{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T19:36:27Z","timestamp":1789414587939,"version":"build-2803163510"},"reference-count":21,"publisher":"SAGE Publications","issue":"4","license":[{"start":{"date-parts":[[2016,4,1]],"date-time":"2016-04-01T00:00:00Z","timestamp":1459468800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["OMICS: A Journal of Integrative Biology"],"published-print":{"date-parts":[[2016,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The frequency of\n                    <jats:italic toggle=\"yes\">Candida<\/jats:italic>\n                    infections is currently rising, and thus adversely impacting global health. The situation is exacerbated by azole resistance developed by fungal pathogens.\n                    <jats:italic toggle=\"yes\">Candida tropicalis<\/jats:italic>\n                    is an opportunistic pathogen that causes candidiasis, for example, in immune-compromised individuals, cancer patients, and those who undergo organ transplantation. It is a member of the non-albicans group of\n                    <jats:italic toggle=\"yes\">Candida<\/jats:italic>\n                    that are known to be azole-resistant, and is frequently seen in individuals being treated for cancers, HIV-infection, and those who underwent bone marrow transplantation. Although the genome of\n                    <jats:italic toggle=\"yes\">C. tropicalis<\/jats:italic>\n                    was sequenced in 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out proteomics profiling of\n                    <jats:italic toggle=\"yes\">C. tropicalis<\/jats:italic>\n                    using high-resolution Fourier transform mass spectrometry. We identified 2743 proteins, thus mapping nearly 44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2591 proteins in the cell lysate of this yeast, we also analyzed the proteome of the conditioned media of\n                    <jats:italic toggle=\"yes\">C. tropicalis<\/jats:italic>\n                    culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons, and corrected 49 computationally-predicted gene models. To our knowledge, this is the first high-throughput proteomics study of\n                    <jats:italic toggle=\"yes\">C. tropicalis<\/jats:italic>\n                    validating predicted protein coding genes and refining the current genome annotation. The findings may prove useful in future global health efforts to fight against\n                    <jats:italic toggle=\"yes\">Candida<\/jats:italic>\n                    infections.\n                  <\/jats:p>","DOI":"10.1089\/omi.2015.0197","type":"journal-article","created":{"date-parts":[[2016,4,19]],"date-time":"2016-04-19T10:29:09Z","timestamp":1461061749000},"page":"239-247","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":19,"title":["Proteogenomics of\n                    <i>Candida tropicalis<\/i>\n                    \u2014An Opportunistic Pathogen with Importance for Global Health"],"prefix":"10.1177","volume":"20","author":[{"given":"Keshava K.","family":"Datta","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"KIIT University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun H.","family":"Patil","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"KIIT University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna","family":"Patel","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Amrita Vishwa Vidyapeetham","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gourav","family":"Dey","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Manipal University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anil K.","family":"Madugundu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Pondicherry University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santosh","family":"Renuse","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Amrita Vishwa Vidyapeetham","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyothi E.","family":"Kaviyil","sequence":"additional","affiliation":[{"name":"National Institute of Mental Health and Neurosciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raja","family":"Sekhar","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Pondicherry University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aryashree","family":"Arunima","sequence":"additional","affiliation":[{"name":"KIIT University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhavna","family":"Daswani","sequence":"additional","affiliation":[{"name":"National Institute for Research in Reproductive Health (ICMR)","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inderjeet","family":"Kaur","sequence":"additional","affiliation":[{"name":"International Center for Genetic Engineering and Biotechnology (ICGEB)","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyotirmaya","family":"Mohanty","sequence":"additional","affiliation":[{"name":"ICAR\u2014Central Institute of Freshwater Aquaculture","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ranjana","family":"Sinha","sequence":"additional","affiliation":[{"name":"ITC LSTC","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sangeeta","family":"Jaiswal","sequence":"additional","affiliation":[{"name":"KIIT University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Sivapriya","sequence":"additional","affiliation":[{"name":"Vision Research Foundation","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeshwanth","family":"Sonnathi","sequence":"additional","affiliation":[{"name":"Great Eastern Medical School & Hospital","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bharat B.","family":"Chattoo","sequence":"additional","affiliation":[{"name":"The M. S. University of Baroda","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harsha","family":"Gowda","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"KIIT University","place":["India"]},{"name":"Yenepoya University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raju","family":"Ravikumar","sequence":"additional","affiliation":[{"name":"National Institute of Mental Health and Neurosciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T. S. Keshava","family":"Prasad","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Yenepoya University","place":["India"]},{"name":"National Institute of Mental Health and Neurosciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2016,4,1]]},"reference":[{"key":"e_1_3_3_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/1559-0275-11-6"},{"key":"e_1_3_3_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08064"},{"key":"e_1_3_3_4_1","doi-asserted-by":"publisher","DOI":"10.3109\/1040841X.2010.489506"},{"key":"e_1_3_3_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201400157"},{"key":"e_1_3_3_6_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.4315"},{"key":"e_1_3_3_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201400168"},{"key":"e_1_3_3_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf543"},{"key":"e_1_3_3_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/1559-0275-11-5"},{"key":"e_1_3_3_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-011-1455-z"},{"key":"e_1_3_3_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3144"},{"key":"e_1_3_3_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1701"},{"key":"e_1_3_3_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2009.05.007"},{"key":"e_1_3_3_14_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr200827k"},{"key":"e_1_3_3_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/138.3.609"},{"key":"e_1_3_3_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jdermsci.2013.06.006"},{"key":"e_1_3_3_17_1","doi-asserted-by":"publisher","DOI":"10.1021\/ac026117i"},{"key":"e_1_3_3_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201000615"},{"key":"e_1_3_3_19_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.15.2.601"},{"key":"e_1_3_3_20_1","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6968.12049"},{"key":"e_1_3_3_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/ajcp\/3.5.347"},{"key":"e_1_3_3_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbs017"}],"container-title":["OMICS: A Journal of Integrative Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/omi.2015.0197","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/omi.2015.0197","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/omi.2015.0197","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T11:45:11Z","timestamp":1779191111000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1089\/omi.2015.0197"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,1]]},"references-count":21,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,4,1]]}},"alternative-id":["10.1089\/omi.2015.0197"],"URL":"https:\/\/doi.org\/10.1089\/omi.2015.0197","relation":{},"ISSN":["1536-2310","1557-8100"],"issn-type":[{"value":"1536-2310","type":"print"},{"value":"1557-8100","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,4,1]]}}}