{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:19:15Z","timestamp":1785417555034,"version":"3.56.0"},"reference-count":48,"publisher":"SAGE Publications","issue":"3","license":[{"start":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T00:00:00Z","timestamp":1709251200000},"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":[[2024,3]]},"abstract":"<jats:p>\n                    <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                    is an opportunistic multidrug-resistant bacterial pathogen responsible for various health care-associated infections. The prediction of proteins that are essential for the survival of bacterial pathogens can greatly facilitate the drug development and discovery pipeline toward target identification. To this end, the present study reports a comprehensive computational approach integrating bioinformatics and systems biology-based methods to identify essential proteins of\n                    <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                    involved in vital processes. From the proteome of this pathogen, we predicted a total of 854 essential proteins based on sequence, protein\u2013protein interaction (PPI) and genome-scale metabolic model methods. These predicted essential proteins are involved in vital processes for cellular regulation such as translation, metabolism, and biosynthesis of essential factors, among others. Cluster analysis of the PPI network revealed the highly connected modules involved in the basic functionality of the organism. Further, the predicted consensus set of essential proteins of\n                    <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                    was evaluated by comparing them with existing resources (NetGenes and PATHOgenex) and literature. The findings of this study offer guidance toward understanding cell functionality, thereby facilitating the understanding of pathogen systems and providing a way forward to shortlist potential therapeutic candidates for developing novel antimicrobial agents against\n                    <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                    . In addition, the research strategy presented herein is a fusion of sequence and systems biology-based approaches that offers prospects as a model to predict essential proteins for other pathogens.\n                  <\/jats:p>","DOI":"10.1089\/omi.2024.0001","type":"journal-article","created":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T15:52:56Z","timestamp":1710345176000},"page":"138-147","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":1,"title":["Prediction of Essential Proteins of\n                    <i>Klebsiella pneumoniae<\/i>\n                    using Integrative Bioinformatics and Systems Biology Approach: Unveiling New Avenues for Drug Discovery"],"prefix":"10.1177","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4854-8238","authenticated-orcid":false,"given":"Gnanasekar","family":"Pranavathiyani","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3568-7047","authenticated-orcid":false,"given":"Archana","family":"Pan","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2024,3,25]]},"reference":[{"key":"e_1_3_6_2_1","doi-asserted-by":"publisher","DOI":"10.1242\/jcs.02714"},{"key":"e_1_3_6_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/elab038"},{"key":"e_1_3_6_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab128"},{"key":"e_1_3_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23588-w"},{"key":"e_1_3_6_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10081007"},{"key":"e_1_3_6_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-2"},{"key":"e_1_3_6_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2021.645955"},{"key":"e_1_3_6_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-023-03039-w"},{"key":"e_1_3_6_10_1","unstructured":"CDC.gov. Klebsiella pneumoniae in Healthcare Settings. 2023. Available from: https:\/\/www.cdc.gov\/hai\/organisms\/klebsiella\/klebsiella.html [Last accessed: December29 2023]."},{"key":"e_1_3_6_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.750662"},{"key":"e_1_3_6_12_1","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S418523"},{"key":"e_1_3_6_13_1","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-8-S4-S11"},{"key":"e_1_3_6_14_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00048-16"},{"key":"e_1_3_6_15_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00031-07"},{"key":"e_1_3_6_16_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.8b00702"},{"issue":"1","key":"e_1_3_6_17_1","first-page":"171","article-title":"Comprehensive review of the identification of essential genes using computational methods: Focusing on feature implementation and assessment","volume":"21","author":"Dong C","year":"2020","unstructured":"Dong C, , Jin Y-T, , Hua H-L, et al. Comprehensive review of the identification of essential genes using computational methods: Focusing on feature implementation and assessment. Brief Bioinform, 2020; 21(1):171\u2013181; doi: 10.1093\/bib\/bby116.","journal-title":"Brief Bioinform"},{"key":"e_1_3_6_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbabio.2015.12.004"},{"key":"e_1_3_6_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2021.105293"},{"key":"e_1_3_6_20_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.803608"},{"issue":"5","key":"e_1_3_6_21_1","first-page":"1004","article-title":"A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality","volume":"32","author":"Hawkey J","year":"2022","unstructured":"Hawkey J, , Vezina B, , Monk JM, et al. A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome Res, 2022; 32(5):1004\u20131014; doi: 10.1101\/gr.276289.121.","journal-title":"Genome Res"},{"key":"e_1_3_6_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2022.110301"},{"key":"e_1_3_6_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf693"},{"key":"e_1_3_6_24_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1157010"},{"key":"e_1_3_6_25_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01218-10"},{"key":"e_1_3_6_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1131"},{"key":"e_1_3_6_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa992"},{"issue":"1","key":"e_1_3_6_28_1","first-page":"D402","article-title":"BiGG Models 2020: Multi-strain genome-scale models and expansion across the phylogenetic tree","volume":"48","author":"Norsigian CJ","year":"2020","unstructured":"Norsigian CJ, , Pusarla N, , McConn JL, et al. BiGG Models 2020: Multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res, 2020; 48(D1):D402\u2013D406; doi: 10.1093\/nar\/gkz1054.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"e_1_3_6_29_1","first-page":"934","article-title":"Treatment options for colistin resistant Klebsiella pneumoniae: Present and future","volume":"8","author":"Petrosillo N","year":"2019","unstructured":"Petrosillo N, , Taglietti F, , Granata G. Treatment options for colistin resistant Klebsiella pneumoniae: Present and future. J Clin Med Res, 2019; 8(7): 934; doi: 10.3390\/jcm8070934.","journal-title":"J Clin Med Res"},{"key":"e_1_3_6_30_1","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-4-56"},{"key":"e_1_3_6_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-28916-7"},{"key":"e_1_3_6_32_1","doi-asserted-by":"publisher","DOI":"10.1042\/bj3350159"},{"key":"e_1_3_6_33_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.722198"},{"key":"e_1_3_6_34_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.773405"},{"key":"e_1_3_6_35_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2020.566702"},{"key":"e_1_3_6_36_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0059126"},{"key":"e_1_3_6_37_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"e_1_3_6_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-01052-5"},{"key":"e_1_3_6_39_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-26689-7"},{"key":"e_1_3_6_40_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1131"},{"key":"e_1_3_6_41_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-6382-6_19"},{"key":"e_1_3_6_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejps.2017.11.014"},{"key":"e_1_3_6_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1052"},{"key":"e_1_3_6_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad560"},{"key":"e_1_3_6_45_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01236"},{"key":"e_1_3_6_46_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep07187"},{"key":"e_1_3_6_47_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12941-017-0191-3"},{"key":"e_1_3_6_48_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-04868-8"},{"key":"e_1_3_6_49_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000140"}],"container-title":["OMICS: A Journal of Integrative Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/omi.2024.0001","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/omi.2024.0001","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/omi.2024.0001","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T23:06:53Z","timestamp":1777676813000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/full\/10.1089\/omi.2024.0001"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3]]},"references-count":48,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3]]}},"alternative-id":["10.1089\/omi.2024.0001"],"URL":"https:\/\/doi.org\/10.1089\/omi.2024.0001","relation":{},"ISSN":["1536-2310","1557-8100"],"issn-type":[{"value":"1536-2310","type":"print"},{"value":"1557-8100","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3]]}}}