Ryan C. Thompson
Contact Address: 8656 Via Mallorca
Unit G
La Jolla, CA 92037
Phone: (908) 922-7470
Email: rct@thompsonclan.org
Website: https://github.com/DarwinAwardWinner
Summary
Education
The Scripps Research Institute

Ph. D. in Bioinformatics, expected Summer 2018
University of Virginia

B.S. in Biology, B.A. in Mathematics, 2009
Echols Scholar
Research Experience
Salomon Lab, The Scripps Research Institute La Jolla, CA   2012 - 2018
Contact:
Dr. Andrew Su, asu@scripps.edu
Summer Internship, Informatics IT, Merck & Co. Boston, MA   2011
Contact:
Adnan Derti, adnan.derti@gmail.com
Gaasterland Lab, UCSD Bioinformatcs La Jolla, CA   2010 - 2012
Contact:
Terry Gaasterland, gaasterland@ucsd.edu
Timko Lab, U. of Virginia BiologyCharlottesville, VA   2007 - 2009
Contact:
Paul J. Rushton, Paul.Rushton@sdstate.edu
Skills
Computing Skills
R/BioConductor, Python, Perl, Lisp, Java, C#, C++; Git version control; Remote UNIX system administration & software compilation, computing cluster job management & parallel computation
Public code: https://github.com/DarwinAwardWinner
StackOverflow Profile: http://stackoverflow.com/users/125921
Statistics & Data Analysis
Multi-omics NGS & microarray analysis, multi-factor linear and generalized linear regression, experimental design and parametrization, empirical Bayesian methods, predictive modeling of clinical outcomes, machine learning classifier training & validation, survival analysis, data visualization & presentation, reproducible research practices
Wet Lab:
PCR, molecular cloning, recombinant protein purification, epitope mapping, site-directed mutagenesis, 2D gels, real-time PCR, and associated data analysis
Languages:
English: native speaker; German: written and spoken
Other Work Experience
Computing Advisor & Help Desk, U. Va. IT Dept. Charlottesville, VA    2005 - 2007
Summer Sailing Instructor, Raritan Yacht Club Perth Amboy, NJ    2006 - 2009

References

Ryan C. Thompson, Paul J. Rushton, Tom W. Laudeman, and Michael P. Timko, "http://darwinawardwinner.github.io/resume/examples/UVa/contigfarmer.pdfContig Farmer: a tool for extracting maximal-length contiguous sequences from a database of short sequence reads (Undergraduate Thesis)" (2009).
Sunil Kurian, Enrique Velazquez, Ryan Thompson, Thomas Whisenant, Stanley Rose, Nicole Riley, Frank Harrison, Terri Gelbart, John Friedewald, Susan Brietigam, Michael Abecassis, and Daniel Salomon, "Orthogonal Comparison of Molecular Signatures of Kidney Transplants with Subclinical and Clinical Acute Rejection -- Equivalent Performance is Agnostic to either Technology or Platform", American Journal of Transplantation (2017).
Ryan C. Thompson, Terri Gelbart, Steven R. Head, Phillip Ordoukhanian, Courtney Mullen, Dongmei Han, Dora M. Berman, Amelia Bartholomew, Norma S. Kenyon, and Daniel R. Salomon, "Optimizing yield of deep RNA sequencing for gene expression profiling of peripheral blood samples from cynomolgus monkeys (Macaca fascicularis)", Journal of Biological Methods (in review) (2016).
SM Kurian, AN Williams, T Gelbart, D Campbell, TS Mondala, SR Head, S Horvath, L Gaber, R Thompson, T Whisenant, "Molecular Classifiers for Acute Kidney Transplant Rejection in Peripheral Blood by Whole Genome Gene Expression Profiling", American Journal of Transplantation 14, 5 (2014), pp. 1164--1172.
Sarah LaMere, Ryan C. Thompson, H. Kiyomi Komori, Adam Mark, and Daniel R. Salomon, "Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells", Genes & Immunity (2016).
Sarah LaMere, Ryan C. Thompson, Xiangzhi Meng, H. Kiyomi Komori, A. Mark, and Daniel R. Salomon, "H3K27 methylation dynamics during CD4 T cell activation: regulation of JAK/STAT and IL12RB2 expression by JMJD3", Journal of Immunology (accepted) (2017).
Ryan C. Thompson, "http://darwinawardwinner.github.io/resume/examples/UVa/math-history-paper.pdfThe sources and limits of geometric rigor from Euclid through Descartes" (2008).
Sunitha Rangaraju, Gregory M Solis, Ryan C Thompson, Rafael L Gomez-Amaro, Leo Kurian, Sandra E Encalada, Alexander B Niculescu, Daniel R Salomon, and Michael Petrascheck, "Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality", eLife 4 (2015).
Erick R. Scott, H. Benjamin Larman, Ali Torkamani, Nicholas J. Schork, Nathan Wineinger, Max Nanis, Ryan C. Thompson, Reza B. Beheshti Zavareh, Luke L. Lairson, Peter G. Schultz, and Andrew I. Su, "RASLseqTools: open-source methods for designing and analyzing RNA-mediated oligonucleotide Annealing, Selection, and, Ligation sequencing (RASL-seq) experiments", Nucleic Acids Research (in review) (2016).
Filip Van Nieuwerburgh, Ryan C. Thompson, Jessica Ledesma, Dieter Deforce, Terry Gaasterland, Phillip Ordoukhanian, and Steven R Head, "Illumina Mate-Paired DNA Sequencing Library Preparation Using Cre-Lox Recombination", Nucleic Acids Research (2011), pp. gkr1000.