Publications

• Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity. 2018 Apr 17. PMID: 29628290 (TCGA Pan-Cancer Atlas overview.)
• Rothchild AC, Sissons JR, Shafiani S, Plaisier C, Min D, Mai D, Gilchrist M, Peschon JJ, Larson RP, Bergthaler A, Baliga N, Urdahl KB, Aderem A. A miR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis.  Proc Natl Acad Sci U S A. 2016 Sep 28. PMID: 27681624
• Plaisier CL*, O’Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS. Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. Cell Syst. 2016 Jul 14. PMID: 27426982 (* = corresponding author)
• Reiss DJ, Plaisier CL, Wu WJ, Baliga NS. cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res. 2015 Apr 14. PMID: 25873626
• Plaisier CL, Pan M, Baliga NS. A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. 2012 Nov. PMID: 22745231
• Plaisier CL, Bare JC, Baliga NS. miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res. 2011 Jul. PMID: 21602264 (http://mirvestigator.systemsbiology.net)
• Plaisier CL, Horvath S, Huertas-Vazquez A, Cruz-Bautista I, Herrera M, Tusie-Luna T, Aguilar-Salinas C, Pajukanta P. A Systems Genetics Approach Implicates USF1, FADS3, and Other Causal Candidate Genes for Familial Combined Hyperlipidemia. PLoS Genetics. 2009 Sep. PMID: 19750004

* = corresponding author