{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T03:41:14Z","timestamp":1768016474433,"version":"3.49.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Network reconstruction of biological entities is very important for understanding biological processes and the organizational principles of biological systems. This work focuses on integrating both the literatures and microarray gene-expression data, and a combined literature mining and microarray analysis (LMMA) approach is developed to construct gene networks of a specific biological system.<\/jats:p>\n               <jats:p>Results: In the LMMA approach, a global network is first constructed using the literature-based co-occurrence method. It is then refined using microarray data through a multivariate selection procedure. An application of LMMA to the angiogenesis is presented. Our result shows that the LMMA-based network is more reliable than the co-occurrence-based network in dealing with multiple levels of KEGG gene, KEGG Orthology and pathway.<\/jats:p>\n               <jats:p>Availability: The LMMA program is available upon request.<\/jats:p>\n               <jats:p>Contact: \u00a0shaoli@mail.tsinghua.edu.cn<\/jats:p>\n               <jats:p>Supplementary Information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl363","type":"journal-article","created":{"date-parts":[[2006,7,6]],"date-time":"2006-07-06T01:54:39Z","timestamp":1152150879000},"page":"2143-2150","source":"Crossref","is-referenced-by-count":78,"title":["Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach"],"prefix":"10.1093","volume":"22","author":[{"given":"Shao","family":"Li","sequence":"first","affiliation":[{"name":"Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University \u00a0 Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lijiang","family":"Wu","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University \u00a0 Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongqi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University \u00a0 Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,7,4]]},"reference":[{"key":"2023012409134915800_b1","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell's functional organization","volume":"5","author":"Barabasi","year":"2004","journal-title":"Nat. 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