Curriculum Vitae

Christopher L. Plaisier

Research Experience:

Baliga Lab (Institute for Systems Biology) – Currently conducting postdoctoral studies on the inference of transcriptional regulatory networks in higher eukaryotic systems, such as arabidopsis, mouse and humans. Working both computationally to extend current algorithms and develop the necessary new components, and experimentally to validate the models inferred in relevant biological systems.

Pajukanta Lab (UCLA) – Identified genes related to the complex disease familial combined hyperlipidemia (FCHL) utilizing systems genetics approaches. Used phenotype-genotype correlations to identify galanin preproprotein (GAL) as a gene involved in elevated plasma triglycerides. Planned, organized and executed collection of 81 FCHL case/control fat biopsies and hybridization to gene expression microarrays. Utilized these FCHL case/control fat biopsies with systems genetics approaches to identify the function of a previously associated SNP in the gene upstream transcription factor 1 (USF1). Further demonstrated that this SNP has an effect on an FCHL associated co-expression module and identified 18 FCHL causal candidate genes in the module.

Drews Lab (University of Utah) – Adapted a targeted mutagenesis strategy involving recombinant zinc finger nucleases to Arabidopsis thaliana. This required utilizing many molecular biological techniques including cloning. Extracted total RNA for use in qRT-PCR and Affymetrix gene expression microarray experiments to identify genes needed for female gametophyte development and function.

Kropf Lab (Unviersity of Utah) Studied the polar growth of developing zygotes of Pelvetia compressa utilizing developmental and physiological assays while treating with different ionophores.

Ehleringer Lab (University of Utah) Worked on a project studying the water uptake and retention of plants in a desert terrain near Canyonlands National Park in Utah. 

Related Professional Experience:

University of Utah Drews Lab Lab Technician / Lab Manager, Learned and developed molecular biology techniques, instructed other lab members in these techniques, and managed the undergraduate lab dishwasher, August 2002 – August 2004. Manager: Gary N. Drews.

InterNAP was VPNX.comSoftware Engineer / Web Developer / Graphics Designer, Designed and developed a web based application that configured and monitored Virtual Private Networks (VPNs) for large business utilizing entirely open source components (PHP, Apache web server, Interbase database, Python backend). Developed a Java SNMP library by wrapping an existing open source SNMP library and modifying it to be compatible with core Internap technologies, June 2000 – June 2002. Manager: Richard Russell.

University of Utah Ehleringer LabIllustrator / Graphics Designer / Web Designer, Created and traced illustrations and graphics to be published in two books written by Dr. Jim Ehleringer. Also designed and developed web page for the lab, September 1998 – June 2000. Manager: James R. Ehleringer. 

Fellowships and Awards:

American Cancer Society Postdoctoral Fellowship, Institute for Systems Biology, July 2012-July 2014. Project Title: Constructing a Glioma Gene Regulatory Network.

Genomic Analysis and Interpretation Training Grant, UCLA, June 2005 – July 2007.

Advanced Gene Mapping/Linkage Analysis Course Travel Stipend, Rockefeller University, Laboratory of Statistical Genetics, December 2006.

Education:

Doctor of Philosophy in Human Genetics, UCLA, June 2009. Advisor: Paivi Pajukanta, Dissertation Title: Genetical Genomics Approaches to Familial Combined Hyperlipidemia. (Full Dissertation)

Masters of Science in Bioinformatics, UCLA, June 2009. Advisor: Steve Horvath, Thesis Title: Transcription Factor Binding in a Familial Combined Hyperlipidemia Weighted Gene Co-expression Network. (Full Thesis)

Advanced Gene Mapping/Linkage Analysis Course, Rockefeller University, Laboratory of Statistical Genetics, December 2006.

Statistical Genetics Short Course Featuring Mendel, Universita Degli Studi Di Pavia, July 2005.

Cisco Certified Network Associate (CCNA), Internap, Inc., March 2001.

B.S. with an emphasis on Biology, University of Utah, May 2000.

 

Peer Reviewed Research Papers:

1. Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS. A system-level model for the microbial regulatory genome. Mol Syst Biol. 2014 Jul 15;10(7):740. doi: 10.15252/msb.20145160. PubMed PMID: 25028489.

2. Plaisier CL, Bennett B, He A, Guan B, Lusis AJ, Reue K, Vergnes L: Zbtb16 has a role in brown adipocyte bioenergetics. Nutr Diabetes. 2012 Sep 17;2:e46. doi:10.1038/nutd.2012.21. PubMed PMID: 23446662

3. Plaisier CL, Pan M, Baliga NSA 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

4. Plaisier CL, Baliga NS: Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment Cell Melanoma Res. 2012 Jul;25(4):406-8. doi: 10.1111/j.1755-148X.2012.01020.x. PMID: 22781216

5. Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS: Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol. 2011 Nov 22;7:554. doi: 10.1038/msb.2011.87. PMID: 22108796

6. 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;39 Suppl 2:W125-31. Epub 2011 May 20. PMID: 21602264 (http://mirvestigator.systemsbiology.net)

7. Romanoski CE, Lee S, Kim MJ, Ingram-Drake L, Plaisier CL, Yordanova R, Tilford C, Guan B, Guan B, He A, Gargalovic P, Kirchgessner T, Berliner JA, Lusis AJ: Systems Genetics Analysis of Gene-by-Environment Interactions in Human Cells. Am J Hum Genet. 2010 Mar 12;86(3):399-410. Epub 2010 Feb 17. PMID: 20170901

8. Weissglas-Volkov D, Plaisier CL, Huertas-Vazquez A, Cruz-Bautista I, Riano-Barros D, Herrera-Hernandez M, Riba L, Cantor RM, Sinsheimer JS, Aguilar-Salinas CA, Tusie-Luna T, Pajukanta P: Identification of two common variants contributing to serum apolipoprotein B levels in Mexicans. Arterioscler Thromb Vasc Biol. Epub 2009 Dec 3. PMID: 19965785

9. Huertas-Vazquez A, Plaisier CL, Geng R, Haas BE, Lee J, Greevenbroek MM, van der Kallen C, de Bruin TWA, Taskinen M-R, Alagramam KN, Pajukanta P:  A nonsynonymous SNP within PCDH15 is associated with lipid traits in Familial Combined Hyperlipidemia. Hum Genet. Epub 2009 Oct 9. PMID: 19816713

10. 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 

11. Aldave AJ, Vivek SY, Vo RC, Kamal KM, Rayner SA, Plaisier CL, Chen MC, Damani MR, Pham MN, Gorin MB, Papp J, Sobel E:  Exclusion of Positional Candidate Gene Coding Region Mutations in the Common Posterior Polymorphous Corneal Dystrophy 1 Candidate Gene Interval. Cornea. 2009 Aug;28(7): 801-7. PMID: 19574904

12. Plaisier CL, Kyttälä M, Weissglas-Volkov D, Sinsheimer JS, Huertas-Vazquez A, Riba L, Ramírez-Jiménez S, de BruinTWA, Tusié-Luna T, Aouizerat BE, Pullinger CR, Malloy MJ, Kane JP, Cruz-Bautista I, Herrera MF, Aguilar-Salinas C, Kuusisto J, Laakso M, Taskinen M-R, van der Kallen CJH, Pajukanta P:  Galanin is associated with elevated plasma triglycerides. Arterioscler Thromb Vasc Biol. 2009 Jan;29(1):147-52. PMID: 18988886

13. Lee JC, Weissglas-Volkov D, Kyttälä M, Dastani Z, Cantor RM, Sobel EM, Plaisier CL, Engert JC, van Greevenbroek MMJ, Kane JP, Malloy MJ, Pullinger CR, Huertas-Vazquez A, Aguilar-Salinas CA, Tusié-Luna T, de BruinTWA, Aouizerat BE, van der Kallen CJH, Croce CM, Aqeilan RI, Marcil M, Viikari JSA, Lehtimäki T, Raitakari OT, Kuusisto J, Laakso M, Taskinen M-R, Genest J, Pajukanta P: Identification of WW domain-containing oxidoreductase as a novel HDL-C susceptibility gene. Am J Hum Genet. 2008 Aug;83(2):180-92. PMID: 18674750

14. Presson AP, Sobel EM, Pajukanta P, Plaisier C, Weeks DE, Aberg K, Papp JC: Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis. BMC Bioinformatics. 2008 Jul 21;9(1):317 pg-1-16. PMID: 18644149

15. Mar-Heyming R, Miyazaki M, Weisglas-Volkov D, Kolaitis N, Sadaat N, Plaisier C, Pajukanta P, Cantor RM, de Bruin TW, Ntambi JM, Lusis AJ:  Association of Stearoyl-CoA Desaturase 1 Activity With Familial Combined Hyperlipidemia. Arterioscler Thromb Vasc Biol. 2008 Jun;28(6):1193-9. PMID: 18340007

16. Sinsheimer JS, Plaisier CL, Huertas-Vazquez A, Aguilar-Salinas C, Tusié-Luna T, Pajukanta P, Lange K:  Estimating Ethnic Admixture from Pedigree Data. Am J Hum Genet. 2008 Mar;82(3):748-55. PMID: 18319077

17. Huertas-Vazquez A, Plaisier C, Weissglas-Volkov D, Sinsheimer J, Canizales-Quinteros S, Cruz-Bautista I, Nikkola E, Herrera-Hernandez M, Davila-Cervantes A, Tusié-Luna T, Taskinen M-R, Aguilar-Salinas C, Pajukanta P:  TCF7L2 is associated with high serum triacylglycerol and differentially expressed in adipose tissue in families with familial combined hyperlipidaemia. Diabetologia. 2008 Jan;51(1):62-9. PMID: 17972059

18. Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, Castellanos R, Brozell A, Schadt EE, Drake TA, Lusis AJ, Horvath S:  Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight. PLoS Genet. 2006 Aug 18;2(8):e130 pg-1182-92. PMID: 16934000

19. Weissglas-Volkov D, Huertas-Vazquez A, Suviolahti E, Lee J, Plaisier C, Canizales-Quinteros S, Tusié-Luna T, Aguilar-Salinas C, Taskinen MR, Pajukanta P:  Common hepatic nuclear factor-4alpha variants are associated with high serum lipid levels and the metabolic syndrome. Diabetes. 2006 Jul;55(7):1970-7. PMID: 16804065

20. Dastani Z, Quiogue L, Plaisier C, Engert JC, Marcil M, Genest J, Pajukanta P:  Evidence for a Gene Influencing High-Density Lipoprotein Cholesterol on Chromosome 4q31.21. Arterioscler Thromb Vasc Biol. 2006 Feb;26(2):392-7. PMID: 16322534

21. Lloyd A, Plaisier CL, Carroll D, Drews GN:  Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2232-7. PMID: 15677315

Presentations in International Scientific Meetings:

1. Plaisier CL, Baliga NS:  Identifying miRNAs that Bind Co-Regulated TranscriptsMicroRNAs and Non-Coding RNAs and Cancer (J5), Keystone Symposium, Feb. 2011. (Poster)

2. Plaisier CL, Reiss DJ, Baliga NS:  Gene Expression Regulatory Networks of Human Disease:  High Grade Glioma. Institute for Systems Biology 9th Annual International Symposium: Systems Biology and Global Health, April 18-19, 2010. (Poster)

3. Plaisier CL, Haas B, Laakso M, Pajukanta P:  Cross-species Comparisons of GWAS Data as a Screening Tool to Identify Novel Loci for LDL-C. XV International Symposium on Atherosclerosis, June 14-18, 2009. (Oral Presentation)

4. Plaisier CL, van der Kallen CJ, de Bruin TW, Schadt EE, Pajukanta P:  Identification of Downstream Targets of USF1. European Atherosclerosis Society 76th Congress, June 10-13, 2007. (Oral Presentation)

5. Kyttälä M, Plaisier CL, Aouizerat B, de Bruin TW, van der Kallen CJ, Pajukanta P:  Identification of a Gene on Chromosome 11p Regulating Plasma Triglyceride Levels. European Atherosclerosis Society 76th Congress, June 10-13, 2007. (Oral Presentation)

6. Plaisier CL, van der Kallen CJ, de Bruin TW, Pajukanta P:  Constriction of the Region for Familial Combined Hyperlipidemia on 11p. American Society of Human Genetics Annual Meeting, Oct 9-13, 2006. (Poster)

7. Plaisier CL, Lusis AJ, Naoumova RP, Shoulders CC, de Bruin TW, Pajukanta P:  Fine mapping a Region on Chromosome 11p for Familial Combined Hyperlipidemia. International Symposium on Atherosclerosis, International Atherosclerosis Society, Jun 18-22, 2006. (Poster)

8. Plaisier CL, Lusis AJ, Cantor RM, Naoumova RP, Shoulders CC, de Bruin TW, Pajukanta P:  Fine mapping a Locus for Familial Combined Hyperlipidemia on 11p. Genome Sequence Variation and the Inherited Basis of Common Disease and Complex Traits, Keystone Symposium, Jan. 2006. (Poster)

Teaching Experience:

Systems Biology of Disease Summer 2014 – Instructor, Week long summer course to introduce the core concepts of systems biology and their application to systems biomedicine. We demonstrated the importance of cross-disciplinary interactions for the success of systems biology programs. Current class website is: http://course.systemsbiology.net/

Bioinformatics and Genomics (CM 160/260) Winter 2006Teaching Assistant, Professor: Christopher Lee, Conducted one discussion section a week, and had office hours for two hours per week. Developed and designed laboratory sessions involving scripts in R to demonstrate the topics covered that week in class. Wrote and graded all homework and tests. Covered topics including:  Basic Probability, Maximum Likelihood, Hidden Markov Models, Dynamic Programming, Sequence Alignment, Microarray Analysis, Phylogeny and Evolution. Current class website is: http://c260a.bioinformatics.ucla.edu/

Human Genetics (CM 156/256) Winter 2007Teaching Assistant, Professors: John Merriam, Karen Reue and Aldons Lusis. Conducted three discussion sections a week, and had office hours two hours per week. Presented a representative primary literature article to students during discussion section. Created several PowerPoint presentations for these discussion sections. Proctored and graded weekly quizzes on the primary literature. Wrote questions for exams and graded exams.

 

Relevant Graduate Course Work:

Statistics and Bioinformatics Related Courses

Introduction to Probability Theory (STATS 100A)

Genomic Technology (HUM GEN C244)

Bioinformatics and Genomics (CHEM CM260)

Statistical Methods in Computational Biology (STATS M254)

Biology & Genetics Related Courses

Cell Biology (BIOL CH CM267 A & B)

Macromolecular Structure (BIOL CH CM253)

Molecular Genetics (BIOL CH CM248)

Mouse Molecular Genetics (MIMG CM222)

Current Topics in Atherosclerosis and Mycocardium (MOL BIO 298)

Advanced Human Genetics (HUM GEN 236 A & B)

Human Genetics Seminar (HUM GEN 282)

Ethics Related Courses

Ethics in Biomedical Research (MIMG CM234)

Ethical Issues in Human Genetics (HUM GEN 220)

Teaching Related Courses

Teaching College Chemistry (CHEM 495)

 

Computer Proficiencies:

Operating Systems – DOS, Linux, MacOS, Windows

Programming Languages – C++, HTML, Java, Javascript, PHP, Python, R, SQL

Web Development FrameworksDjango

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