Teacher Details

Urmila Kulkarni Kale

Bioinformatics Centre


Research Areas : Bioinformatics, Comparative genomics, phyloinformatics, immunoinformatics, structural bioinformatics, database development, algorithm design

Google Scholar Profile | ResearchGate Profile

1)    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
2)    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. ISSN(print/online): 1567-1348/1567-7257, URL/DOI: http://dx.doi.org/10.1016/j.meegid.2021.104869
3)    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. ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v13112238
4)    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. ISSN(print/online): 1999-4915, URL/DOI: http://dx.doi.org/10.3390/v13112266
5)    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. ISSN(print/online): 0146-6615/1096-9071, URL/DOI: http://dx.doi.org/10.1002/jmv.25675
6)    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: 6, ISSN(print/online): 0146-6615/1096-9071, URL/DOI: http://dx.doi.org/10.1002/jmv.25909
7)    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: http://dx.doi.org/10.1016/j.jinf.2019.11.025
8)    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: http://dx.doi.org/10.1128/genomeA.00467-18
9)    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: http://dx.doi.org/10.1016/j.meegid.2017.01.022
10)    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: http://dx.doi.org/10.1371/journal.pone.0173408
11)    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: http://dx.doi.org/10.1093/database/bax066
12)    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: http://dx.doi.org/10.1371/journal.pone.0149350
13)    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: http://dx.doi.org/10.1111/myc.12439
14)    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: http://dx.doi.org/10.1038/srep27436
15)    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: http://dx.doi.org/10.1016/j.molonc.2015.10.011
16)    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: http://dx.doi.org/10.1007/s00705-016-2886-8
17)    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, e2326. Google Scholar Citations: 45, WoS Citations: 32, ISSN(print/online): 2167-8359, URL/DOI: http://dx.doi.org/10.7717/peerj.2326
18)    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: http://dx.doi.org/10.1186/s13040-016-0081-9
19)    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: http://dx.doi.org/10.1186/s13040-015-0067-z
20)    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: http://dx.doi.org/10.1016/j.jviromet.2013.12.012
21)    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: http://dx.doi.org/10.1371/journal.pone.0088981
22)    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: http://dx.doi.org/10.2174/2210315511303010005
23)    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: http://dx.doi.org/10.3109/15419061.2013.791683
24)    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: http://dx.doi.org/10.1166/asl.2013.4499
25)    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: http://dx.doi.org/10.1007/s12079-012-0168-0
26)    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: http://dx.doi.org/10.1016/j.ympev.2012.07.003
27)    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: http://dx.doi.org/10.2174/157489312803900910

Publications Before 2011

28)    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: http://dx.doi.org/10.1093/bib/bbq027
29)    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: http://dx.doi.org/10.2174/092986607780989921
30)    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: http://dx.doi.org/10.1016/j.virol.2006.09.040
31)    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: http://dx.doi.org/10.1186/1471-2105-7-S5-S12
32)    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: http://dx.doi.org/10.1093/nar/gki460
33)    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: http://dx.doi.org/10.1093/nar/gkh098
34)    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: http://dx.doi.org/10.1006/viro.1999.9859
35)    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
36)    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: http://dx.doi.org/10.1016/S0161-5890(97)00024-2
37)    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: http://dx.doi.org/10.1093/bioinformatics/9.4.397
38)    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
39)    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: http://dx.doi.org/10.1016/0022-2836(92)90261-H