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)    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
2)    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
3)    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
4)    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. ISSN(print/online): 0022-2615/1473-5644, URL/DOI: http://dx.doi.org/10.1099/jmm.0.001475
5)    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
6)    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
7)    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, ISSN(print/online): 1080-6040/1080-6059, URL/DOI: http://dx.doi.org/10.3201/eid2804.211845
8)    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
9)    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
10)    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
11)    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
12)    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, ISSN(print/online): 2673-7647, URL/DOI: http://dx.doi.org/10.3389/fbinf.2021.709951
13)    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
14)    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. ISSN(print/online): 0146-6615/1096-9071, URL/DOI: http://dx.doi.org/10.1002/jmv.25909
15)    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
16)    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. ISSN(print/online): 2169-8287, URL/DOI: http://dx.doi.org/10.1128/genomeA.00467-18
17)    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, ISSN(print/online): 1567-1348/1567-7257, URL/DOI: http://dx.doi.org/10.1016/j.meegid.2017.01.022
18)    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, ISSN(print/online): 1932-6203, URL/DOI: http://dx.doi.org/10.1371/journal.pone.0173408
19)    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
20)    Kulkarni-Kale, U. D. (2017). Disease to therapeutics via 3D structures: stories from viral world. Acta Crystallographica Section A: Foundations and Advances, 73, C576-C576. ISSN(print/online): 2053-2733, URL/DOI: http://dx.doi.org/10.1107/S2053273317089975
21)    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, ISSN(print/online): 1932-6203, URL/DOI: http://dx.doi.org/10.1371/journal.pone.0149350
22)    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, ISSN(print/online): 1439-0507, URL/DOI: http://dx.doi.org/10.1111/myc.12439
23)    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, ISSN(print/online): 2045-2322, URL/DOI: http://dx.doi.org/10.1038/srep27436
24)    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, ISSN(print/online): 1574-7891/1878-0261, URL/DOI: http://dx.doi.org/10.1016/j.molonc.2015.10.011
25)    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, ISSN(print/online): 0304-8608/1432-8798, URL/DOI: http://dx.doi.org/10.1007/s00705-016-2886-8
26)    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, ISSN(print/online): 2167-8359, URL/DOI: http://dx.doi.org/10.7717/peerj.2326
27)    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
28)    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, ISSN(print/online): 1756-0381, URL/DOI: http://dx.doi.org/10.1186/s13040-015-0067-z
29)    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, ISSN(print/online): 0166-0934/1879-0984, URL/DOI: http://dx.doi.org/10.1016/j.jviromet.2013.12.012
30)    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, ISSN(print/online): 1932-6203, URL/DOI: http://dx.doi.org/10.1371/journal.pone.0088981
31)    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, ISSN(print/online): 2210-3155/2210-3163, URL/DOI: http://dx.doi.org/10.2174/2210315511303010005
32)    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, ISSN(print/online): 1541-9061/1543-5180, URL/DOI: http://dx.doi.org/10.3109/15419061.2013.791683
33)    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
34)    Radhakrishnan, A., Raju, R., Tuladhar, N., Subbannayya, T., Thomas, J.K., Goel, R., Telikicherla, D., Palapetta, S.M., Rahiman, B.A., Venkatesh, D.D., Kulkarni-Kale, U., 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, ISSN(print/online): 1873-9601/1873-961X, URL/DOI: http://dx.doi.org/10.1007/s12079-012-0168-0
35)    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, ISSN(print/online): 1055-7903/1095-9513, URL/DOI: http://dx.doi.org/10.1016/j.ympev.2012.07.003
36)    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, ISSN(print/online): 1574-8936/2212-392X, URL/DOI: http://dx.doi.org/10.2174/157489312803900910

Publications Before 2011

38)    Kulkarni-Kale, U., Sawant, S., Chavan, V. (2010). Bioinformatics education in India. Briefings in Bioinformatics, 11 (6), 616-625. Google Scholar Citations, ISSN(print/online): 1467-5463/1477-4054, URL/DOI: http://dx.doi.org/10.1093/bib/bbq027
39)    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, ISSN(print/online): 0929-8665 /1875-5305 , URL/DOI: http://dx.doi.org/10.2174/092986607780989921
40)    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, ISSN(print/online): 0042-6822/1096-0341, URL/DOI: http://dx.doi.org/10.1016/j.virol.2006.09.040
41)    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, ISSN(print/online): 1471-2105, URL/DOI: http://dx.doi.org/10.1186/1471-2105-7-S5-S12
42)    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, ISSN(print/online): 0305-1048/1362-4962, URL/DOI: http://dx.doi.org/10.1093/nar/gki460
43)    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, ISSN(print/online): 0305-1048/1362-4962, URL/DOI: http://dx.doi.org/10.1093/nar/gkh098
45)    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, ISSN(print/online): 0090-1229, URL/DOI: http://dx.doi.org/10.1006/clin.1998.4582
46)    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, ISSN(print/online): 0161-5890/1872-9142, URL/DOI: http://dx.doi.org/10.1016/S0161-5890(97)00024-2
47)    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, ISSN(print/online): 0266-7061, URL/DOI: http://dx.doi.org/10.1093/bioinformatics/9.4.397
48)    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, ISSN(print/online): 0129-6264/1793-642X, URL/DOI: http://dx.doi.org/10.1142/S0129626493000289
49)    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, ISSN(print/online): 0022-2836/1089-8638, URL/DOI: http://dx.doi.org/10.1016/0022-2836(92)90261-H