{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T13:14:51Z","timestamp":1783257291543,"version":"3.54.6"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T00:00:00Z","timestamp":1783209600000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Science Foundation","award":["450627322"],"award-info":[{"award-number":["450627322"]}]},{"name":"German Science Foundation","award":["520750254"],"award-info":[{"award-number":["520750254"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Published biomedical experiments provide an increasingly rich collection of results and identify genes potentially involved in diverse biological mechanisms. However, individual studies are often confined to narrow experimental contexts and are restricted to single omics layers. Cross-study knowledge aggregation can broaden this perspective and enable the construction of global, context-aware gene rankings. Recent developments in natural language processing have made large-scale literature mining increasingly feasible. This enables the systematic extraction and fusion of symbolic knowledge from published experiments. We present pathXcite, a software that extracts genes associated with specific contexts, such as diseases or biological mechanisms from the literature, and ranks them by contextual relevance. These relevance-based gene rankings can compress a scientific context into a symbolic representation. This representation enables diverse downstream analyses, including cross-context comparisons, network-based analysis, enrichment analysis, and integration with experimental omics data. In multiple use cases, we show how our extraction and fusion strategy can be applied to uncover hidden aspects in biological data.<\/jats:p>","DOI":"10.1093\/bib\/bbag348","type":"journal-article","created":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T12:31:58Z","timestamp":1783254718000},"source":"Crossref","is-referenced-by-count":0,"title":["Literature-informed gene extraction and ranking for multimodal data fusion"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1261-3969","authenticated-orcid":false,"given":"Marietta","family":"Hamberger","sequence":"first","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Albert-Einstein-Allee 11, 89081 Ulm ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5153-0269","authenticated-orcid":false,"given":"Silke D","family":"Werle","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Albert-Einstein-Allee 11, 89081 Ulm ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9534-6295","authenticated-orcid":false,"given":"Johann M","family":"Kraus","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Albert-Einstein-Allee 11, 89081 Ulm ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4759-5254","authenticated-orcid":false,"given":"Hans A","family":"Kestler","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Albert-Einstein-Allee 11, 89081 Ulm ,","place":["Germany"]},{"name":"Leibniz Institute on Aging \u2013 Fritz Lipmann Institute , Beutenbergstra\u00dfe 11, 07745 Jena ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,5]]},"reference":[{"key":"2026070508315361600_ref1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mex.2024.102788","volume":"13","author":"Hagenauer","journal-title":"MethodsX"},{"key":"2026070508315361600_ref2","doi-asserted-by":"publisher","first-page":"3161","DOI":"10.1016\/j.csbj.2022.06.035","article-title":"Boolean modelling as a logic-based dynamic approach in systems medicine","volume":"20","author":"Hemedan","year":"2022","journal-title":"Comput Struct Biotechnol J"},{"key":"2026070508315361600_ref3","doi-asserted-by":"publisher","first-page":"2014","DOI":"10.3389\/fnhum.2014.00692","article-title":"Toward literature-based feature selection for diagnostic classification: a meta-analysis of resting-state fMRI in depression","volume":"8","author":"Sundermann","year":"2014","journal-title":"Front Hum Neurosci"},{"key":"2026070508315361600_ref4","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1186\/s12859-017-1905-4","article-title":"ADAGE signature analysis: differential expression analysis with data-defined gene sets","volume":"18","author":"Tan","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2026070508315361600_ref5","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.3390\/healthcare11091268","article-title":"A review on electronic health record text-mining for biomedical name entity recognition in healthcare domain","volume":"11","author":"Ahmad","year":"2023","journal-title":"Healthcare"},{"key":"2026070508315361600_ref6","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1093\/bib\/6.4.357","article-title":"What makes a gene name? Named entity recognition in the biomedical literature","volume":"6","author":"Leser","year":"2005","journal-title":"Brief Bioinform"},{"key":"2026070508315361600_ref7","doi-asserted-by":"publisher","first-page":"673","DOI":"10.3389\/fcell.2020.00673","article-title":"Named entity recognition and relation detection for biomedical information extraction","volume":"8","author":"Perera","year":"2020","journal-title":"Front Cell Dev Biol"},{"key":"2026070508315361600_ref8","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1038\/s42003-024-06177-7","article-title":"Rummagene: massive mining of gene sets from supporting materials of biomedical research publications","volume":"7","author":"Clarke","year":"2024","journal-title":"Commun Biol"},{"key":"2026070508315361600_ref9","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1016\/j.csbj.2021.03.022","article-title":"The language of proteins: NLP, machine learning & protein sequences","volume":"19","author":"Ofer","year":"2021","journal-title":"Comput Struct Biotechnol J"},{"key":"2026070508315361600_ref10","first-page":"949","article-title":"Application of natural language processing (NLP) in machine learning","volume-title":"3rd International Conference on Advancement in Electronics & Communication Engineering (AECE)","author":"Shetty","year":"2023"},{"key":"2026070508315361600_ref11","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1093\/jamia\/ocz200","article-title":"Deep learning in clinical natural language processing: a methodical review","volume":"27","author":"Wu","year":"2020","journal-title":"J Am Med Inform Assoc"},{"key":"2026070508315361600_ref12","doi-asserted-by":"publisher","first-page":"lqab090","DOI":"10.1093\/nargab\/lqab090","article-title":"OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis","volume":"3","author":"Baltoumas","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2026070508315361600_ref13","doi-asserted-by":"publisher","first-page":"W455","DOI":"10.1093\/nar\/gkr246","article-title":"G\u00e9nie: literature-based gene prioritization at multi genomic scale","volume":"39","author":"Fontaine","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref14","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad490","volume":"39","author":"Karatzas","journal-title":"Bioinformatics"},{"key":"2026070508315361600_ref15","doi-asserted-by":"publisher","first-page":"1973","DOI":"10.1093\/bioinformatics\/btz807","article-title":"GenCLiP 3: mining human genes\u2019 functions and regulatory networks from PubMed based on co-occurrences and natural language processing","volume":"36","author":"Wang","year":"2019","journal-title":"Bioinformatics"},{"key":"2026070508315361600_ref16","doi-asserted-by":"publisher","first-page":"W571","DOI":"10.1093\/nar\/gkz393","article-title":"Geneshot: search engine for ranking genes from arbitrary text queries","volume":"47","author":"Lachmann","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref17","doi-asserted-by":"publisher","first-page":"i277","DOI":"10.1093\/bioinformatics\/btn182","article-title":"Identifying gene-disease associations using centrality on a literature mined gene-interaction network","volume":"24","author":"\u00d6zg\u00fcr","year":"2008","journal-title":"Bioinformatics"},{"key":"2026070508315361600_ref18","doi-asserted-by":"publisher","first-page":"185","DOI":"10.6026\/97320630002185","article-title":"Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature","volume":"2","author":"Natarajan","year":"2007","journal-title":"Bioinformation"},{"key":"2026070508315361600_ref19","volume-title":"Modern Information Retrieval","author":"Baeza-Yates","year":"1999"},{"key":"2026070508315361600_ref20","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1145\/361219.361220","article-title":"A vector space model for automatic indexing","volume":"18","author":"Salton","year":"1975","journal-title":"Commun ACM"},{"key":"2026070508315361600_ref21","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1108\/eb026526","article-title":"A statistical interpretation of term specificity and its application in retrieval","volume":"28","author":"Sparck Jones","year":"1972","journal-title":"J Doc"},{"key":"2026070508315361600_ref22","article-title":"A general introduction to the E-utilities","volume-title":"Entrez Programming Utilities Help [Internet]","author":"Sayers","year":"2010"},{"key":"2026070508315361600_ref23","doi-asserted-by":"publisher","first-page":"W587","DOI":"10.1093\/nar\/gkz389","article-title":"PubTator central: automated concept annotation for biomedical full text articles","volume":"47","author":"Wei","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref24","doi-asserted-by":"publisher","first-page":"W540","DOI":"10.1093\/nar\/gkae235","article-title":"PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge","volume":"52","author":"Wei","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref25","doi-asserted-by":"publisher","first-page":"D672","DOI":"10.1093\/nar\/gkae909","article-title":"KEGG: biological systems database as a model of the real world","volume":"53","author":"Kanehisa","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref26","doi-asserted-by":"publisher","first-page":"D672","DOI":"10.1093\/nar\/gkad1025","article-title":"The Reactome pathway knowledgebase 2024","volume":"52","author":"Milacic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref27","doi-asserted-by":"crossref","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"The Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"2026070508315361600_ref28","doi-asserted-by":"crossref","first-page":"D1333","DOI":"10.1093\/nar\/gkad1005","article-title":"The human phenotype ontology in 2024: phenotypes around the world","volume":"52","author":"Gargano","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref29","doi-asserted-by":"publisher","first-page":"3069","DOI":"10.1093\/bioinformatics\/btv313","article-title":"DSigDB: drug signatures database for gene set analysis","volume":"31","author":"Yoo","year":"2015","journal-title":"Bioinformatics"},{"key":"2026070508315361600_ref30","doi-asserted-by":"publisher","first-page":"btad310","DOI":"10.1093\/bioinformatics\/btad310","article-title":"AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning","volume":"39","author":"Luo","year":"2023","journal-title":"Bioinformatics"},{"key":"2026070508315361600_ref31","doi-asserted-by":"publisher","first-page":"btad599","DOI":"10.1093\/bioinformatics\/btad599","article-title":"GNorm2: an improved gene name recognition and normalization system","volume":"39","author":"Wei","year":"2023","journal-title":"Bioinformatics"},{"key":"2026070508315361600_ref32","doi-asserted-by":"crossref","first-page":"baw005","DOI":"10.1093\/database\/baw005","article-title":"EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation","volume":"2016","author":"Pafilis","year":"2016","journal-title":"Database"},{"key":"2026070508315361600_ref33","doi-asserted-by":"publisher","DOI":"10.1007\/s10462-025-11321-8","volume":"58","author":"Seow","journal-title":"Artif Intell Rev"},{"key":"2026070508315361600_ref34","doi-asserted-by":"publisher","first-page":"bbac282","DOI":"10.1093\/bib\/bbac282","article-title":"BioRED: a rich biomedical relation extraction dataset","volume":"23","author":"Luo","year":"2022","journal-title":"Brief Bioinform"},{"key":"2026070508315361600_ref35","volume-title":"Nearest Neighbor (NN) Norms: NN Pattern Classification Techniques","author":"Dasarathy","year":"1991"},{"key":"2026070508315361600_ref36","volume-title":"Data Analysis, Machine Learning and Knowledge Discovery","author":"Burkovski"},{"key":"2026070508315361600_ref37","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1111\/cge.14026","article-title":"Hypermobile Ehlers\u2013Danlos syndrome: a review and a critical appraisal of published genetic research to date","volume":"101","author":"Scicluna","year":"2022","journal-title":"Clin Genet"},{"key":"2026070508315361600_ref38","doi-asserted-by":"publisher","first-page":"4040","DOI":"10.3390\/cells11244040","article-title":"RNA-Seq of dermal fibroblasts from patients with hypermobile Ehlers\u2013Danlos syndrome and hypermobility Spectrum disorders supports their categorization as a single entity with involvement of extracellular matrix degrading and proinflammatory Pathomechanisms","volume":"11","author":"Ritelli","year":"2022","journal-title":"Cells"},{"key":"2026070508315361600_ref39","first-page":"657","article-title":"M\u00e9moire Sur les \u00e9lections au scrutin","volume":"1781","author":"Borda","year":"1784","journal-title":"Histoire de l\u2019Acad\u00e9mie Royale des Sciences"},{"key":"2026070508315361600_ref40","doi-asserted-by":"publisher","first-page":"D845","DOI":"10.1093\/nar\/gkz1021","article-title":"The DisGeNET knowledge platform for disease genomics: 2019 update","volume":"48","author":"Pi\u00f1ero","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref41","doi-asserted-by":"publisher","first-page":"102436","DOI":"10.1016\/j.ctrv.2022.102436","article-title":"Beyond HER2: targeting the ErbB receptor family in breast cancer","volume":"109","author":"Drago","year":"2022","journal-title":"Cancer Treat Rev"},{"key":"2026070508315361600_ref42","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/s41523-023-00533-2","article-title":"Estrogen\/HER2 receptor crosstalk in breast cancer: combination therapies to improve outcomes for patients with hormone receptor-positive\/HER2-positive breast cancer","volume":"9","author":"Pegram","year":"2023","journal-title":"NPJ Breast Cancer"},{"key":"2026070508315361600_ref43","doi-asserted-by":"publisher","first-page":"788987","DOI":"10.3389\/fbioe.2021.788987","article-title":"Small-molecule induction promotes corneal endothelial cell differentiation from human iPS cells","volume":"9","author":"Chen","year":"2021","journal-title":"Front Bioeng Biotechnol"},{"key":"2026070508315361600_ref44","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1186\/s13578-021-00700-7","article-title":"Role of FoxO transcription factors in aging and age-related metabolic and neurodegenerative diseases","volume":"11","author":"Du","year":"2021","journal-title":"Cell Biosci"},{"key":"2026070508315361600_ref45","doi-asserted-by":"publisher","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref46","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1038\/nmeth.4077","article-title":"OmniPath: guidelines and gateway for literature-curated signaling pathway resources","volume":"13","author":"T\u00fcrei","year":"2016","journal-title":"Nat Methods"},{"key":"2026070508315361600_ref47","doi-asserted-by":"publisher","first-page":"3128","DOI":"10.1016\/j.molcel.2021.06.011","article-title":"Replication gaps are a key determinant of PARP inhibitor synthetic lethality with BRCA deficiency","volume":"81","author":"Cong","year":"2021","journal-title":"Mol Cell"},{"key":"2026070508315361600_ref48","doi-asserted-by":"publisher","first-page":"6579","DOI":"10.18632\/aging.204231","article-title":"ALKBH family members as novel biomarkers and prognostic factors in human breast cancer","volume":"14","author":"Chen","year":"2022","journal-title":"Aging"},{"key":"2026070508315361600_ref49","doi-asserted-by":"publisher","first-page":"8873","DOI":"10.12659\/MSM.919046","article-title":"Identification of hub genes using co-expression network analysis in breast cancer as a tool to predict different stages","volume":"25","author":"Fu","year":"2019","journal-title":"Med Sci Monit"},{"key":"2026070508315361600_ref50","doi-asserted-by":"publisher","first-page":"D679","DOI":"10.1093\/nar\/gkad960","article-title":"Wikipathways 2024: next generation pathway database","volume":"52","author":"Agrawal","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026070508315361600_ref51","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1080\/01621459.1963.10500845","article-title":"Hierarchical grouping to optimize an objective function","volume":"58","author":"Ward","year":"1963","journal-title":"J Am Stat Assoc"},{"key":"2026070508315361600_ref52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1145\/1852102.1852106","article-title":"A similarity measure for indefinite rankings","volume":"28","author":"Webber","year":"2010","journal-title":"ACM Trans Inf Syst"},{"key":"2026070508315361600_ref53","first-page":"583","article-title":"Cluster ensembles \u2013 a knowledge reuse framework for combining multiple partitions","volume":"3","author":"Strehl","year":"2002","journal-title":"J Mach Learn Res"},{"key":"2026070508315361600_ref54","first-page":"42","article-title":"The hematological complications of alcoholism","volume":"21","author":"Ballard","year":"1997","journal-title":"Alcohol Health Res World"},{"key":"2026070508315361600_ref55","doi-asserted-by":"publisher","first-page":"6390","DOI":"10.1128\/IAI.73.10.6390-6398.2005","article-title":"Massive destruction of malaria-parasitized red blood cells despite spleen closure","volume":"73","author":"Kr\u00fccken","year":"2005","journal-title":"Infect Immun"},{"key":"2026070508315361600_ref56","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1002\/hep.24256","article-title":"Hepatocyte-specific hypoxia-inducible factor-1$\\alpha$ is a determinant of lipid accumulation and liver injury in alcohol-induced steatosis in mice","volume":"53","author":"Nath","year":"2011","journal-title":"Hepatology"},{"key":"2026070508315361600_ref57","volume":"13","author":"Wei","journal-title":"Front Immunol"},{"key":"2026070508315361600_ref58","doi-asserted-by":"publisher","first-page":"3133096","DOI":"10.1155\/2022\/3133096","article-title":"To explore the molecular mechanism of acupuncture alleviating inflammation and treating obesity based on text mining","volume":"2022","author":"Du","year":"2022","journal-title":"Biomed Res Int"},{"key":"2026070508315361600_ref59","doi-asserted-by":"publisher","first-page":"4740141","DOI":"10.1155\/2022\/4740141","article-title":"Identification of key genes and molecular pathways in keratoconus: integrating text mining and bioinformatics analysis","volume":"2022","author":"Hu","year":"2022","journal-title":"Biomed Res Int"},{"key":"2026070508315361600_ref60","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.12677\/ACM.2020.107206","article-title":"Analysis of gene function enrichment and drug treatment of oral mucositis after radiotherapy and chemotherapy for head and neck tumor based on computer text mining","volume":"10","author":"Rong","year":"2020","journal-title":"Adv Clin Med"},{"key":"2026070508315361600_ref61","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1097\/RD9.0000000000000035","article-title":"Drug discovery and potential gene and pathway associated with polycystic ovary syndrome through text mining and biomedical databases","volume":"7","author":"Wang","year":"2022","journal-title":"Reprod Dev Med"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/4\/bbag348\/68697712\/bbag348.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/4\/bbag348\/68697712\/bbag348.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T12:32:00Z","timestamp":1783254720000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag348\/8724996"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7]]},"references-count":61,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag348","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7]]},"published":{"date-parts":[[2026,7]]},"article-number":"bbag348"}}