Teacher Details
Urmila Kulkarni Kale
Bioinformatics Centre
urmila.kulkarni.kale@gmial.com
Research Areas : Bioinformatics, Comparative genomics, phyloinformatics, immunoinformatics, structural bioinformatics, database development, algorithm design
| 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
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| 2) | 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
|
| 3) | 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
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| 4) | 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
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| 5) | 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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| 6) | 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
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| 7) | 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
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| 8) | 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
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| 9) | 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
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| 10) | 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
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| 11) | 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
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| 12) | 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
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| 13) | 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
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| 14) | 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
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| 15) | 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
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| 16) | 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
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| 17) | 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
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| 18) | 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
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| 19) | 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
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| 20) | 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
|
| 21) | 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
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| 22) | 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
|
| 23) | 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
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| 24) | 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
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| 25) | 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
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| 26) | 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
|
| 27) | 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
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| 28) | 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
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| 29) | 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
|
| 30) | 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
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| 31) | 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
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| 32) | 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
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| 33) | 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
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| 34) | 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
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| 35) | 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
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| 36) | 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,
ISSN(print/online): 1745-7580,
URL/DOI: https://www.longdom.org/archive/imr-volume-7-issue-3-year-2011.html
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Publications Before 2011 |
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| 37) | 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
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| 38) | 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
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| 39) | 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
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| 40) | 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
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| 41) | 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
|
| 42) | 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
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| 43) | 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,
ISSN(print/online): 0042-6822/1096-0341,
URL/DOI: http://dx.doi.org/10.1006/viro.1999.9859
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| 44) | 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
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| 45) | 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
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| 46) | 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
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| 47) | 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
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| 48) | 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
|