{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T18:21:18Z","timestamp":1764872478869,"version":"3.41.2"},"reference-count":44,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,11,28]],"date-time":"2020-11-28T00:00:00Z","timestamp":1606521600000},"content-version":"vor","delay-in-days":332,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The exponential growth of genomic\/genetic data in the era of Big Data demands new solutions for making these data findable, accessible, interoperable and reusable. In this article, we present a web-based platform named Gene Expression Time-Course Research (GETc) Platform that enables the discovery and visualization of time-course gene expression data and analytical results from the NIH\/NCBI-sponsored Gene Expression Omnibus (GEO). The analytical results are produced from an analytic pipeline based on the ordinary differential equation model. Furthermore, in order to extract scientific insights from these results and disseminate the scientific findings, close and efficient collaborations between domain-specific experts from biomedical and scientific fields and data scientists is required. Therefore, GETc provides several recommendation functions and tools to facilitate effective collaborations. GETc platform is a very useful tool for researchers from the biomedical genomics community to present and communicate large numbers of analysis results from GEO. It is generalizable and broadly applicable across different biomedical research areas. GETc is a user-friendly and efficient web-based platform freely accessible at http:\/\/genestudy.org\/<\/jats:p>","DOI":"10.1093\/database\/baaa074","type":"journal-article","created":{"date-parts":[[2020,8,11]],"date-time":"2020-08-11T12:26:18Z","timestamp":1597148778000},"source":"Crossref","is-referenced-by-count":4,"title":["An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries"],"prefix":"10.1093","volume":"2020","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2997-5314","authenticated-orcid":false,"given":"Braja Gopal","family":"Patra","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health,The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00a0Babak","family":"Soltanalizadeh","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00a0Nan","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00a0Leqing","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vahed","family":"Maroufy","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00a0Canglin","family":"Wu","sequence":"additional","affiliation":[{"name":"TechWave International. Inc., Houston, TX, USA\u00a0and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00a0W Jim","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00a0Kirk","family":"Roberts","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hulin","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"},{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashraf","family":"Yaseen","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,28]]},"reference":[{"key":"2020112809064884600_R1","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"Ncbi geo: archive for functional genomics data sets\u2013update","volume":"41","author":"Barrett","year":"2012","journal-title":"Nucleic acids research"},{"volume-title":"Database","year":"2017","author":"Roberts","key":"2020112809064884600_R2"},{"key":"2020112809064884600_R3","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1093\/jamia\/ocx121","article-title":"Datamed\u2013an open source discovery index for finding biomedical datasets","volume":"25","author":"Chen","year":"2018","journal-title":"Journal of the American Medical Informatics Association"},{"key":"2020112809064884600_R4","first-page":"pages 257","article-title":"Datacite-a global registration agency for research data","author":"Brase","year":"2009"},{"key":"2020112809064884600_R5","doi-asserted-by":"crossref","first-page":"S231","DOI":"10.1093\/bioinformatics\/18.suppl_2.S231","article-title":"The mutual information: detecting and evaluating dependencies between variables","volume":"18","author":"Steuer","year":"2002","journal-title":"Bioinformatics"},{"key":"2020112809064884600_R6","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1126\/science.1087447","article-title":"A gene-coexpression network for global discovery of conserved genetic modules","volume":"302","author":"Stuart","year":"2003","journal-title":"Science"},{"key":"2020112809064884600_R7","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-7-S1-S7","article-title":"Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context","volume":"7","author":"Margolin","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2020112809064884600_R8","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/0022-5193(73)90247-6","article-title":"Boolean formalization of genetic control circuits","volume":"42","author":"Thomas","year":"1973","journal-title":"Journal of theoretical biology"},{"key":"2020112809064884600_R9","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1093\/bioinformatics\/16.8.727","article-title":"Inferring qualitative relations in genetic networks and metabolic pathways","volume":"16","author":"Akutsu","year":"2000","journal-title":"Bioinformatics"},{"key":"2020112809064884600_R10","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/bioinformatics\/18.2.261","article-title":"Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks","volume":"18","author":"Shmulevich","year":"2002","journal-title":"Bioinformatics"},{"key":"2020112809064884600_R11","doi-asserted-by":"crossref","first-page":"S85","DOI":"10.1098\/rsif.2008.0132.focus","article-title":"Boolean network models of cellular regulation: prospects and limitations","volume":"5","author":"Bornholdt","year":"2008","journal-title":"Journal of the Royal Society Interface"},{"key":"2020112809064884600_R12","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1089\/106652700750050961","article-title":"Using Bayesian networks to analyze expression data","volume":"7","author":"Friedman","year":"2000","journal-title":"Journal of Computational Biology"},{"key":"2020112809064884600_R13","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/bib\/4.3.228","article-title":"Inferring gene networks from time series microarray data using dynamic Bayesian networks","volume":"4","author":"Kim","year":"2003","journal-title":"Briefings in Bioinformatics"},{"key":"2020112809064884600_R14","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/bioinformatics\/bth463","article-title":"A new dynamic Bayesian network (dbn) approach for identifying gene regulatory networks from time course microarray data","volume":"21","author":"Zou","year":"2004","journal-title":"Bioinformatics"},{"key":"2020112809064884600_R15","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.0030129","article-title":"A primer on learning in Bayesian networks for computational biology","volume":"3","author":"Needham","year":"2007","journal-title":"PLoS computational biology"},{"key":"2020112809064884600_R16","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1198\/jasa.2011.ap10194","article-title":"High-dimensional odes coupled with mixed-effects modeling techniques for dynamic gene regulatory network identification","volume":"106","author":"Lu","year":"2011","journal-title":"Journal of the American Statistical Association"},{"key":"2020112809064884600_R17","article-title":"Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations","volume":"9","author":"Wu","year":"2014","journal-title":"PloS one"},{"key":"2020112809064884600_R18","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1007\/s10928-014-9365-1","article-title":"Dynamic transcriptional signatures and network responses for clinical symptoms in influenza-infected human subjects using systems biology approaches","volume":"41","author":"Linel","year":"2014","journal-title":"Journal of Pharmacokinetics and Pharmacodynamics"},{"key":"2020112809064884600_R19","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1177\/0962280217746719","article-title":"A big data pipeline: Identifying dynamic gene regulatory networks from time-course gene expression omnibus data with applications to influenza infection","volume":"27","author":"Carey","year":"2018","journal-title":"Statistical methods in medical research"},{"key":"2020112809064884600_R20","first-page":"pages 1149","article-title":"Determining the user intent of web search engine queries","author":"Jansen","year":"2007"},{"key":"2020112809064884600_R21","first-page":"pages 548","article-title":"Combining a co-occurrence-based and a semantic measure for entity linking","author":"Nunes","year":"2013"},{"key":"2020112809064884600_R22","first-page":"pages 36","article-title":"Dataset recommendation for data linking: An intensional approach","author":"Ellefi","year":"2016"},{"volume-title":"Predicting and recommending relevant datasets in complex environments","year":"2018","author":"Srivastava","key":"2020112809064884600_R23"},{"key":"2020112809064884600_R24","first-page":"pages 116","article-title":"Citeseer: An autonomous web agent for automatic retrieval and identification of interesting publications","author":"Bollacker","year":"1998"},{"key":"2020112809064884600_R25","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/s00799-015-0156-0","article-title":"Research-paper recommender systems: a literature survey","volume":"17","author":"Beel","year":"2016","journal-title":"International Journal on Digital Libraries"},{"key":"2020112809064884600_R26","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0158423","article-title":"Science concierge: A fast content-based recommendation system for scientific publications","volume":"11","author":"Achakulvisut","year":"2016","journal-title":"PloS one"},{"key":"2020112809064884600_R27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0184516","article-title":"A collaborative approach for research paper recommender system","volume":"12","author":"Haruna","year":"2017","journal-title":"PloS one"},{"key":"2020112809064884600_R28","first-page":"pages 459","article-title":"Introducing Docear\u2019s research paper recommender system","author":"Beel","year":"2013"},{"key":"2020112809064884600_R29","first-page":"pages 448","article-title":"Collaborative topic modeling for recommending scientific articles","author":"Wang","year":"2011"},{"key":"2020112809064884600_R30","first-page":"pages 316","article-title":"Scientific publication recommendations based on collaborative citation networks","author":"Huynh","year":"2012"},{"key":"2020112809064884600_R31","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1093\/bioinformatics\/btp049","article-title":"Sciminer: web-based literature mining tool for target identification and functional enrichment analysis","volume":"25","author":"Hur","year":"2009","journal-title":"Bioinformatics"},{"key":"2020112809064884600_R32","first-page":"267","article-title":"Pure: a Pubmed article recommendation system based on content-based filtering","volume":"18","author":"Yoneya","year":"2007","journal-title":"Genome informatics"},{"key":"2020112809064884600_R33","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-8-423","article-title":"Pubmed related articles: a probabilistic topic-based model for content similarity","volume":"8","author":"Lin","year":"2007","journal-title":"BMC bioinformatics"},{"key":"2020112809064884600_R34","first-page":"pages 121","article-title":"Co-author relationship prediction in heterogeneous bibliographic networks","author":"Sun","year":"2011"},{"key":"2020112809064884600_R35","first-page":"pages 231","article-title":"Collabseer: a search engine for collaboration discovery","author":"Chen","year":"2011"},{"key":"2020112809064884600_R36","first-page":"pages 1285","article-title":"Cross-domain collaboration recommendation","author":"Tang","year":"2012"},{"key":"2020112809064884600_R37","first-page":"pages 1870","article-title":"Context-aware academic collaborator recommendation","author":"Liu","year":"2018"},{"key":"2020112809064884600_R38","first-page":"pages 1209","article-title":"Acrec: a co-authorship based random walk model for academic collaboration recommendation","author":"Li","year":"2014"},{"key":"2020112809064884600_R39","first-page":"pages 639","article-title":"Collaborator recommendation for isolated researchers","author":"Huynh","year":"2014"},{"key":"2020112809064884600_R40","doi-asserted-by":"crossref","first-page":"2798","DOI":"10.1093\/bioinformatics\/btn520","article-title":"Geometadb: powerful alternative search engine for the gene expression omnibus","volume":"24","author":"Zhu","year":"2008","journal-title":"Bioinformatics"},{"key":"2020112809064884600_R41","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/jamia\/ocw177","article-title":"Metamap lite: an evaluation of a new Java implementation of metamap","volume":"24","author":"Demner-Fushman","year":"2017","journal-title":"Journal of the American Medical Informatics Association"},{"volume-title":"Database","year":"2019","author":"Chen","key":"2020112809064884600_R42"},{"key":"2020112809064884600_R43","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbi.2020.103399","article-title":"A content-based literature recommendation system for datasets to improve data reusability-a case study on gene expression omnibus (geo) datasets","author":"Patra","year":"2020","journal-title":"Journal of Biomedical Informatics"},{"volume-title":"Database","year":"2020","author":"Patra","key":"2020112809064884600_R44"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa074\/34568783\/baaa074.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa074\/34568783\/baaa074.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,28]],"date-time":"2020-11-28T14:07:10Z","timestamp":1606572430000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa074\/6008704"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"references-count":44,"URL":"https:\/\/doi.org\/10.1093\/database\/baaa074","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2020]]},"published":{"date-parts":[[2020]]},"article-number":"baaa074"}}