Christopher Plaisier

Senior Research Scientist

401 Terry Ave N
206-732-2139
Christopher.Plaisier@systemsbiology.org

Dr. Plaisier’s research 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 he integrates genetic, transcriptional, functional and clinical data together into one comprehensive gene regulatory network. He then designs and conducts experiments which validate the predictions from these gene regulatory networks using in vitro cell culture models. Recently he described a cancer miRNA regulatory network (http://cmrn.systemsbiology.net) which required the development of a novel tool the miRvestigator (http://mirvestigator.systemsbiology.net) and provided a comprehensive picture of miRNA mediated regulation for 46 cancer sub-types. He is currently working to extend the gene regulatory network construction to provide transcription factor mediated regulation for glioblastoma multiforme by integrating genetic, mRNA and miRNA expression, as well as clinical data from The Cancer Genome Atlas (TCGA).

Publications

Peterson, Eliza J. R., David J. Reiss, Serdar Turkarslan, Kyle J. Minch, Tige Rustad, Christopher L. Plaisier, William J. R. Longabaugh, David R. Sherman, and Nitin S. Baliga. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Research 42, no. 18 (October 2014): 11291–303. https://doi.org/10.1093/nar/gku777. Cite
Plaisier, Christopher L., Min Pan, and Nitin S. Baliga. “A MiRNA-Regulatory Network Explains How Dysregulated MiRNAs Perturb Oncogenic Processes across Diverse Cancers.” Genome Research 22, no. 11 (November 2012): 2302–14. https://doi.org/10.1101/gr.133991.111. Cite
Brooks, Aaron N., David J. Reiss, Antoine Allard, Wei-Ju Wu, Diego M. Salvanha, Christopher L. Plaisier, Sriram Chandrasekaran, Min Pan, Amardeep Kaur, and Nitin S. Baliga. “A System-Level Model for the Microbial Regulatory Genome.” Molecular Systems Biology 10 (2014): 740. Cite
Danziger, Samuel A., David J. Reiss, Alexander V. Ratushny, Jennifer J. Smith, Christopher L. Plaisier, John D. Aitchison, and Nitin S. Baliga. “Bicluster Sampled Coherence Metric (BSCM) Provides an Accurate Environmental Context for Phenotype Predictions.” BMC Systems Biology 9 Suppl 2 (2015): S1. https://doi.org/10.1186/1752-0509-9-S2-S1. Cite
Plaisier, Christopher L., Sofie O’Brien, Brady Bernard, Sheila Reynolds, Zac Simon, Chad M. Toledo, Yu Ding, David J. Reiss, Patrick J. Paddison, and Nitin S. Baliga. “Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.” Cell Systems 3, no. 2 (August 2016): 172–86. https://doi.org/10.1016/j.cels.2016.06.006. Cite
Reiss, David J., Christopher L. Plaisier, Wei-Ju Wu, and Nitin S. Baliga. “CMonkey2: Automated, Systematic, Integrated Detection of Co-Regulated Gene Modules for Any Organism.” Nucleic Acids Research 43, no. 13 (July 27, 2015): e87. https://doi.org/10.1093/nar/gkv300. Cite
Plaisier, Christopher L., Fang-Yin Lo, Justin Ashworth, Aaron N. Brooks, Karlyn D. Beer, Amardeep Kaur, Min Pan, David J. Reiss, Marc T. Facciotti, and Nitin S. Baliga. “Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins.” BMC Systems Biology 8 (2014): 122. https://doi.org/10.1186/s12918-014-0122-2. Cite
Toledo, Chad M., Yu Ding, Pia Hoellerbauer, Ryan J. Davis, Ryan Basom, Emily J. Girard, Eunjee Lee, et al. “Genome-Wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.” Cell Reports 13, no. 11 (December 22, 2015): 2425–39. https://doi.org/10.1016/j.celrep.2015.11.021. Cite
Plaisier, Christopher L., and Nitin S. Baliga. “Harnessing the Power of Human Tumor-Derived Cell Lines for the Rational Design of Cancer Therapies.” Pigment Cell & Melanoma Research 25, no. 4 (July 2012): 406–8. https://doi.org/10.1111/j.1755-148X.2012.01020.x. Cite
Ashworth, Justin, Christopher L. Plaisier, Fang Yin Lo, David J. Reiss, and Nitin S. Baliga. “Inference of Expanded Lrp-like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction.” PloS One 9, no. 9 (2014): e107863. https://doi.org/10.1371/journal.pone.0107863. Cite
Plaisier, Christopher L., J. Christopher Bare, and Nitin S. Baliga. “MiRvestigator: Web Application to Identify MiRNAs Responsible for Co-Regulated Gene Expression Patterns Discovered through Transcriptome Profiling.” Nucleic Acids Research 39, no. Web Server issue (July 2011): W125-131. https://doi.org/10.1093/nar/gkr374. Cite
Rothchild, Alissa C., James R. Sissons, Shahin Shafiani, Christopher Plaisier, Deborah Min, Dat Mai, Mark Gilchrist, et al. “MiR-155-Regulated Molecular Network Orchestrates Cell Fate in the Innate and Adaptive Immune Response to Mycobacterium Tuberculosis.” Proceedings of the National Academy of Sciences of the United States of America, September 2016. https://doi.org/10.1073/pnas.1608255113. Cite
Turkarslan, Serdar, David J. Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J. Christopher Bare, Christopher L. Plaisier, and Nitin S. Baliga. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors.” Molecular Systems Biology 7 (2011): 554. https://doi.org/10.1038/msb.2011.87. Cite
Ashworth, Justin, Brady Bernard, Sheila Reynolds, Christopher L. Plaisier, Ilya Shmulevich, and Nitin S. Baliga. “Structure-Based Predictions Broadly Link Transcription Factor Mutations to Gene Expression Changes in Cancers.” Nucleic Acids Research 42, no. 21 (December 1, 2014): 12973–83. https://doi.org/10.1093/nar/gku1031. Cite
Keller, Mark P., Pradyut K. Paul, Mary E. Rabaglia, Donnie S. Stapleton, Kathryn L. Schueler, Aimee Teo Broman, Shuyun Isabella Ye, et al. “The Transcription Factor Nfatc2 Regulates Beta-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.” PLoS Genetics 12, no. 12 (December 2016): e1006466. https://doi.org/10.1371/journal.pgen.1006466. Cite