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Storch","year":"2002","journal-title":"Nature"},{"issue":"25","key":"ref11","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"MB Eisen","year":"1998","journal-title":"Proc Natl Acad Sci USA"},{"issue":"12","key":"ref12","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1101\/gr.9.12.1198","article-title":"Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes","volume":"9","author":"MG Walker","year":"1999","journal-title":"Genome Res"},{"issue":"3","key":"ref13","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/10343","article-title":"Systematic determination of genetic network architecture","volume":"22","author":"S Tavazoie","year":"1999","journal-title":"Nat 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Bayesian hierarchical clustering. In: Proc 22nd Intl Conf Mach Learn. 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Sch\u00f6lkopf","year":"2002"},{"key":"ref76","article-title":"Gaussian Processes for Machine Learning","author":"CE Rasmussen","year":"2006"},{"issue":"2","key":"ref77","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1080\/10618600.2000.10474879","article-title":"Markov chain sampling methods for Dirichlet process mixture models","volume":"9","author":"RM Neal","year":"2000","journal-title":"J Comput Graph Stat"},{"key":"ref78","article-title":"SciPy: Open source scientific tools for Python","author":"E Jones","year":"2015"},{"issue":"1","key":"ref79","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/1471-2105-14-252","article-title":"Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters","volume":"14","author":"J Hensman","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref80","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"J Mach Learn Res"},{"issue":"22","key":"ref81","doi-asserted-by":"crossref","first-page":"12176","DOI":"10.1073\/pnas.190337797","article-title":"Genome sequence of Halobacterium species NRC-1","volume":"97","author":"WV Ng","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"ref82","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"issue":"16","key":"ref83","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"12","key":"ref84","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"7","key":"ref85","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1016\/j.cell.2009.12.018","article-title":"A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection","volume":"139","author":"SD Shapira","year":"2009","journal-title":"Cell"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"ref87","unstructured":"Tang H, Pedersen B, Ramirez F, Naldi A, Flick P, Yunes J, et al. goatools; 2016. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/tanghaibao\/goatools\" xlink:type=\"simple\">https:\/\/github.com\/tanghaibao\/goatools<\/ext-link>."},{"issue":"7","key":"ref88","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Y Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref89","article-title":"The Elements of Statistical Learning","volume":"vol. 1","author":"J Friedman","year":"2001"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005896","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T00:00:00Z","timestamp":1516924800000}}],"container-title":["PLOS Computational 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