Department Details

Bioinformatics Centre

1)    Doiphode, S., Ghosh, P., Swamy, K.V., Nagar, S. (2026). An In Silico Study of Resveratrol Derivatives as Dual Inhibitors of Cyclooxygenase-2 (COX-2) and 5-Lipoxygenase (5-LOX) in Cancer Therapy. Biotechnology and Applied Biochemistry, ISSN(print/online): 0885-4513/1470-8744, URL/DOI: http://dx.doi.org/10.1002/bab.70150
2)    Vaidya, S.R., Sharma, S., Kamble, M.B., Sreedeep, K.S., Deepthi, B., Kulkarni, S., Gade, S., Pandey, P.G., Joshi, M., Divatia, J., Dhamne, C.A. (2026). Clinico-virological investigation of measles complications in immunocompromised pediatric patients. Infection, Genetics and Evolution, 139, 105918. ISSN(print/online): 1567-1348/1567-7257, URL/DOI: http://dx.doi.org/10.1016/j.meegid.2026.105918
3)    Koulgi, S., Harman, T.H., Jones, A.J., Sonavane, U., Nietlispach, D., Sengupta, D., Joshi, M. (2026). Unique Microswitches Positioned Extracellular to the Orthosteric Binding Site Initiate Activation in the β1-Adrenergic Receptor. Journal of Chemical Information and Modeling, ISSN(print/online): 1549-9596/1549-960X, URL/DOI: http://dx.doi.org/10.1021/acs.jcim.5c02542
4)    Anjulal, H., Saha, A., Barvkar, V.T., Pawar, H., Joshi, M., Zinjarde, S.S. (2026). Overexpression, biochemical characterization, and structural modeling of polyhydroxybutyrate depolymerase from Nocardiopsis dassonvillei. Enzyme and Microbial Technology, 193, 110767. ISSN(print/online): 0141-0229/1879-0909, URL/DOI: http://dx.doi.org/10.1016/j.enzmictec.2025.110767
5)    Jagtap, R.A., Jagdale, B.S., Dhonnar, S.L., Shaikh, S.A., More, R.A., Alavala, R.R., Muteeb, G., Fernandez-Conde, D., Pawar, T.J., Meshram, R.J., Escobar-Cabrera, J. (2026). Efficient synthesis, dual anti-tubercular and antioxidant activity of triazole-acetophenone derivatives: enhanced efficacy via esterification and quantum mechanical validation of CYP121 binding. RSC Advances, 16 (4), 3609-3622. ISSN(print/online): 2046-2069, URL/DOI: http://dx.doi.org/10.1039/d5ra09368f
6)    Birla, S.S., Meshram, R.J., Rai, M.K. (2026). Integrative evaluation of mycosynthesized silver nanoparticles against multidrug-resistant pathogens using microbiological and in silico approaches. Inorganic and Nano-Metal Chemistry, ISSN(print/online): 2470-1556/2470-1564, URL/DOI: http://dx.doi.org/10.1080/24701556.2025.2583080
7)    Kadam, M.B., Shaikh, S.A., Chobe, S.S., Meshram, R.J., More, R.A., Madje, B.R., Vaidya, S.R. (2026). Triazolo-pyridine derivatives: Synthesis, characterization and biological evaluation. Journal of Molecular Structure, 1356, ISSN(print/online): 0022-2860/1872-8014, URL/DOI: http://dx.doi.org/10.1016/j.molstruc.2025.144958
8)    Ahire, P.S., Gaikwad, N.D., Mahale, K.A., Sharma, A.B., Mourya, A.A., Patil, R.K., Chobe, S.S., More, R.A., Sarnikar, Y.P., Mondal, S., Meshram, R.J. (2026). Maleimide-based scaffolds as potent antitubercular agents: Synthesis, InhA targeting and biological evaluation. Journal of Molecular Structure, 1365, 145998. ISSN(print/online): 0022-2860/1872-8014, URL/DOI: http://dx.doi.org/10.1016/j.molstruc.2026.145998
9)    Patel, S., Saxena, S. (2025). Skin lesion classification using convolutional neural networks. International Journal of Advanced Research in Computer Science, 16 (3), 104-108. ISSN(print/online): 0976-5697, URL/DOI: http://dx.doi.org/10.26483/ijarcs.v16i3.7284
10)    Dasgupta, A., Tripathi, A., Mitra, A., Ghosh, P., Santra, M.K., Mitra, D. (2025). Human microRNA miR-197-3p positively regulates HIV-1 virion infectivity through its target DDX52 by stabilizing Vif protein expression. Journal of Biological Chemistry, 301 (2), 108198. ISSN(print/online): 0021-9258/1083-351X, URL/DOI: http://dx.doi.org/10.1016/j.jbc.2025.108198
11)    Mahajan, P., Gor, H., Joshi, M., Nema, V. (2025). DapB is a conserved target for tackling antimicrobial resistance in Mycobacterium tuberculosis. Journal of Biomolecular Structure and Dynamics, ISSN(print/online): 0739-1102/1538-0254, URL/DOI: http://dx.doi.org/10.1080/07391102.2025.2581074
12)    Suneesh, N.S., Dhotre, K., Mahajan, P., Dass, D., Banerjee, A., Siddiqi, N.J., Malik, A., Joshi, M., Khan, A.A., Nema, V., Mukherjee, A. (2025). Reverse vaccinology-based design of multivalent multiepitope mRNA vaccines targeting key viral proteins of Herpes Simplex Virus type-2. Frontiers in Immunology, 16, 1586271. Google Scholar Citations: 1, WoS Citations: 1, ISSN(print/online): 1664-3224, URL/DOI: http://dx.doi.org/10.3389/fimmu.2025.1586271
13)    Mahajan, M., Ghodke, G., Joshi, M., Chaudhary, A., Kaul-Ghanekar, R. (2025). Matairesinol Targets Lipid Metabolism Reprogramming in AR-Independent Prostate Cancer Cells. Asian Pacific Journal of Cancer Prevention, 26 (8), 2855-2867. ISSN(print/online): 1513-7368/2476-762X, URL/DOI: http://dx.doi.org/10.31557/APJCP.2025.26.8.2855
14)    Gotkhindikar, A., Chakravorty, D., Sengupta, D., Joshi, M., Assmann, S.M. (2025). Is GCR1 the GPR157 of plants?. Plant Physiology, 197 (2), 057. ISSN(print/online): 0032-0889/1532-2548, URL/DOI: http://dx.doi.org/10.1093/plphys/kiaf057
15)    Mahajan, P., Gor, H. R., Jadhav, S., Joshi, M., Nema, V. (2025). Host-Directed Therapeutic for the treatment of Mycobacterium tuberculosis. Microbiological Research, 299, 128253. ISSN(print/online): 0944-5013/1618-0623, URL/DOI: http://dx.doi.org/10.1016/j.micres.2025.128253
16)    Sadawarte, S., Kale, M., Kulkarni Kale, U., Mittal, S., Kulkarni, A.P. (2025). Decoding circadian moonlighting proteins nexus with TP53: cornerstone to understand cancer and mental health disorders. Biological Rhythm Research, 56 (11), 830-854. ISSN(print/online): 0929-1016/1744-4179, URL/DOI: http://dx.doi.org/10.1080/09291016.2025.2518411
17)    Mulla, J.A., Palod, P.S., Bhagwat, S.A., Sonawane, A.P., Acharya, S.K., Kulkarni, A.P., Tamhane, V.A. (2025). Genomic and functional insights into the diversity of Capsicum annuum defensin gene family. 3 Biotech, 15, 95. ISSN(print/online): 2190-572X/2190-5738, URL/DOI: http://dx.doi.org/10.1007/s13205-025-04256-y
18)    Shaikh, S.A., Wakchaure, S.N., Meshram, R.J., Deokar, S.C., More, R.A., Nerkar, C.K., Chobe, S.S. (2025). Resynthesis, Antimicrobial Evaluation and Molecular Docking Studies of Thiazolyl-2-Chloroacetamide Derivatives as Potential Broad-Spectrum Agents. Chemistry and Biodiversity, 22 (11), e01486. ISSN(print/online): 1612-1872/1612-1880, URL/DOI: http://dx.doi.org/10.1002/cbdv.202501486
19)    Suryavanshi, H., Chabukswar, A., Meshram, R., Waghmare, P., Jagdale, S., Sakharkar, A., Patil, V., Navin, J. (2025). Design, Synthesis, and Inhibitory Activity of Benzimidazole-2-thiol Derivatives on SHSY-5Y Neuroblastoma Cancer Cell Line. ChemistrySelect, 10 (25), e06047. ISSN(print/online): 2365-6549, URL/DOI: http://dx.doi.org/10.1002/slct.202406047
20)    Ballabh, D., Shaikh, S., More, R.A., Meshram, R.J. (2025). Dynamics, mechanistic and energetic evaluation of thiazole-thiadiazole compounds in flavin dependent thymidylate synthase of Mycobacterium tuberculosis. International Journal of Biological Macromolecules, 289, 138839. ISSN(print/online): 0141-8130/1879-0003, URL/DOI: http://dx.doi.org/10.1016/j.ijbiomac.2024.138839
21)    Joshi, R., Gaikwad, H., Soge, B., Alshammari, A., Albekairi, N.A., Kabra, A., Yashwante, U., Kolte, B., Lokhande, P., Meshram, R.J. (2025). Exploring pyrazolines as potential inhibitors of NSP3-macrodomain of SARS-CoV-2: synthesis and in silico analysis. Scientific Reports, 15 (1), 767. ISSN(print/online): 2045-2322, URL/DOI: http://dx.doi.org/10.1038/s41598-024-81711-5
22)    Kamble, S.C., Ghosh, P.D. (2024). Defining omics-based biomarker signatures of metabolic dysfunction-associated steatotic liver disease (MASLD): In vitro studies. Current Opinion in Biomedical Engineering, 30, 100534. ISSN(print/online): 2468-4511, URL/DOI: http://dx.doi.org/10.1016/j.cobme.2024.100534
23)    Singh, S., Ghosh, P., Sharma, S., Bhargava, S., Kumar, A.R. (2024). Tetrahydropalmatine from medicinal plants activates human glucokinase to regulate glucose homeostasis. Biotechnology and Applied Biochemistry, 71 (2), 295-313. ISSN(print/online): 0885-4513/1470-8744, URL/DOI: http://dx.doi.org/10.1002/bab.2541
24)    Lokhande, K.B., Pawar, S.V., Madkaiker, S., Shrivastava, A., Venkateswara, S.K., Nawani, N., Wani, M., Ghosh, P.D., Singh, A. (2024). Screening of potential phytomolecules against MurG as drug target in nosocomial pathogen Pseudomonas aeruginosa: perceptions from computational campaign. Journal of Biomolecular Structure and Dynamics, 42 (1), 1-14. ISSN(print/online): 0739-1102/1538-0254, URL/DOI: http://dx.doi.org/10.1080/07391102.2023.2194005
25)    Rajan, B. R. S., Joshi, M., Tillu, G. (2024). Unlocking ancient wisdom with technology – A special issue on Ayurveda and technology. Journal of Ayurveda and Integrative Medicine, 15 (3), 101020. ISSN(print/online): 0975-9476/0976-2809, URL/DOI: http://dx.doi.org/10.1016/j.jaim.2024.101020
26)    Nikte, S.V., Joshi, M., Sengupta, D. (2024). State-dependent dynamics of extramembrane domains in the β2-adrenergic receptor. Proteins: Structure, Function and Bioinformatics, 92 (3), 1-12. ISSN(print/online): 0887-3585/1097-0134, URL/DOI: http://dx.doi.org/10.1002/prot.26613
27)    Gawai, T., Sadawarte, S., Khandagale, K., Raj, A., Kulkarni, A., Jaiswal, D.K., Ade, A.B., Gawande, S. (2024). Phylogenetic and population genetic analyses of Thrips tabaci Lindeman (Thysanoptera: Thripidae) on Allium host in India. PeerJ, 12, e17679. Google Scholar Citations: 2, WoS Citations: 1, ISSN(print/online): 2167-8359, URL/DOI: http://dx.doi.org/10.7717/peerj.17679
28)    Bose, G.S., Jindal, S., Landage, K.G., Jindal, A., Mahale, M.P., Kulkarni, A.P., Mittal, S. (2024). SMAR1 and p53-regulated lncRNA RP11-431M3.1 enhances HIF1A translation via miR-138 in colorectal cancer cells under oxidative stress. FEBS Journal, 291 (21), 4696-4713. ISSN(print/online): 1742-464X/1742-4658, URL/DOI: http://dx.doi.org/10.1111/febs.17253
29)    Bose, G.S., Kalakoti, G., Kulkarni, A.P., Mittal, S. (2024). AP-1/C-FOS and AP-1/FRA2 differentially regulate early and late adipogenic differentiation of mesenchymal stem cells. Journal of Cellular Biochemistry, 125 (10), e30543. ISSN(print/online): 0730-2312/1097-4644, URL/DOI: http://dx.doi.org/10.1002/jcb.30543
30)    Gire, D., Inamdar, S., Acharya, J., Sadawarte, S., Kulkarni, A., Ghaskadbi, S. (2024). Dynamic changes in the gene expression during adipogenesis in hMSCs. Gene Reports, 34, 101860. ISSN(print/online): 2452-0144, URL/DOI: http://dx.doi.org/10.1016/j.genrep.2023.101860
31)    Limaye, S., Shelke, A., Kale, M.M., Kulkarni-Kale, U., Kuchipudi, S.V. (2024). IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution. Viruses, 16 (3), 373. ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v16030373
32)    Karbhal, R., Sawant, S., Kulkarni-Kale, U. (2024). iCEED: Integrated customized extraction of enzyme data. Journal of Bioinformatics and Computational Biology, 22 (2), 2450005. ISSN(print/online): 0219-7200/1757-6334, URL/DOI: http://dx.doi.org/10.1142/s0219720024500057
33)    Limaye, S., Lohar, T., Dube, H., Ramasamy, S., Kale, M., Kulkarni-Kale, U., Kuchipudi, S.V., (2024). Rapid evolution leads to extensive genetic diversification of cattle flu Influenza D virus. Communications Biology, 7, 1276. ISSN(print/online): 2399-3642, URL/DOI: http://dx.doi.org/10.1038/s42003-024-06954-4
34)    Shaikh, S.A., Labhade, S.R., Kale, R.R., Pachorkar, P.Y., Meshram, R.J., Jain, K.S., Labhade, H.S., Bhanushali, D.D., More, R.A., Nerkar, C.K., Chobe, S.S. (2024). Thiadiazole-thiazole derivatives as potent anti-tubercular agents: Synthesis, biological evaluation, and In silico docking studies. European Journal of Medicinal Chemistry Reports, 12, 100183. ISSN(print/online): 2772-4174, URL/DOI: http://dx.doi.org/10.1016/j.ejmcr.2024.100183
35)    Dahiwade, M., Vyawahare, N., Garade, P., Marathe, A., Meshram, R., Suryawanshi, M., Palake, A., Kodam, K., Ottoor, D. (2024). Biological activity and biomolecule interaction of pyridyl thiazole derivative and its copper complex. Journal of Molecular Liquids, 404, 124936. ISSN(print/online): 0167-7322/1873-3166, URL/DOI: http://dx.doi.org/10.1016/j.molliq.2024.124936
36)    Meshram, R., Kolte, B., Gacche, R. (2024). Reverse vaccinology approach for identification of epitopes from E1 protein as peptide vaccine against HCV: A proof of concept. Vaccine, 42 (24), 1-13. ISSN(print/online): 0264-410X/1873-2518, URL/DOI: http://dx.doi.org/10.1016/j.vaccine.2024.07.007
37)    Vane, V., Mokal, R., Yashwante, U., Meshram, R. J., Jadhava, S. (2024). Synthesis and In-Vitro/Silico Evaluation of Fluorinated Chalcones. Oriental Journal of Chemistry, 40 (4), 1077-1086. ISSN(print/online): 0970-020X/2231-5039, URL/DOI: http://dx.doi.org/10.13005/ojc/400419
38)    Shaikh, S.A., Pachorkar, P.Y., Meshram, R.J., Boraste, D.R., More, R.A., Chobe, S.S., Ballabh, D., Wakchaure, S.N., Labhade, S.R., Kale, R.R., Labhade, H.S. (2024). Synthesis, Biological and Molecular Docking Studies of Thiazole-Thiadiazole derivatives as potential Anti-Tuberculosis Agents. Chemistry and Biodiversity, 21 (6), e202400496. ISSN(print/online): 1612-1872/1612-1880, URL/DOI: http://dx.doi.org/10.1002/cbdv.202400496
39)    Hublikar, M., Kadu, V., Edake, N., Raut, D., Shirame, S., Z. Ahmed, M., Makam, P., Ahmad, M.S., Meshram, R.J., Bhosale, R. (2024). Design, Synthesis, Anti-Cancer, Anti-inflammatory and In Silico Studies of 3-Substituted-2-Oxindole Derivatives. Chemistry and Biodiversity, 21 (11), e202400844. ISSN(print/online): 1612-1872/1612-1880, URL/DOI: http://dx.doi.org/10.1002/cbdv.202400844
40)    Jani, V., Sonavane, U., Sawant, S. (2024). Structural insights into the activation mechanism of phosphoinositide 3-kinase alpha. Computational Biology and Chemistry, 108, 1-16. ISSN(print/online): 1476-9271/1476-928X, URL/DOI: http://dx.doi.org/10.1016/j.compbiolchem.2023.107994
41)    Saxena, A., Saxena, S. (2023). Pancreatic Cancer Data Classification with Quantum Machine Learning. Journal of Quantum Computing, 5 (1), 1-13. ISSN(print/online): 2579-0137/2579-0145, URL/DOI: http://dx.doi.org/10.32604/jqc.2023.044555
42)    Doiphode, S., Lokhande, K.B., Ghosh, P., Swamy, K.V., Nagar, S. (2023). Dual inhibition of cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) by resveratrol derivatives in cancer therapy: in silico approach. Journal of Biomolecular Structure and Dynamics, 41 (17), 8571-8586. Google Scholar Citations: 1, ISSN(print/online): 0739-1102/1538-0254, URL/DOI: http://dx.doi.org/10.1080/07391102.2022.2135599
43)    Ballav, S., Lokhande, K.B., Yadav, R.S., Ghosh, P.D., Swamy, K.V., Basu, S. (2023). Exploring binding mode assessment of novel kaempferol, resveratrol, and quercetin derivatives with PPAR-α as potent drug candidates against canc. Molecular Diversity, 27 (6), 2867 - 2885. ISSN(print/online): 1381-1991/1573-501X, URL/DOI: http://dx.doi.org/10.1007/s11030-022-10587-2
44)    Chand, K., Barman, M.K., Ghosh, P., Mitra, D. (2023). DNAJB8 facilitates autophagic-lysosomal degradation of viral Vif protein and restricts HIV-1 virion infectivity by rescuing APOBEC3G expression in host cells. FASEB Journal, 37 (3), 1-23. ISSN(print/online): 0892-6638/1530-6860, URL/DOI: http://dx.doi.org/10.1096/fj.202201738R
45)    Lokhande, K.B., Pawar, S.V., Madkaiker, S., Nawani, N., Venkateswara, S.K., Ghosh, P. (2023). High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign. Journal of Biomolecular Structure and Dynamics, 41 (7), 2698-2712. WoS Citations: 5, ISSN(print/online): 0739-1102/1538-0254, URL/DOI: http://dx.doi.org/10.1080/07391102.2022.2038271
46)    Joshi, M.S., Lin, S.J., Vona, B., Lau, T., Huang, K., Zaki, M.S., Aldeen, H.S., Karimiani, E.G., Rocca, C., Noureldeen, M.M., Saad, A.K., Petree, C....ed. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. . Genome Medicine, 15 (1), 102. ISSN(print/online): 1756-994X, URL/DOI: http://dx.doi.org/10.1186/s13073-023-01258-4
47)    Yadav, S., Raazi, Z., Shivaraj, S.M., Somani, D., Prashant, R., Kulkarni, A., Kumar, R., Biradar, S., Desai, S., Kadoo, N. (2023). Whole Genome Sequencing and Comparative Genomics of Indian Isolates of Wheat Spot Blotch Pathogen Bipolaris sorokiniana Reveals Expansion of Pathogenicity Gene Clusters . Pathogens, 12 (1), 1-20. ISSN(print/online): 2076-0817, URL/DOI: http://dx.doi.org/10.3390/pathogens12010001
48)    Sawant, P., Kulkarni, A.P., Lavania, M. (2023). Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India. Frontiers in Cellular and Infection Microbiology, 13, 1258660. ISSN(print/online): 2235-2988, URL/DOI: http://dx.doi.org/10.3389/fcimb.2023.1258660
49)    Gedam, P.A., Khandagale, K., Shirsat, D., Thangasamy, A., Kulkarni, O., Kulkarni, A., Barvkar, V., Mahajan, V., Gupta, A.J., Bhagat, K.P., Khade, Y.P. (2023). Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling. Frontiers in Plant Science, 14, 1150909. ISSN(print/online): 1664-462X, URL/DOI: http://dx.doi.org/10.3389/fpls.2023.1150909
50)    Vaidya, S.R., Kumbhar, N.S., Andhare, G.K., Pawar, N., Walimbe, A.M., Kinikar, M., Kasibhatla, S.M., Kulkarni-Kale, U. (2023). Neutralizing Antibody Response to Genotypically Diverse Measles Viruses in Clinically Suspected Measles Cases . Viruses, 15 (11), 2243. ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v15112243
51)    Lodha, K., Wavhal, D., Bhujbal, N., Mazire, P., Bhujbal, S., Korde, A., Bagul, K., Roy, A., Meshram, R., Shinde, V. (2023). Synthesis and biological evaluation of 9-aryl-1,8-dioxo-octahydroxanthene derivatives as antileishmanial agents. Results in Chemistry, 5, 100943. ISSN(print/online): 2211-7156, URL/DOI: http://dx.doi.org/10.1016/j.rechem.2023.100943
52)    Patil, A.M., Lagad, P.M., Soge, B., Meshram, R., Lokhande, M.N., Lokhande, P.D. (2023). Ammonium chloride mediated synthesis of 2-aryl-phthalazinone from O-formyl benzoic acid and in silico applications. ARKIVOC, 2023 (7), 1-11. ISSN(print/online): 1551-7004/1551-7012, URL/DOI: http://dx.doi.org/10.24820/ark.5550190.p011.972
53)    Kamble, R.P., Ghosh, P., Kulkarni, A.A. (2022). Identification of α-amylase inhibitory compounds from leaves of Careya arborea Roxb. and in silico docking studies. South African Journal of Botany, 151, 493-503. ISSN(print/online): 0254-6299/1727-9321, URL/DOI: http://dx.doi.org/10.1016/j.sajb.2022.05.018
54)    Joshi, S., Ghosh, P., Barage, S., Basu, B., Deobagkar, D.D. (2022). Genome-wide lone strand adenine methylation in Deinococcus radiodurans R1: Regulation of gene expression through DR0643-dependent adenine methylation. Microbiological Research, 257, 126964. ISSN(print/online): 0944-5013/1618-0623, URL/DOI: http://dx.doi.org/10.1016/j.micres.2022.126964
55)    Lokhande, K.B., Banerjee, T., Swamy, K.V., Ghosh, P., Deshpande, M. (2022). An in silico scientific basis for LL-37 as a therapeutic for Covid-19. Proteins: Structure, Function and Bioinformatics, 90 (5), 1029-1043. Google Scholar Citations: 1, WoS Citations: 6, ISSN(print/online): 0887-3585/1097-0134, URL/DOI: http://dx.doi.org/10.1002/prot.26198
56)    Lokhande, K.B., Ghosh, P., Nagar, S., Venkateswara Swamy, K. (2022). Novel B, C-ring truncated deguelin derivatives reveals as potential inhibitors of cyclin D1 and cyclin E using molecular docking and molecular dynamic simulation. Molecular Diversity, 26 (4), 2295–2309. WoS Citations: 3, ISSN(print/online): 1381-1991/1573-501X, URL/DOI: http://dx.doi.org/10.1007/s11030-021-10334-z
57)    Paithankar, H., Tarang, G.S., Parvez, F., Marathe, A., Joshi, M., Chugh, J. (2022). Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs. Biophysical Journal, 121 (6), 1038-1055. WoS Citations: 1, ISSN(print/online): 0006-3495/1542-0086, URL/DOI: http://dx.doi.org/10.1016/j.bpj.2022.02.005
58)    Khandagale, K., Roylawar, P., Kulkarni, O., Khambalkar, P., Ade, A., Kulkarni, A., Singh, M., Gawande, S. (2022). Comparative Transcriptome Analysis of Onion in Response to Infection by Alternaria porri (Ellis) Cifferi. Frontiers in Plant Science, 13, 857306-857306. ISSN(print/online): 1664-462X, URL/DOI: http://dx.doi.org/10.3389/fpls.2022.857306
59)    Mane, A., Kasibhatla, S.M., Vidhate, P., Saxena, V., Patil, S., Rao, A., Nirmalkar, A., Kulkarni-Kale, U., Panda, S (2022). Phylogenetic Analysis of Spread of Hepatitis C Virus Identified during HIV Outbreak Investigation, Unnao, India. Emerging infectious diseases, 28 (4), 725–733. Google Scholar Citations: 1, ISSN(print/online): 1080-6040/1080-6059, URL/DOI: http://dx.doi.org/10.3201/eid2804.211845
60)    Hufsky, F., Abecasis, A., Agudelo R. P., Bletsa, M., Brown, K., Claus, C., Deinhardt E. S., Deng, L., Friedel, C.C., Gismondi, M.I., Kostaki, E.G., Kühnert, D., Kulkarni-Kale, U., Metzner, K.J., Meyer, I.M., Miozzi, L., Nishimura, L., Paraskevopoulou, S., Pérez C. A., Rahlff, J., Thomson, E., Tumescheit, C., van der Hoek, L., Van Espen, L., Vandamme, A. M., Zaheri, M., Zuckerman, N., Marz, M. (2022). Women in the European Virus Bioinformatics Center. Viruses, 14 (7), 1522. ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v14071522
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179)    Vikhe, P.P., Gaikar, R.B., Vikhe, G.P., Meshram, R.J., Karale, B.K. (2011). Molecular Properties and Docking Studies on Chromone Pyrazolones as Potential Inhibitors of P38 Map Kinase. International Journal of Pharmacy and Pharmaceutical Sciences, 3 (5), 321-324. Google Scholar Citations: 2, ISSN(print/online): 2656-0097/0975-1491, URL/DOI: https://www.researchgate.net/profile/Dr-Rohan-Meshram/publication/258878549_Molecular_properties_and_docking_studies_on_chromone_pyrazolones_as_potential_inhibitors_of_p38_MAP_kinase/links/0c9605294e07d3dfa3000000/Molecular-properties-and-docking-studies-on-chromone-pyrazolones-as-potential-inhibitors-of-p38-MAP-kinase.pdf
180)    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: http://www.cisjournal.org/journalofcomputing/archive/vol2no7/vol2no7_4.pdf
  

Publications Before 2011
181)    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: http://nopr.niscair.res.in/bitstream/123456789/8272/1/IJBB%2047%282%29%2067-74.pdf
182)    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, WoS Citations: 1, ISSN(print/online): 0021-8979/1089-7550, URL/DOI: http://dx.doi.org/10.1063/1.3471815
183)    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: 12, ISSN(print/online): 1467-5463/1477-4054, URL/DOI: http://dx.doi.org/10.1093/bib/bbq027
184)    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: http://dx.doi.org/10.1002/prot.22241
185)    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: 13, ISSN(print/online): 1071-5762/1029-2470, URL/DOI: http://dx.doi.org/10.1080/10715760903179673
186)    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: http://barc.gov.in/publications/nl/2008/20081010.pdf
187)    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: http://dx.doi.org/10.1080/10425170701461730
188)    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: http://dx.doi.org/10.3233/KES-2008-125-602
189)    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: 8, ISSN(print/online): 0278-4491/1547-5921, URL/DOI: http://dx.doi.org/10.1002/ep.10251
190)    Ghate, A.D., Bhagwat, B.U., Bhosle, S.G., Gadepalli, S.M., Kulkarni-Kale, U. (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: 12, ISSN(print/online): 0929-8665 /1875-5305 , URL/DOI: http://dx.doi.org/10.2174/092986607780989921
191)    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: 28, ISSN(print/online): 0042-6822/1096-0341, URL/DOI: http://dx.doi.org/10.1016/j.virol.2006.09.040
192)    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: http://dx.doi.org/10.2174/092986607780989877
193)    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: http://dx.doi.org/10.1007/s11033-006-9029-3
194)    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: 166, ISSN(print/online): 0952-3499/1099-1352, URL/DOI: http://dx.doi.org/10.1002/jmr.815
195)    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: 7, ISSN(print/online): 1471-2105, URL/DOI: http://dx.doi.org/10.1186/1471-2105-7-S5-S12
196)    Baladhye, V.B., Kamble, S.P., Fawade, M.M. (2006). Phenobarbitone Induced Changes in Yeast Mitochondrial Proteome. Journal of Bioinfolet, 3 (2), 123-125.
197)    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: 12, ISSN(print/online): 0048-3575/1095-9939, URL/DOI: http://dx.doi.org/10.1016/j.pestbp.2005.10.006
198)    Ghosh, I. (2006). Target based high throughput screening and lead designing in pharmaceutical drug industry. Indian Journal of Chemistry - Section A Inorganic, Physical, Theoretical and Analytical Chemistry, 45 (1), 163-173. Google Scholar Citations: 1, ISSN(print/online): 0376-4710/0975-0975, URL/DOI: http://nopr.niscair.res.in/bitstream/123456789/19962/1/IJCA%2045A%281%29%20163-173.pdf
199)    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: 23, ISSN(print/online): 1549-9596/1549-960X, URL/DOI: http://dx.doi.org/10.1021/ci050115s
200)    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: 46, ISSN(print/online): 1742-4682, URL/DOI: http://dx.doi.org/10.1186/1742-4682-3-27
201)    Sarkar, A., Kulkarni, A., Chattopadhyay, S., Mogare, D., Sharma, K.K., Singh, K., Pal, J.K. (2005). Lead-induced upregulation of the 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: 8, ISSN(print/online): 0167-4781, URL/DOI: http://dx.doi.org/10.1016/j.bbaexp.2005.12.003
202)    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: 179, ISSN(print/online): 0305-1048/1362-4962, URL/DOI: http://dx.doi.org/10.1093/nar/gki460
203)    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: 8, ISSN(print/online): 0166-6851/1872-9428, URL/DOI: http://dx.doi.org/10.1016/j.molbiopara.2004.05.014
204)    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: http://biochempress.com/Files/iejmd_2004_3_0350.pdf
205)    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: 16, ISSN(print/online): 0305-1048/1362-4962, URL/DOI: http://dx.doi.org/10.1093/nar/gkh098
206)    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: 78, ISSN(print/online): 0022-1007/1540-9538, URL/DOI: http://dx.doi.org/10.1084/jem.20022033
207)    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: 31, ISSN(print/online): 1367-4803/1460-2059, URL/DOI: http://dx.doi.org/10.1093/bioinformatics/18.9.1266
208)    Kolaskar, A.S., Naik, P.S. (2000). Online identification of viruses. Journal of Microbiology, Immunology and Infection, 32 (2), 69-78. ISSN(print/online): 1684-1182/1995-9133, URL/DOI: http://europepmc.org/abstract/med/10917875
209)    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: 86, ISSN(print/online): 0042-6822/1096-0341, URL/DOI: http://dx.doi.org/10.1006/viro.1999.9859
210)    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: http://dx.doi.org/10.1080/07391102.1998.10509009
211)    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: http://dx.doi.org/10.1006/clin.1998.4582
212)    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: http://dx.doi.org/10.1007/s007050050394
213)    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: 8, ISSN(print/online): 0161-5890/1872-9142, URL/DOI: http://dx.doi.org/10.1016/S0161-5890(97)00024-2
214)    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: 19, ISSN(print/online): 0367-8377, URL/DOI: http://dx.doi.org/10.1111/j.1399-3011.1996.tb00817.x
215)    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: 8, ISSN(print/online): 0266-7061, URL/DOI: http://dx.doi.org/10.1093/bioinformatics/9.4.397
216)    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: http://dx.doi.org/10.1142/S0129626493000289
217)    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: 30, ISSN(print/online): 0022-2836/1089-8638, URL/DOI: http://dx.doi.org/10.1016/0022-2836(92)90261-H
218)    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: http://dx.doi.org/10.1159/000150273
219)    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: http://bioinfo.net.in/publications/36-bio-1.pdf
220)    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: 32, ISSN(print/online): 0161-5890/1872-9142, URL/DOI: http://dx.doi.org/10.1016/0161-5890(91)90098-5
221)    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: http://bioinfo.net.in/publications/protsc-data-anal-1991.pdf
222)    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: 840, ISSN(print/online): 0014-5793/1873-3468, URL/DOI: http://dx.doi.org/10.1016/0014-5793(90)80535-Q
223)    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: http://dx.doi.org/10.1007/BF02703165
224)    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: http://dx.doi.org/10.1080/07391102.1988.10506509
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