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Christopher Plaisier

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Asst Professor
Faculty, TEMPE Campus, Mailcode 9709

Dr. Plaisier’s laboratory is focused on constructing gene regulatory networks from patient data that can be used to discover diagnostic and prognostic biomarkers as well as novel drug targets. To accomplish this they integrate genetic, transcriptional, functional and clinical data together into one comprehensive gene regulatory network. They then design and conduct experiments which validate the predictions from these gene regulatory networks using in vitro cell culture models. In 2012 Dr. Plaisier described a cancer miRNA regulatory network ( which required the development of a novel tool the miRvestigator ( and provided a comprehensive picture of miRNA mediated regulation for 46 cancer sub-types. More recently, Dr. Plaisier described the development and application of the Systems Genetics Network AnaLysis (SYGNAL) pipeline to the deadly brain cancer glioblastoma multiforme ( In the process of building the SYGNAL pipeline Dr. Plaisier also compiled the Transcription Factor (TF) Target Gene database ( which houses a very powerful TF to target interactions inferred from human genome sequence, a compendium of TF DNA binding motifs, and ENCODE digital genomic footprints. The SYGNAL pipeline is powerful in that it extends gene regulatory network inferrence by discovering both TF and miRNA regulatory influences by integrating across genetic, mRNA and miRNA expression, as well as clinical data from The Cancer Genome Atlas (TCGA). He demonstrated that the resulting gene regultory network can be used to discover novel biological findings and synergistic drug combinations for glioblastoma multiforme. Most importantly the SYGNAL pipeline is generalizable to any mamalian system (currently human and mouse) with a minimum data requirement of transcriptional profiles across relevant conditions.


Postdoctoral Fellow, Institute for Systems Biology, August 2009 – August 2012.  Advisor:  Nitin Baliga.

Doctor of Philosophy in Human Genetics, University of California, Los Angeles, June 2009. Advisor: Paivi Pajukanta, Dissertation Title: Genetical Genomics Approaches to Familial Combined Hyperlipidemia.

Masters of Science in Bioinformatics, University of California, Los Angeles, June 2009. Advisor: Steve Horvath, Thesis Title: Transcription Factor Binding in a Familial Combined Hyperlipidemia Weighted Gene Co-expression Network.

Bachelor of Science in Biology, University of Utah, May 2000.

  1. 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;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. PubMed PMID: 29628290.
  2. 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. pii: 201608255. [Epub ahead of print] PubMed PMID: 27681624
  3. 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. pii: S2405-4712(16)30189-2. doi: 10.1016/j.cels.2016.06.006. [Epub ahead of print] PubMed PMID: 27426982
  4. Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, Baliga NS, Moffat J, Lin Q, Li XN, Nam DH, Lee J, Pollard SM, Zhu J, Delrow JJ, Clurman BE, Olson JM, Paddison PJ. Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells. Cell Rep. 2015 Dec 22;13(11):2425-39. doi:10.1016/j.celrep.2015.11.021. Epub 2015 Dec 7. PubMed PMID: 26673326
  5. 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. pii: gkv300. [Epub ahead of print] PMID: 25873626
  6. Plaisier CL, Pan M, Baliga NS: A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. 2012 Nov;22(11):2302-14. doi: 10.1101/gr.133991.111. Epub 2012 Jun 28. PubMed PMID: 22745231
  7. 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;5(9): e1000642. Epub 2009 Sep 11. PMID: 19750004
Spring 2018
Course NumberCourse Title
BME 394Special Topics
BME 493Honors Thesis
BME 494Special Topics
BME 598Special Topics

Volunteer Experience

STEM Fellow, Industry Expert
Washington Alliance for Better Schools
Sep 2013 – Jun 2014
Advised 10th grade teachers on developing new curriculum around antibiotic resistance that met Next Generation Science Standards (NGSS) for STEM (science, technology, engineering and math) learning in Washington classrooms.


Science Communication Fellowship
Pacific Science Center
Aug 2015 – August 2017
Science and Technology
Learned how to communicate my science to the broader public by developing my communication skills and an interactive activity and presenting it to visitors at the Pacific Science Center.


Big Data Mentor
Washington State Board for Community and Technical Colleges
Oct 2014 – August 2017
Worked with community college faculty to develop ideas of how they could incorporate quantitative reasoning and big data into their classes.


Masterclass Instructor
University of Cape Town
Aug 2015 – Aug 2015
Taught three day masterclass on patient stratification and biomarker discovery to 16 researchers from the University of Cape Town. This was a shortened form of the Systems Biology of Disease course that we have developed at the Institute for Systems Biology. It was tailored specifically to bring skills that would help the trainees meet their research goals.