{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:59:47Z","timestamp":1791223187289,"version":"4.1.0"},"reference-count":66,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key R&D Program of Xinjiang Uygur Autonomous Region","award":["2022B03018-2, 2022B03018-3"],"award-info":[{"award-number":["2022B03018-2, 2022B03018-3"]}]},{"DOI":"10.13039\/501100004761","name":"Natural Science Foundation of Hainan Province","doi-asserted-by":"publisher","award":["823QN249"],"award-info":[{"award-number":["823QN249"]}],"id":[{"id":"10.13039\/501100004761","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32322020"],"award-info":[{"award-number":["32322020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82060472"],"award-info":[{"award-number":["82060472"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>Genomic or transcriptomic sequencing guides the precision of cervical cancer (CC) diagnosis; however, the molecular profile of Asian patients remains poorly understood. We established a comprehensive multi-omics cohort comprising 112 tumor-normal adjacent tissue pairs from Chinese CC patients. Our integrated analysis revealed a mutational burden comparable to other populations, with three major mutational signatures primarily attributed to APOBEC-associated, age-associated, and DNA repair-associated biological categories. Multi-omics profiling elucidated the functional consequences of somatic mutations and copy number variations, identifying PIK3CA, EP300, and MPRIP as key driver events. We further uncovered both concordant and discordant activation patterns across cancer-related signaling pathways. Transcriptomic and proteomic analyses nominated cell cycle regulation, epithelial-mesenchymal transition, and LAMC2 as promising diagnostic and therapeutic targets. Comprehensive immune characterization enabled stratification of patients into three major immune phenotypes with varying microenvironmental profiles. This study provides valuable resources and novel insights into the molecular architecture of cervical cancer in the Chinese population, identifying potential biomarkers to guide precision detection and immunotherapy strategies.<\/jats:p>","DOI":"10.1371\/journal.pbio.3004029","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:39:23Z","timestamp":1791221963000},"page":"e3004029","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated multi-omics analysis reveals the molecular landscape and therapeutic strategies in Chinese cervical cancer patients"],"prefix":"10.1371","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9244-9950","authenticated-orcid":true,"given":"Tao","family":"Pan","sequence":"first","affiliation":[{"name":"Hainan Medical University","place":["Haikou, China"],"department":["Key Laboratory of Reproductive Health Diseases Research and Translation of Ministry of Education & Key Laboratory for Human Reproductive Medicine and Genetic Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Schoo..."]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xucui","family":"Zhuang","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology","place":["Wuhan, China"],"department":["Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College"]},{"name":"Huazhong University of Science and Technology","place":["Wuhan, China"],"department":["Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hainan Medical University","place":["Haikou, China"],"department":["Key Laboratory of Reproductive Health Diseases Research and Translation of Ministry of Education & Key Laboratory for Human Reproductive Medicine and Genetic Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Schoo..."]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiyu","family":"Guo","sequence":"additional","affiliation":[{"name":"Harbin Medical University","place":["Harbin, China"],"department":["School of Interdisciplinary Medicine and Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Si","family":"Li","sequence":"additional","affiliation":[{"name":"Harbin Medical University","place":["Harbin, China"],"department":["School of Interdisciplinary Medicine and Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Can","family":"Zhang","sequence":"additional","affiliation":[{"name":"Harbin Medical University","place":["Harbin, China"],"department":["School of Interdisciplinary Medicine and Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Han","sequence":"additional","affiliation":[{"name":"People\u2019s Hospital of Xinjiang Uygur Autonomous Region","place":["Urumqi, China"],"department":["Department of Gynecology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuxia","family":"Li","sequence":"additional","affiliation":[{"name":"Shihezi University","place":["Shihezi, China"],"department":["Department of Gynecology, First Affiliated Hospital"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yueying","family":"Gao","sequence":"additional","affiliation":[{"name":"Harbin Medical University","place":["Harbin, China"],"department":["School of Interdisciplinary Medicine and Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyang","family":"Yu","sequence":"additional","affiliation":[{"name":"Hainan Medical University","place":["Haikou, China"],"department":["Key Laboratory of Reproductive Health Diseases Research and Translation of Ministry of Education & Key Laboratory for Human Reproductive Medicine and Genetic Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Schoo..."]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1914-0727","authenticated-orcid":true,"given":"Yongsheng","family":"Li","sequence":"additional","affiliation":[{"name":"Hainan Medical University","place":["Haikou, China"],"department":["Key Laboratory of Reproductive Health Diseases Research and Translation of Ministry of Education & Key Laboratory for Human Reproductive Medicine and Genetic Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Schoo..."]},{"name":"Harbin Medical University","place":["Harbin, China"],"department":["School of Interdisciplinary Medicine and Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaoyang","family":"Sun","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology","place":["Wuhan, China"],"department":["Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College"]},{"name":"Huazhong University of Science and Technology","place":["Wuhan, China"],"department":["Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"issue":"2","key":"pbio.3004029.ref001","doi-asserted-by":"crossref","DOI":"10.1016\/S2214-109X(19)30482-6","article-title":"Estimates of incidence and mortality of cervical cancer in 2018: a worldwide analysis","volume":"8","author":"M Arbyn","year":"2020","journal-title":"Lancet Glob Health"},{"issue":"7488","key":"pbio.3004029.ref002","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nature12881","article-title":"Landscape of genomic alterations in cervical carcinomas","volume":"506","author":"AI Ojesina","year":"2014","journal-title":"Nature"},{"issue":"7645","key":"pbio.3004029.ref003","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/nature21386","article-title":"Integrated genomic and molecular characterization of cervical cancer","volume":"543","year":"2017","journal-title":"Nature"},{"issue":"1","key":"pbio.3004029.ref004","doi-asserted-by":"crossref","first-page":"5818","DOI":"10.1038\/s41467-022-33544-x","article-title":"Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance","volume":"13","author":"A Chakravarthy","year":"2022","journal-title":"Nat Commun"},{"issue":"6","key":"pbio.3004029.ref005","doi-asserted-by":"crossref","first-page":"1833","DOI":"10.1016\/j.celrep.2014.05.012","article-title":"APOBEC-mediated cytosine deamination links PIK3CA helical domain mutations to human papillomavirus-driven tumor development","volume":"7","author":"S Henderson","year":"2014","journal-title":"Cell Rep"},{"issue":"8","key":"pbio.3004029.ref006","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1038\/s41588-020-0673-7","article-title":"Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes","volume":"52","author":"A Gagliardi","year":"2020","journal-title":"Nat Genet"},{"issue":"3","key":"pbio.3004029.ref007","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/s11912-020-0873-4","article-title":"PARP inhibitors in gynecologic cancers: what is the next big development?","volume":"22","author":"M Lightfoot","year":"2020","journal-title":"Curr Oncol Rep"},{"issue":"7959","key":"pbio.3004029.ref008","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1038\/s41586-023-05940-w","article-title":"PI3K\u03b2 controls immune evasion in PTEN-deficient breast tumours","volume":"617","author":"JS Bergholz","year":"2023","journal-title":"Nature"},{"issue":"2","key":"pbio.3004029.ref009","article-title":"Integrated proteogenomic characterization of HBV-related hepatocellular carcinoma","volume":"179","author":"Q Gao","year":"2019","journal-title":"Cell"},{"issue":"4","key":"pbio.3004029.ref010","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2019.10.007","article-title":"Integrated proteogenomic characterization of clear cell renal cell carcinoma","volume":"179","author":"DJ Clark","year":"2019","journal-title":"Cell"},{"issue":"12","key":"pbio.3004029.ref011","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1080\/14737140.2018.1527688","article-title":"A comprehensive review of protein kinase inhibitors for cancer therapy","volume":"18","author":"R Kannaiyan","year":"2018","journal-title":"Expert Rev Anticancer Ther"},{"issue":"4","key":"pbio.3004029.ref012","doi-asserted-by":"crossref","first-page":"908","DOI":"10.3390\/molecules23040908","article-title":"PKIDB: a curated, annotated and updated database of protein kinase inhibitors in clinical trials","volume":"23","author":"F Carles","year":"2018","journal-title":"Molecules"},{"issue":"10","key":"pbio.3004029.ref013","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1158\/0008-5472.CAN-19-2687","article-title":"LncSpA: LncRNA spatial atlas of expression across normal and cancer tissues","volume":"80","author":"D Lv","year":"2020","journal-title":"Cancer Res"},{"issue":"10","key":"pbio.3004029.ref014","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1038\/s41419-021-04229-y","article-title":"Stat1 confers sensitivity to radiation in cervical cancer cells by controlling Parp1 levels: a new perspective for Parp1 inhibition","volume":"12","author":"G Raspaglio","year":"2021","journal-title":"Cell Death Dis"},{"issue":"1","key":"pbio.3004029.ref015","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s13059-017-1349-1","article-title":"xCell: digitally portraying the tissue cellular heterogeneity landscape","volume":"18","author":"D Aran","year":"2017","journal-title":"Genome Biol"},{"issue":"1","key":"pbio.3004029.ref016","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13073-020-0721-z","article-title":"Large-scale public data reuse to model immunotherapy response and resistance","volume":"12","author":"J Fu","year":"2020","journal-title":"Genome Med"},{"issue":"4","key":"pbio.3004029.ref017","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1002\/(SICI)1098-2264(199708)19:4<233::AID-GCC5>3.0.CO;2-Y","article-title":"Advanced-stage cervical carcinomas are defined by a recurrent pattern of chromosomal aberrations revealing high genetic instability and a consistent gain of chromosome arm 3q","volume":"19","author":"K Heselmeyer","year":"1997","journal-title":"Genes Chromosomes Cancer"},{"issue":"8801","key":"pbio.3004029.ref018","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1016\/0140-6736(92)90662-M","article-title":"Clonal p53 mutation in primary cervical cancer: association with human-papillomavirus-negative tumours","volume":"339","author":"T Crook","year":"1992","journal-title":"Lancet"},{"issue":"3","key":"pbio.3004029.ref019","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/j.ygyno.2012.12.019","article-title":"PIK3CA mutational status and overall survival in patients with cervical cancer treated with radical chemoradiotherapy","volume":"128","author":"JB McIntyre","year":"2013","journal-title":"Gynecol Oncol"},{"issue":"3","key":"pbio.3004029.ref020","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.ygyno.2007.01.045","article-title":"Inverse correlation between RASSF1A hypermethylation, KRAS and BRAF mutations in cervical adenocarcinoma","volume":"105","author":"S Kang","year":"2007","journal-title":"Gynecol Oncol"},{"key":"pbio.3004029.ref021","doi-asserted-by":"crossref","first-page":"17588359211038477","DOI":"10.1177\/17588359211038477","article-title":"TGFBR2 mutation predicts resistance to immune checkpoint inhibitors in patients with non-small cell lung cancer","volume":"13","author":"T Li","year":"2021","journal-title":"Ther Adv Med Oncol"},{"issue":"7700","key":"pbio.3004029.ref022","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s41586-018-0018-1","article-title":"Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive breast cancer","volume":"556","author":"S Dasgupta","year":"2018","journal-title":"Nature"},{"key":"pbio.3004029.ref023","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/1471-230X-13-122","article-title":"Gene expression analysis of a Helicobacter pylori-infected and high-salt diet-treated mouse gastric tumor model: identification of CD177 as a novel prognostic factor in patients with gastric cancer","volume":"13","author":"T Toyoda","year":"2013","journal-title":"BMC Gastroenterol"},{"issue":"12","key":"pbio.3004029.ref024","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1038\/nbt.2038","article-title":"Single-cell dissection of transcriptional heterogeneity in human colon tumors","volume":"29","author":"P Dalerba","year":"2011","journal-title":"Nat Biotechnol"},{"issue":"11","key":"pbio.3004029.ref025","doi-asserted-by":"crossref","first-page":"110970","DOI":"10.1016\/j.celrep.2022.110970","article-title":"YAP1 maintains active chromatin state in head and neck squamous cell carcinomas that promotes tumorigenesis through cooperation with BRD4","volume":"39","author":"N Chen","year":"2022","journal-title":"Cell Rep"},{"issue":"1","key":"pbio.3004029.ref026","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1038\/s41467-023-39901-8","article-title":"ACTL6A protects gastric cancer cells against ferroptosis through induction of glutathione synthesis","volume":"14","author":"Z Yang","year":"2023","journal-title":"Nat Commun"},{"key":"pbio.3004029.ref027","doi-asserted-by":"crossref","first-page":"17002","DOI":"10.1038\/sigtrans.2017.2","article-title":"Let\u2019s talk about Secs: Sec61, Sec62 and Sec63 in signal transduction, oncology and personalized medicine","volume":"2","author":"M Linxweiler","year":"2017","journal-title":"Signal Transduct Target Ther"},{"issue":"12","key":"pbio.3004029.ref028","doi-asserted-by":"crossref","first-page":"2175","DOI":"10.1038\/s41588-023-01570-0","article-title":"Multiomic analysis of cervical squamous cell carcinoma identifies cellular ecosystems with biological and clinical relevance","volume":"55","author":"J Fan","year":"2023","journal-title":"Nat Genet"},{"key":"pbio.3004029.ref029","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/j.biopha.2017.09.143","article-title":"MicroRNA-150 promotes cell proliferation, migration, and invasion of cervical cancer through targeting PDCD4","volume":"97","author":"Z Zhang","year":"2018","journal-title":"Biomed Pharmacother"},{"issue":"39","key":"pbio.3004029.ref030","doi-asserted-by":"crossref","first-page":"5106","DOI":"10.1038\/onc.2016.54","article-title":"Scaffold protein FHL2 facilitates MDM2-mediated degradation of IER3 to regulate proliferation of cervical cancer cells","volume":"35","author":"H Jin","year":"2016","journal-title":"Oncogene"},{"issue":"2","key":"pbio.3004029.ref031","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1002\/cac2.12240","article-title":"Proteomics profiling of colorectal cancer progression identifies PLOD2 as a potential therapeutic target","volume":"42","author":"Y Shao","year":"2022","journal-title":"Cancer Commun (Lond)"},{"key":"pbio.3004029.ref032","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s12935-017-0420-z","article-title":"Hypoxia and TGF-\u03b21 induced PLOD2 expression improve the migration and invasion of cervical cancer cells by promoting epithelial-to-mesenchymal transition (EMT) and focal adhesion formation","volume":"17","author":"F Xu","year":"2017","journal-title":"Cancer Cell Int"},{"issue":"6","key":"pbio.3004029.ref033","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1158\/1078-0432.CCR-22-0794","article-title":"LAMC2 regulates key transcriptional and targetable effectors to support pancreatic cancer growth","volume":"29","author":"O Erice","year":"2023","journal-title":"Clin Cancer Res"},{"issue":"1","key":"pbio.3004029.ref034","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1186\/s13046-022-02516-w","article-title":"LAMC2 marks a tumor-initiating cell population with an aggressive signature in pancreatic cancer","volume":"41","author":"DD Cave","year":"2022","journal-title":"J Exp Clin Cancer Res"},{"issue":"29","key":"pbio.3004029.ref035","article-title":"Single-nucleus RNA sequencing and spatial transcriptomics reveal the immunological microenvironment of cervical squamous cell carcinoma","volume":"9","author":"Z Ou","year":"2022","journal-title":"Adv Sci (Weinh)"},{"issue":"6","key":"pbio.3004029.ref036","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/s41568-019-0143-7","article-title":"The broken cycle: E2F dysfunction in cancer","volume":"19","author":"LN Kent","year":"2019","journal-title":"Nat Rev Cancer"},{"issue":"1","key":"pbio.3004029.ref037","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/s13046-022-02412-3","article-title":"NCAPD3 enhances Warburg effect through c-myc and E2F1 and promotes the occurrence and progression of colorectal cancer","volume":"41","author":"Z Jing","year":"2022","journal-title":"J Exp Clin Cancer Res"},{"issue":"1","key":"pbio.3004029.ref038","doi-asserted-by":"crossref","first-page":"2835","DOI":"10.1038\/s41467-022-30264-0","article-title":"Inhibition of the CDK2 and Cyclin A complex leads to autophagic degradation of CDK2 in cancer cells","volume":"13","author":"J Zhang","year":"2022","journal-title":"Nat Commun"},{"issue":"1","key":"pbio.3004029.ref039","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.cell.2015.08.063","article-title":"CDK7-dependent transcriptional addiction in triple-negative breast cancer","volume":"163","author":"Y Wang","year":"2015","journal-title":"Cell"},{"issue":"1","key":"pbio.3004029.ref040","doi-asserted-by":"crossref","DOI":"10.1016\/j.ccell.2019.11.003","article-title":"CDK7 inhibition potentiates genome instability triggering anti-tumor immunity in small cell lung cancer","volume":"37","author":"H Zhang","year":"2020","journal-title":"Cancer Cell"},{"issue":"11","key":"pbio.3004029.ref041","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41590-021-01047-4","article-title":"Tumor-induced reshuffling of lipid composition on the endoplasmic reticulum membrane sustains macrophage survival and pro-tumorigenic activity","volume":"22","author":"G Di Conza","year":"2021","journal-title":"Nat Immunol"},{"issue":"34","key":"pbio.3004029.ref042","article-title":"Peroxidation of polyunsaturated fatty acids by lipoxygenases drives ferroptosis","volume":"113","author":"WS Yang","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pbio.3004029.ref043","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nchembio.2238","article-title":"Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis","volume":"13","author":"VE Kagan","year":"2017","journal-title":"Nat Chem Biol"},{"issue":"7","key":"pbio.3004029.ref044","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/s41568-022-00459-0","article-title":"Targeting ferroptosis as a vulnerability in cancer","volume":"22","author":"G Lei","year":"2022","journal-title":"Nat Rev Cancer"},{"issue":"1","key":"pbio.3004029.ref045","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/s12967-022-03370-2","article-title":"TPI1 activates the PI3K\/AKT\/mTOR signaling pathway to induce breast cancer progression by stabilizing CDCA5","volume":"20","author":"X Jin","year":"2022","journal-title":"J Transl Med"},{"issue":"1","key":"pbio.3004029.ref046","doi-asserted-by":"crossref","first-page":"100211","DOI":"10.1016\/j.xgen.2022.100211","article-title":"Multi-omics characterization of silent and productive HPV integration in cervical cancer","volume":"3","author":"J Fan","year":"2023","journal-title":"Cell Genom"},{"issue":"12","key":"pbio.3004029.ref047","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"J Cox","year":"2008","journal-title":"Nat Biotechnol"},{"issue":"14","key":"pbio.3004029.ref048","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"14","key":"pbio.3004029.ref049","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1093\/bioinformatics\/bts271","article-title":"Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs","volume":"28","author":"CT Saunders","year":"2012","journal-title":"Bioinformatics"},{"issue":"3","key":"pbio.3004029.ref050","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"DC Koboldt","year":"2012","journal-title":"Genome Res"},{"issue":"3","key":"pbio.3004029.ref051","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btr665","article-title":"SomaticSniper: identification of somatic point mutations in whole genome sequencing data","volume":"28","author":"DE Larson","year":"2012","journal-title":"Bioinformatics"},{"issue":"9","key":"pbio.3004029.ref052","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"issue":"16","key":"pbio.3004029.ref053","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"K Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pbio.3004029.ref054","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004873","article-title":"CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing","volume":"12","author":"E Talevich","year":"2016","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"pbio.3004029.ref055","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"CH Mermel","year":"2011","journal-title":"Genome Biol"},{"issue":"7457","key":"pbio.3004029.ref056","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature12213","article-title":"Mutational heterogeneity in cancer and the search for new cancer-associated genes","volume":"499","author":"MS Lawrence","year":"2013","journal-title":"Nature"},{"issue":"12","key":"pbio.3004029.ref057","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/btl117","article-title":"Pvclust: an R package for assessing the uncertainty in hierarchical clustering","volume":"22","author":"R Suzuki","year":"2006","journal-title":"Bioinformatics"},{"key":"pbio.3004029.ref058","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1038\/s41523-018-0066-6","article-title":"Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer","volume":"4","author":"Z Sztupinszki","year":"2018","journal-title":"NPJ Breast Cancer"},{"issue":"17","key":"pbio.3004029.ref059","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"S Chen","year":"2018","journal-title":"Bioinformatics"},{"issue":"9","key":"pbio.3004029.ref060","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown","volume":"11","author":"M Pertea","year":"2016","journal-title":"Nat Protoc"},{"issue":"43","key":"pbio.3004029.ref061","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"pbio.3004029.ref062","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"G Yu","year":"2012","journal-title":"OMICS"},{"issue":"12","key":"pbio.3004029.ref063","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"A Liberzon","year":"2011","journal-title":"Bioinformatics"},{"issue":"12","key":"pbio.3004029.ref064","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btq170","article-title":"ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking","volume":"26","author":"MD Wilkerson","year":"2010","journal-title":"Bioinformatics"},{"key":"pbio.3004029.ref065","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"K Yoshihara","year":"2013","journal-title":"Nat Commun"},{"key":"pbio.3004029.ref066","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"S H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinformatics"}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3004029","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:39:35Z","timestamp":1791221975000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3004029"}},"subtitle":[],"editor":[{"given":"Elena","family":"Rainero","sequence":"first","affiliation":[{"name":"The University of Sheffield","place":["UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,5]]},"references-count":66,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,10,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.3004029","relation":{},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,5]]}}}