Department Details

Bioinformatics Centre

1)    Lokhande, K.B., Pawar, S.V., Madkaiker, S., Nawani, N., Venkateswara, S.K., Ghosh, P. (2022). 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, WoS Citations: 4, ISSN(print/online): 0739-1102/1538-0254, URL/DOI: http://dx.doi.org/10.1080/07391102.2022.2038271
2)    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, ISSN(print/online): 0254-6299/1727-9321, URL/DOI: http://dx.doi.org/10.1016/j.sajb.2022.05.018
3)    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, 2295–2309. WoS Citations: 3, ISSN(print/online): 1381-1991/1573-501X, URL/DOI: http://dx.doi.org/10.1007/s11030-021-10334-z
4)    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 (S) (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
5)    Doiphode, S., Lokhande, K.B., Ghosh, P., Swamy, K.V., Nagar, S. (2022). 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, 1-16. ISSN(print/online): 0739-1102/1538-0254, URL/DOI: https://doi.org/10.1080/07391102.2022.2135599
6)    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
7)    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, URL/DOI: http://dx.doi.org/10.1016/j.bpj.2022.02.005
8)    Mane, A., Limaye, S., Patil, L., Kulkarni-Kale, U. (2022). Genetic variability in minor capsid protein (L2 gene) of human papillomavirus type 16 among Indian women. Medical Microbiology and Immunology, 211, 153-160. ISSN(print/online): 0300-8584/1432-1831, URL/DOI: http://dx.doi.org/10.1007/s00430-022-00739-4
9)    Mane, A., Limaye, S., Patil, L., Kulkarni-Kale, U. (2022). Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis. Journal of Medical Microbiology, 71 (1), 001475. WoS Citations: 2, ISSN(print/online): 0022-2615/1473-5644, URL/DOI: http://dx.doi.org/10.1099/jmm.0.001475
10)    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
11)    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
12)    More, N.A., Jadhao, N.L., Meshram, R.J., Tambe, P., Salve, R.A., Sabane, J.K., Sawant, S.N., Gajbhiye, V., Gajbhiye, J.M. (2022). Novel 3-fluoro-4-morpholinoaniline derivatives: Synthesis and assessment of anti-cancer activity in breast cancer cells. Journal of Molecular Structure, 1253, 132127. ISSN(print/online): 0022-2860/1872-8014, URL/DOI: http://dx.doi.org/10.1016/j.molstruc.2021.132127
13)    Meshram, R.J., Kathwate, G.H., Gacche, R.N. (2022). Progress, evolving therapeutic/diagnostic approaches, and challenges in the management of hepatitis C virus infections. Archives of Virology, 167, 717-736. WoS Citations: 1, ISSN(print/online): 0304-8608/1432-8798, URL/DOI: http://dx.doi.org/10.1007/s00705-022-05375-0
14)    Lodha, K.K., Wavhal, D.S., Bhalekar, S.B., Meshram, R.J., Shinde, V.S. (2022). Exploring New Tetrahydrothienopyridine Derivatives as Platelet Agglutination Inhibitors: Synthesis, Biological Evaluation and In Silico Study. ChemistrySelect, 7 (2), 202103428. ISSN(print/online): 2365-6549, URL/DOI: http://dx.doi.org/10.1002/slct.202103428
15)    Ghosh, P., Hajra, A. (2021). Fluorination of 2 H-Indazoles Using N-Fluorobenzenesulfonimide. The Journal of Organic Chemistry, 86 (15), 10883–10888. Google Scholar Citations: 6, ISSN(print/online): 0022-3263/1520-6904, URL/DOI: http://dx.doi.org/10.1021/acs.joc.1c01253
16)    Joshi, S., Ujaoney, A.K., Ghosh, P., Deobagkar, D.D., Basu, B. (2021). N6-methyladenine and epigenetic immunity of Deinococcus radiodurans. Research in Microbiology, 172 (1), 103789. WoS Citations: 3, ISSN(print/online): 0923-2508, URL/DOI: http://dx.doi.org/10.1016/j.resmic.2020.10.004
17)    Bhattacharjee, S., Laru, S., Ghosh, P., Hajra, A. (2021). Potassium Persulfate Mediated Chemodivergent C-3 Functionalization of 2H-Indazoles with DMSO as C1 Source. The Journal of Organic Chemistry, 86 (15), 10866−10873. Google Scholar Citations: 9, ISSN(print/online): 0022-3263/1520-6904, URL/DOI: https://pubs.acs.org/doi/full/10.1021/acs.joc.1c01188
18)    Roy, A., Behera, S., Kumari, B., Mazire, P.H., Mandal, A., Purkait, B., Ghosh, P., Das, P., Das, P. (2021). The HIV − 1 protease inhibitor Amprenavir targets Leishmania donovani topoisomerase I and induces oxidative stress-mediated programmed cell death. Parasitology International, 82, 102287. WoS Citations: 2, ISSN(print/online): 1383-5769/1873-0329, URL/DOI: http://dx.doi.org/10.1016/j.parint.2021.102287
19)    Kulkarni, A.S., Ramesh, R., Walia, S., Sayyad, S.I., Gathalkar, G.B., Balamkundu, S., Joshi, M., Sen, A., Reddy, D.S. (2021). Identification of a Novel Series of Potent Organosilicon Mosquito Repellents. ACS Omega, 6 (46), 31236-31243. ISSN(print/online): 2470-1343, URL/DOI: http://dx.doi.org/10.1021/acsomega.1c04961
20)    Nikte, S.V., Sonar, K., Tandale, A., Joshi, M., Sengupta, D. (2021). Loss of a water-mediated network results in reduced agonist affinity in a β2-adrenergic receptor clinical variant. Biochimica et Biophysica Acta- Proteins and Proteomics, 1869 (4), 140605. WoS Citations: 3, ISSN(print/online): 1570-9639, URL/DOI: http://dx.doi.org/10.1016/j.bbapap.2021.140605
21)    Gujar, N., Nikte, S.V., Joshi, R.S., Joshi, M. (2021). Molecular Characterization of the β2-like Octopamine Receptor of Helicoverpa armigera. Journal of Membrane Biology, 254, 311-319. WoS Citations: 2, ISSN(print/online): 0022-2631/1432-1424, URL/DOI: http://dx.doi.org/10.1007/s00232-021-00172-3
22)    Alai, S., Gujar, N., Joshi, M., Gautam, M., Gairola, S. (2021). Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Heliyon, 7 (3), e06564. WoS Citations: 11, ISSN(print/online): 2405-8440, URL/DOI: http://dx.doi.org/10.1016/j.heliyon.2021.e06564
23)    Kharche, S., Joshi, M., Chattopadhyay, A., Sengupta, D. (2021). Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1. PLoS Computational Biology, 17 (5), e1008593. Google Scholar Citations: 2, WoS Citations: 6, ISSN(print/online): 1553-7358/1553-734X, URL/DOI: http://dx.doi.org/10.1371/journal.pcbi.1008593
24)    Borse, S., Joshi, M., Saggam, A., Bhat, V., Walia, S., Marathe, A., Sagar, S., Chavan-Gautam, P., Girme, A., Hingorani, L., Tillu, G. (2021). Ayurveda botanicals in COVID-19 management: An in silico multi-target approach. PloS One, 16 (6), e0248479. Google Scholar Citations: 9, WoS Citations: 21, ISSN(print/online): 1932-6203, URL/DOI: http://dx.doi.org/10.1371/journal.pone.0248479
25)    Joshi, M., Lin, S.J., Vona, B., Barbalho, P.G., Kaiyrzhanov, R., Maroofian, R., Petree, C., Severino, M., Stanley, V., Varshney, P., Bahena, P., Alzahrani, F. (2021). Biallelic variants in KARS1 are associated with neurodevelopmental disorders and hearing loss recapitulated by the knockout zebrafish. Genetics in Medicine, 23, 1933-1943. WoS Citations: 4, ISSN(print/online): 1098-3600/1530-0366, URL/DOI: http://dx.doi.org/10.1038/s41436-021-01239-1
26)    Dar, M.S., Dholakia, B.B., Kulkarni, A.P., Oak, P.S., Shanmugam, D., Gupta, V.S., Giri, A.P. (2021). Influence of domestication on specialized metabolic pathways in fruit crops. Planta, 253 (2), 1-15. WoS Citations: 2, ISSN(print/online): 0032-0935/1432-2048, URL/DOI: http://dx.doi.org/10.1007/s00425-020-03554-4
27)    Kolhe, N., Kulkarni, A., Zinjarde, S., Acharya, C. (2021). Transcriptome Response of the Tropical Marine Yeast Yarrowia lipolytica on Exposure to Uranium. Current Microbiology, 78, 2033-2043. WoS Citations: 4, ISSN(print/online): 0343-8651/1432-0991, URL/DOI: http://dx.doi.org/10.1007/s00284-021-02459-z
28)    González-Candelas, F., Shaw, M.A., Phan, T., Kulkarni-Kale, U., Paraskevis, D., Luciani, F., Kimura, H., Sironi, M. (2021). One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages. Infection, Genetics and Evolution, 92, 104869. WoS Citations: 28, ISSN(print/online): 1567-1348/1567-7257, URL/DOI: http://dx.doi.org/10.1016/j.meegid.2021.104869
29)    Gokavi, J., Sadawarte, S., Shelke, A., Kulkarni-Kale, U., Thakar, M., Saxena, V. (2021). Inhibition of miR-155 Promotes TGF-β Mediated Suppression of HIV Release in the Cervical Epithelial Cells . Viruses, 13 (11), 2266. WoS Citations: 2, ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v13112266
30)    Vaidya, S.R., Kasibhatla, S.M., Kamble, M.B., Munivenkatappa, A., Kumbhar, N.S., Jayaswamy, M.M., Ramtirthkar, M.R., Kale, M.M., Kulkarni-Kale, U. (2021). Genetic and antigenic characterization of wild type rubella viruses isolated from India. Vaccine, 39 (6), ISSN(print/online): 0264-410X/1873-2518, URL/DOI: http://dx.doi.org/10.1016/j.vaccine.2020.12.063
31)    Limaye, S., Kasibhatla, S.M., Ramtirthkar, M., Kinikar, M., Kale, M.M., Kulkarni-Kale, U. (2021). Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak. Viruses, 13 (11), 2238. WoS Citations: 5, ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v13112238
32)    Kadam, K., Peerzada, N., Karbhal, R., Sawant, S., Valadi, J., Kulkarni-Kale, U. (2021). Antibody Class(es) Predictor for Epitopes (AbCPE): A Multi-Label Classification Algorithm. Frontiers in Bioinformatics, 1, Google Scholar Citations: 2, ISSN(print/online): 2673-7647, URL/DOI: http://dx.doi.org/10.3389/fbinf.2021.709951
33)    Sharbidre, A., Dhage, P., Duggal, H., Meshram, R. (2021). In silico Investigation of Tridax procumbens Phyto-Constituents Against SARS-CoV-2 Infection. Biointerface Research in Applied Chemistry, 11 (4), 12120-12148. ISSN(print/online): 2069-5837, URL/DOI: http://dx.doi.org/10.33263/BRIAC114.1212012148
34)    Meshram, R.J., Bagul, K.T., Aouti, S.U., Shirsath, A.M., Duggal, H., Gacche, R.N. (2021). Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major. Molecular Diversity, 25, 1679-1700. WoS Citations: 2, ISSN(print/online): 1381-1991/1573-501X, URL/DOI: http://dx.doi.org/10.1007/s11030-020-10129-8
35)    Sawant, A.S., Kamble, S.S., Pisal, P.M., Sawant, S.S., Hese, S.V., Bagul, K.T., Pinjari, R.V., Kamble, V.T., Meshram, R.J., Gacche, R.N. (2021). Synthesis and evaluation of N-(4-(substituted)-3-(trifluoromethyl) phenyl) isobutyramides and their N-ethyl analogous as anticancer, anti-angiogenic & antioxidant agents: In vitro and in silico analysis. Computational Biology and Chemistry, 92, 107484. ISSN(print/online): 1476-9271/1476-928X, URL/DOI: http://dx.doi.org/10.1016/j.compbiolchem.2021.107484
36)    Dandekar, P.D., Kotmale, A.S., Chavan, S.R., Kadlag, P.P., Sawant, S.V., Dhavale, D.D., RaviKumar, A. (2021). Insights into the Inhibition Mechanism of Human Pancreatic α-Amylase, a Type 2 Diabetes Target, by Dehydrodieugenol B Isolated from Ocimum tenuiflorum. ACS Omega, 6 (3), 1780-1786. WoS Citations: 5, ISSN(print/online): 2470-1343, URL/DOI: http://dx.doi.org/10.1021/acsomega.0c00617
37)    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. WoS Citations: 6, ISSN(print/online): 0888-7543/1089-8646, URL/DOI: http://dx.doi.org/10.1016/j.ygeno.2019.07.013
38)    Ghosh, A.K., Ghosh, P., Hajra, A. (2020). Rhodium-Catalyzed Directed C(sp2)–H Bond Addition of 2-Arylindazoles to N-Sulfonylformaldimines and Activated Aldehydes. The Journal of Organic Chemistry, 85 (23), 15752–15759. Google Scholar Citations: 13, ISSN(print/online): 0022-3263/1520-6904, URL/DOI: http://dx.doi.org/10.1021/acs.joc.0c02408
39)    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. WoS Citations: 1, ISSN(print/online): 0006-291X, URL/DOI: http://dx.doi.org/10.1016/j.bbrc.2020.04.096
40)    Datir, S., Ghosh, P. (2020). In silico analysis of the structural diversity and interactions between invertases and invertase inhibitors from potato (Solanum tuberosum L.). 3 Biotech, 10 (4), 1-15. WoS Citations: 2, ISSN(print/online): 2190-572X/2190-5738, URL/DOI: http://dx.doi.org/10.1007/s13205-020-02171-y
41)    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. WoS Citations: 2, ISSN(print/online): 1932-6203, URL/DOI: http://dx.doi.org/10.1371/journal.pone.0234721
42)    Jamalpure, S., Panditrao, G., Kulabhusan, P.K., Hameed, A.S., Paknikar, K.M., Joshi, M., Rajwade, J.M. (2020). In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus. Journal of Molecular Modeling, 26 (10), 264. ISSN(print/online): 1610-2940/0948-5023, URL/DOI: http://dx.doi.org/10.1007/s00894-020-04524-z
43)    Nikte, S., Gahankari, A., Mulla, J., Sengupta, D., Joshi, M., Tamhane, V. (2020). In vitro and in silico studies on membrane interactions of diverse Capsicum annuum flower γ-thionin peptides. Proteins: Structure, Function and Bioinformatics, 88 (1), 227-236. WoS Citations: 4, ISSN(print/online): 0887-3585/1097-0134, URL/DOI: http://dx.doi.org/10.1002/prot.25791
44)    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. WoS Citations: 5, ISSN(print/online): 0141-8130/1879-0003, URL/DOI: http://dx.doi.org/10.1016/j.ijbiomac.2020.01.282
45)    Singh, P., Bharti, N., Singh, A.P., Tripathi, S.K., Pandey, S.P., Chauhan, A.S., Kulkarni, A., Sane, A.P. (2020). Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome. Scientific Reports, 10 (1), 17196. WoS Citations: 5, ISSN(print/online): 2045-2322, URL/DOI: http://dx.doi.org/10.1038/s41598-020-74144-3
46)    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. WoS Citations: 14, ISSN(print/online): 1932-6203, URL/DOI: http://dx.doi.org/10.1371/journal.pone.0237457
47)    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: http://dx.doi.org/10.1093/femspd/ftaa039
48)    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. WoS Citations: 6, ISSN(print/online): 0163-4453/1532-2742, URL/DOI: http://dx.doi.org/10.1016/j.jinf.2019.11.025
49)    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, 92 (8), 1303-1308. WoS Citations: 6, ISSN(print/online): 0146-6615/1096-9071, URL/DOI: http://dx.doi.org/10.1002/jmv.25675
50)    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, 92 (10), ‏ 1932-1937. WoS Citations: 18, ISSN(print/online): 0146-6615/1096-9071, URL/DOI: http://dx.doi.org/10.1002/jmv.25909
51)    Patil, A., Duggal, H., Bagul, K.T., Kamble, S., Lokhande, P., Gacche, R., Meshram, R. (2020). Synthesis of new 3-arylaminophthalides and 3-indolyl-phthalides using ammonium chloride, evaluation of their anti-mycobacterial potential and docking study. Combinatorial Chemistry and High Throughput Screening, 23 (8), 723-739. Google Scholar Citations: 1, WoS Citations: 1, ISSN(print/online): 1386-2073/1875-5402, URL/DOI: http://dx.doi.org/10.2174/1386207323666200422082754
52)    Sawant, A.S., Kamble, S.S., Pisal, P.M., Meshram, R.J., Sawant, S.S., Kamble, V.A., Kamble, V.T., Gacche, R.N. (2020). Synthesis and evaluation of a novel series of 6-bromo-1-cyclopentyl-1H-indazole-4-carboxylic acid-substituted amide derivatives as anticancer, antiangiogenic, and antioxidant agents. Medicinal Chemistry Research, 29 (1), 17-32. WoS Citations: 2, ISSN(print/online): 1054-2523/1554-8120, URL/DOI: http://dx.doi.org/10.1007/s00044-019-02454-x
53)    Meshram, R.J., Bagul, K.T., Pawnikar, S.P., Barage, S.H., Kolte, B.S., Gacche, R.N. (2020). Known compounds and new lessons: structural and electronic basis of flavonoid-based bioactivities. Journal of Biomolecular Structure and Dynamics, 38 (4), 1168-1184. Google Scholar Citations: 12, WoS Citations: 14, ISSN(print/online): 0739-1102/1538-0254, URL/DOI: http://dx.doi.org/10.1080/07391102.2019.1597770
54)    Hartung, F., Patil, A., Meshram, R.J., Weber, G.F. (2020). Gene expression signatures of site-specificity in cancer metastases. Clinical and Experimental Metastasis, 37 (1), 159-171. Google Scholar Citations: 3, WoS Citations: 5, ISSN(print/online): 0262-0898/1573-7276, URL/DOI: http://dx.doi.org/10.1007/s10585-019-09995-w
55)    Meshram, R.J., Shirsath, A., Aouti, S., Bagul, K., Gacche, R.N. (2020). Molecular modeling and simulation study of homoserine kinase as an effective leishmanial drug target. Journal of Molecular Modeling, 26 (8), 218. WoS Citations: 1, ISSN(print/online): 1610-2940/0948-5023, URL/DOI: http://dx.doi.org/10.1007/s00894-020-04473-7
56)    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. WoS Citations: 3, ISSN(print/online): 1874-3919/1876-7737, URL/DOI: http://dx.doi.org/10.1016/j.jprot.2020.103800
57)    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: 3, ISSN(print/online): 1471-2164, URL/DOI: http://dx.doi.org/10.1186/s12864-019-5482-y
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121)    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: 57, ISSN(print/online): 0148-5598/1573-689X, URL/DOI: http://dx.doi.org/10.1007/s10916-011-9780-4
122)    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: http://dx.doi.org/10.6026/97320630008309
123)    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: http://dx.doi.org/10.1007/s10867-011-9219-7
124)    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: 30, ISSN(print/online): 1420-682X/1420-9071, URL/DOI: http://dx.doi.org/10.1007/s00018-011-0722-6
125)    Kolekar, P.S., Kale, M.M., Kulkarni-Kale, U. (2011). Genotyping of Mumps Viruses Based on the SH gene: Development of a Server using Alignment-free and alignment based methods. Immunome Research, 7 (3), 1-7. Google Scholar Citations: 11, ISSN(print/online): 1745-7580, URL/DOI: http://omicsonline.com/open-access/1745-7580/1745-7580-7-051.pdf
126)    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: http://dx.doi.org/10.1007/s10910-010-9760-9
127)    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/publication/258878549_Molecular_properties_and_docking_studies_on_chromone_pyrazolones_as_potential_inhibitors_of_p38_MAP_kinase
128)    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


129)    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
130)    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
131)    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
132)    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
133)    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
134)    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
135)    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
136)    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
137)    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
138)    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: 12, ISSN(print/online): 0929-8665 /1875-5305 , URL/DOI: http://dx.doi.org/10.2174/092986607780989921
139)    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
140)    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
141)    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
142)    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
143)    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
144)    Baladhye, V.B., Kamble, S.P., Fawade, M.M. (2006). Phenobarbitone Induced Changes in Yeast Mitochondrial Proteome. Journal of Bioinfolet, 3 (2), 123-125.
145)    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
146)    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
147)    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
148)    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: http://nopr.niscair.res.in/bitstream/123456789/19962/1/IJCA%2045A%281%29%20163-173.pdf
149)    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: 8, ISSN(print/online): 0167-4781, URL/DOI: http://dx.doi.org/10.1016/j.bbaexp.2005.12.003
150)    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
151)    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
152)    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
153)    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
154)    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
155)    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
156)    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: http://europepmc.org/abstract/med/10917875
157)    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
158)    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
159)    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
160)    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
161)    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
162)    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
163)    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
164)    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
165)    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, URL/DOI: http://dx.doi.org/10.1016/0022-2836(92)90261-H
166)    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
167)    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
168)    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
169)    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
170)    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
171)    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
172)    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