{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:41Z","timestamp":1740185141263,"version":"3.37.3"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T00:00:00Z","timestamp":1656288000000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008333","name":"University of Alabama at Birmingham","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008333","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54TR001005"],"award-info":[{"award-number":["U54TR001005"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,24]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>In biology, graph layout algorithms can reveal comprehensive biological contexts by visually positioning graph nodes in their relevant neighborhoods. A layout software algorithm\/engine commonly takes a set of nodes and edges and produces layout coordinates of nodes according to edge constraints. However, current layout engines normally do not consider node, edge or node-set properties during layout and only curate these properties after the layout is created. Here, we propose a new layout algorithm, distance-bounded energy-field minimization algorithm (DEMA), to natively consider various biological factors, i.e., the strength of gene-to-gene association, the gene\u2019s relative contribution weight and the functional groups of genes, to enhance the interpretation of complex network graphs. In DEMA, we introduce a parameterized energy model where nodes are repelled by the network topology and attracted by a few biological factors, i.e., interaction coefficient, effect coefficient and fold change of gene expression. We generalize these factors as gene weights, protein\u2013protein interaction weights, gene-to-gene correlations and the gene set annotations\u2014four parameterized functional properties used in DEMA. Moreover, DEMA considers further attraction\/repulsion\/grouping coefficient to enable different preferences in generating network views. Applying DEMA, we performed two case studies using genetic data in autism spectrum disorder and Alzheimer\u2019s disease, respectively, for gene candidate discovery. Furthermore, we implement our algorithm as a plugin to Cytoscape, an open-source software platform for visualizing networks; hence, it is convenient. Our software and demo can be freely accessed at http:\/\/discovery.informatics.uab.edu\/dema.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac261","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T11:10:15Z","timestamp":1649934615000},"page":"i359-i368","source":"Crossref","is-referenced-by-count":1,"title":["DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features"],"prefix":"10.1093","volume":"38","author":[{"given":"Zhenyu","family":"Weng","sequence":"first","affiliation":[{"name":"Communication and Information Security Lab, Institute of Big Data Technologies, Shenzhen Graduate School, Peking University, Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zongliang","family":"Yue","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, University of Alabama at Birmingham , Birmingham, AL 35294, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuesheng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Communication and Information Security Lab, Institute of Big Data Technologies, Shenzhen Graduate School, Peking University, Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jake Yue","family":"Chen","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, University of Alabama at Birmingham , Birmingham, AL 35294, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,6,27]]},"reference":[{"key":"2023041407560470400_","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2105-4-2","article-title":"An automated method for finding molecular complexes in large protein interaction networks","volume":"4","author":"Bader","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023041407560470400_","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1126\/science.1173299","article-title":"Scale-free networks: a decade and beyond","volume":"325","author":"Barab\u00e1si","year":"2009","journal-title":"Science"},{"key":"2023041407560470400_","first-page":"361","article-title":"Gephi: an open source software for exploring and manipulating networks, Vol. 8","author":"Bastian","year":"2009","journal-title":"ICWSM, San Jose, California, USA"},{"key":"2023041407560470400_","doi-asserted-by":"crossref","first-page":"11277","DOI":"10.18632\/aging.103524","article-title":"Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response","volume":"12","author":"Bock","year":"2020","journal-title":"Aging (Albany NY)"},{"key":"2023041407560470400_","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s12864-017-3512-1","article-title":"HAPPI-2: a comprehensive and high-quality map of human annotated and predicted protein interactions","volume":"18","author":"Chen","year":"2017","journal-title":"BMC Genomics"},{"key":"2023041407560470400_","first-page":"367","article-title":"Mining Alzheimer disease relevant proteins from integrated protein interactome data","author":"Chen","year":"2006","journal-title":"Pacific Symposium on Biocomputing, Grand Wailea, Maui, Hawaii, USA"},{"key":"2023041407560470400_","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1142\/S0219720007002606","article-title":"A systems biology approach to the study of cisplatin drug resistance in ovarian cancers","volume":"5","author":"Chen","year":"2007","journal-title":"J. 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