173. Google Scholar Citations: 1, ISSN(print/online): 0376-4710/0975-0975, URL/DOI:
102)    Prakash, O., Ghosh, I. (2006). Developing an antituberculosis compounds database and data mining in the search of a motif responsible for the activity of a diverse class of antituberculosis agents. Journal of Chemical Information and Modeling, 46 (1), 17-23. Google Scholar Citations: 23, WoS Citations: 20, ISSN(print/online): 1549-9596/1549-960X, URL/DOI:
103)    Sarkar, A., Kulkarni, A., Chattopadhyay, S., Mogare, D., Sharma, K.K., Singh, K., Pal, J.K. (2005). Lead-induced upregulation of te heme-regulated eukaryotic initiation factor 2α kinase is compromised by hemin in human K562 cells. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression, 1732 (1-3), 15-22. Google Scholar Citations: 11, WoS Citations: 7, ISSN(print/online): 0167-4781, URL/DOI:
104)    Kulkarni-Kale, U., Bhosle, S., Kolaskar, A.S. (2005). CEP: a conformational epitope prediction server. Nucleic Acids Research, 33 (2), 168-171. Google Scholar Citations: 265, WoS Citations: 138, ISSN(print/online): 0305-1048/1362-4962, URL/DOI:
105)    Sarkar, D., Ghosh, I., Datta, S. (2004). Biochemical characterization of Plasmodium falciparum hypoxanthine-guanine-xanthine phosphorybosyltransferase: role of histidine residue in substrate selectivity. Molecular and Biochemical Parasitology, 137 (2), 267-276. Google Scholar Citations: 12, WoS Citations: 6, ISSN(print/online): 0166-6851/1872-9428, URL/DOI:
106)    Raychaudhury, C., Ghosh, I. (2004). Information- Theoretical Measure of Similarity and a Topological Shape and Size Descriptor for Molecular Similarity Analysis. Internet Electronic Journal of Molecular Design, 3 (6), 350-360. Google Scholar Citations: 4, ISSN(print/online): 1538-6414, URL/DOI:
107)    Kulkarni‐Kale, U., Bhosle, S., Manjari, G.S., Kolaskar, A.S. (2004). VirGen: a comprehensive viral genome resource. Nucleic Acids Research, 32 (1), D289-D292. Google Scholar Citations: 27, WoS Citations: 15, ISSN(print/online): 0305-1048/1362-4962, URL/DOI:
108)    Awasthi, A., Mathur, R., Khan, A., Joshi, B.N., Jain, N., Sawant, S., Boppana, R., Mitra, D., Saha, B. (2003). CD40 Signaling Is Impaired in L. major–infected Macrophages and Is Rescued by a p38MAPK Activator Establishing a Host-protective Memory T Cell Response. Journal of Experimental Medicine, 197 (8), 1037-1043. Google Scholar Citations: 98, WoS Citations: 64, ISSN(print/online): 0022-1007/1540-9538, URL/DOI:
109)    Sakharkar, M.K., Kangueane, P., Petrov, D.A., Kolaskar, A.S., Subbiah, S.S. (2002). SEGE: A database on 'intron less/single exonic' genes from eukaryotes. Bioinformatics, 18 (9), 1266-1267. Google Scholar Citations: 42, WoS Citations: 28, ISSN(print/online): 1367-4803/1460-2059, URL/DOI:
110)    Kolaskar, A.S., Naik, P.S. (2000). Online identification of viruses. Journal of Microbiology, Immunology and Infection, 32 (2), 69-78. ISSN(print/online): 1684-1182, URL/DOI:
111)    Kolaskar, A.S., Kulkarni-Kale, U. (1999). Prediction of Three-Dimensional Structure and Mapping of Conformational Epitopes of Envelope Glycoprotein of Japanese Encephalitis Virus. Virology, 261 (1), 31-42. Google Scholar Citations: 185, WoS Citations: 76, ISSN(print/online): 0042-6822/1096-0341, URL/DOI:
112)    Kolaskar, A.S., Joshi, R.R. (1998). Molecular Dynamics Simulation of a 13-mer Duplex DNA: A PvuII Substrate. Journal of Biomolecular Structure and Dynamics, 15 (6), 1155-1165. Google Scholar Citations: 2, WoS Citations: 2, ISSN(print/online): 0739-1102/1538-0254, URL/DOI:
113)    Davis, J.A., Peen, E., Williams, R.C., Perkins, S., Malone, C.C., McCormack, W.T., Csernok, E., Gross, W.L., Kolaskar, A.S., Kulkarni-Kale, U. (1998). Determination of Primary Amino Acid Sequence and Unique Three-Dimensional Structure of WGH1, a Monoclonal Human IgM Antibody with Anti-PR3 Specificity. Clinical Immunology and Immunopathology, 89 (1), 35-43. Google Scholar Citations: 11, WoS Citations: 6, ISSN(print/online): 0090-1229, URL/DOI:
114)    Kolaskar, A.S., Naik, P.S. (1998). Computer-aided virus identification on the World Wide Web. Archives of Virology, 143 (8), 1513-1521. ISSN(print/online): 0304-8608/1432-8798, URL/DOI:
115)    Williams, R.C., Malone, C.C., Kolaskar, A.S., Kulkarni-Kale, U. (1997). Antigenic determinants reacting with rheumatoid factor: Epitopes with different primary sequences share similar conformation. Molecular Immunology, 34 (7), 543-556. Google Scholar Citations: 7, WoS Citations: 7, ISSN(print/online): 0161-5890/1872-9142, URL/DOI:
116)    Kolaskar, A.S., Sawant, S. (1996). Prediction of conformational states of amino acids using a Ramachandran plot. International Journal of Peptide and Protein Research, 47 (1-2), 110-116. Google Scholar Citations: 17, WoS Citations: 15, ISSN(print/online): 0367-8377, URL/DOI:
117)    Date, S., Kulkarni, R., Kulkarni, B., Kulkarni-Kale, U., Kolaskar, A.S. (1993). Multiple alignment of sequences on parallel computers. Computer Applications in the Biosciences, 9 (4), 397-402. Google Scholar Citations: 18, WoS Citations: 7, ISSN(print/online): 0266-7061, URL/DOI:
118)    Kulkarni, R., Date, S., Kulkarni, B., Kulkarni, U., Kolaskar, A.S. (1993). Pras: parallel alignment of sequences algorithm. Parallel Processing Letters, 3 (3), 243-252. Google Scholar Citations: 2, ISSN(print/online): 0129-6264/1793-642X, URL/DOI:
119)    Kolaskar, A.S., Kulkarni-Kale, U. (1992). Sequence alignment approach to pick up conformationally similar protein fragments. Journal of Molecular Biology, 223 (4), 1053-1061. Google Scholar Citations: 41, WoS Citations: 28, ISSN(print/online): 0022-2836, URL/DOI:
120)    Kolaskar, A.S. (1992). Outline of activities as Distributed Bioinformation Centre, University of Poona. Bioinformatics, 1 (4), 3-5. Google Scholar Citations: 2, ISSN(print/online): 1367-4803/1460-2059, URL/DOI:
121)    Kolaskar, A.S., Naik, P.S. (1992). Computerization of Virus Data and Its Usefulness in Virus Classification. Intervirology, 34 (3), 133-141. Google Scholar Citations: 4, WoS Citations: 2, ISSN(print/online): 0300-5526/1423-0100, URL/DOI:
122)    Kolaskar, A.S., Samuel, S.L. (1991). Analysis of inverted repeats in primary structure of proteins. Protein Sequences and Data Analysis, 4 (2), 105-110. Google Scholar Citations: 6, ISSN(print/online): 0931-9506, URL/DOI:
123)    Kutubuddin, M., Kolaskar, A.S., Galande, S., Gore, M.M., Ghosh, S.N., Banerjee, K. (1991). Recognition of helper T cell epitopes in envelope (E) glycoprotein of Japanese encephalitis, West Nile and dengue viruses. Molecular Immunology, 28 (1-2), 149-154. Google Scholar Citations: 44, WoS Citations: 30, ISSN(print/online): 0161-5890/1872-9142, URL/DOI:
124)    Kolaskar, A.S., Tongaonkar, P.C. (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters, 276 (1-2), 172-174. Google Scholar Citations: 912, WoS Citations: 538, ISSN(print/online): 0014-5793/1873-3468, URL/DOI:
125)    Devi, A.S., Rehana, T., Kolaskar, A.S., Pandit, M.W. (1989). Hydrophilicity and antigenicity of proteins-A case study of myoglobin and hemoglobin. Journal of Biosciences, 14 (2), 133-142. Google Scholar Citations: 2, WoS Citations: 1, ISSN(print/online): 0250-5991/0973-7138, URL/DOI:
126)    Thanaraj, T.A., Kolaskar, A.S., Pandit, M.W. (1988). Prediction of the Recognition Sites on 16S and 23S rRNAs from E.coli for the Formation of 16S-23S rRNA Complex. Journal of Biomolecular Structure and Dynamics, 6 (3), 587-592. Google Scholar Citations: 3, ISSN(print/online): 0739-1102/1538-0254, URL/DOI: