{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:21:28Z","timestamp":1772166088739,"version":"3.50.1"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"S3","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2016,8]]},"DOI":"10.1186\/s12918-016-0313-0","type":"journal-article","created":{"date-parts":[[2016,8,26]],"date-time":"2016-08-26T04:41:56Z","timestamp":1472186516000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["XMRF: an R package to fit Markov Networks to high-throughput genetics data"],"prefix":"10.1186","volume":"10","author":[{"given":"Ying-Wooi","family":"Wan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Genevera I.","family":"Allen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yulia","family":"Baker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eunho","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pradeep","family":"Ravikumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Anderson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhandong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,8,26]]},"reference":[{"issue":"3","key":"313_CR1","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1214\/009053606000000281","volume":"34","author":"N Meinshausen","year":"2006","unstructured":"Meinshausen N, Buhlmann P. High-dimensional graphs and variable selection with the lasso. Ann Stat. 2006; 34(3):1436\u201362.","journal-title":"Ann Stat"},{"issue":"3","key":"313_CR2","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1214\/09-AOS691","volume":"38","author":"P Ravikumar","year":"2010","unstructured":"Ravikumar P, Wainwright MJ, Lafferty JD. High-dimensional ising model selection using l1-regularized logistic regression. Ann Stat. 2010; 38(3):1287\u2013319.","journal-title":"Ann Stat"},{"key":"313_CR3","first-page":"1367","volume":"25","author":"E Yang","year":"2012","unstructured":"Yang E, Ravikumar PD, Allen GI, Liu Z. Graphical Models via Generalized Linear Models. Adv Neural Inf Process Syst. 2012; 25:1367\u20131375.","journal-title":"Adv Neural Inf Process Syst"},{"key":"313_CR4","first-page":"3813","volume":"16","author":"E Yang","year":"2015","unstructured":"Yang E, Ravikumar P, Allen GI, Liu Z. Graphical models via univariate exponential family distributions. J Mach Learn Res. 2015; 16:3813\u201347.","journal-title":"J Mach Learn Res"},{"key":"313_CR5","unstructured":"Knaus J. Snowfall: Easier Cluster Computing (based on Snow). R package version 1.84-4. 2013. http:\/\/CRAN.R-project.org\/package=snowfall . Accessed 2012."},{"issue":"2","key":"313_CR6","first-page":"1432","volume":"24","author":"H Liu","year":"2010","unstructured":"Liu H, Roeder K, Wasserman L. Stability approach to regularization selection (stars) for high dimensional graphical models. Adv Neural Inf Process Syst. 2010; 24(2):1432\u201340.","journal-title":"Adv Neural Inf Process Syst"},{"issue":"4","key":"313_CR7","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1111\/j.1467-9868.2010.00740.x","volume":"72","author":"N Meinshausen","year":"2010","unstructured":"Meinshausen N, B\u00fchlmann P. Stability selection. J R Stat Soc Series B (Statistical Methodology). 2010; 72(4):417\u201373.","journal-title":"J R Stat Soc Series B (Statistical Methodology)"},{"issue":"3","key":"313_CR8","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1109\/TNB.2013.2263838","volume":"12","author":"GI Allen","year":"2013","unstructured":"Allen GI, Liu Z. A Local Poisson Graphical Model for Inferring Networks From Sequencing Data. NanoBioscience IEEE Trans. 2013; 12(3):189\u201398.","journal-title":"NanoBioscience IEEE Trans"},{"key":"313_CR9","first-page":"1695","volume":"Complex Systems","author":"G Csardi","year":"2006","unstructured":"Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006; Complex Systems:1695.","journal-title":"InterJournal"},{"key":"313_CR10","unstructured":"Yang E, Ravikumar PD, Allen GI, Liu Z. On Poisson Graphical Models. Adv Neural Inf Process Syst. 2013;:1718\u201326."},{"issue":"11","key":"313_CR11","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498\u2013504.","journal-title":"Genome Res"},{"key":"313_CR12","doi-asserted-by":"crossref","unstructured":"Allen GI, Liu Z. A log-linear graphical model for inferring genetic networks from high-throughput sequencing data. In: Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference: 2012. p. 1\u20136. doi:10.1109\/BIBM.2012.6392619.","DOI":"10.1109\/BIBM.2012.6392619"},{"issue":"7418","key":"313_CR13","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","volume":"490","author":"Cancer Genome Atlas Network","year":"2012","unstructured":"Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490(7418):61\u201370.","journal-title":"Nature"},{"issue":"Database issue","key":"313_CR14","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1093\/nar\/gku1075","volume":"43","author":"SA Forbes","year":"2015","unstructured":"Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ. COSMIC: exploring the world\u2019s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015; 43(Database issue):805\u201311.","journal-title":"Nucleic Acids Res"},{"issue":"7456","key":"313_CR15","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature12222","volume":"499","author":"Cancer Genome Atlas Research Network","year":"2013","unstructured":"Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013; 499(7456):43\u20139.","journal-title":"Nature"},{"issue":"7417","key":"313_CR16","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nature11404","volume":"489","author":"The Cancer Genome Atlas Research Network","year":"2012","unstructured":"The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012; 489(7417):519\u201325.","journal-title":"Nature"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-016-0313-0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T17:26:40Z","timestamp":1498325200000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-016-0313-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8]]},"references-count":16,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2016,8]]}},"alternative-id":["313"],"URL":"https:\/\/doi.org\/10.1186\/s12918-016-0313-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/032219","asserted-by":"object"}]},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8]]},"article-number":"69"}}