resume/ryan_thompson_resume.txt

Ryan C. Thompson, Ph.D.

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
==========

* Accomplished, experienced computational biologist with deep
  knowledge of biology, mathematics, statistics, and programming.
* 11 years of bioinformatics experience answering a wide range of
  complex biological questions through analysis of large NGS- and
  microarray-based whole transcriptome and epigenetic data sets.
* Focus on sound statistical analysis, effective data visualization
  and communication, and making expert knowledge and successful
  analysis methods available as re-usable software tools.
* Supportive team member and experienced mentor with a strong ability
  to help others connect biological, statistical, and computational
  understanding.

Education
==========

2012—2019: Ph.D. in Bioinformatics, Skaggs Graduate School of Chemical and Biological Sciences
The Scripps Research Institute, La Jolla, California
Advisor: Andrew Su

2005—2009: B.S. in Biology with High Distinction; B.A. in Mathematics
University of Virginia, Charlottesville, Virginia
Advisor: Paul J. Rushton

Research Experience
==========

Salomon & Su Labs, The Scripps Research Institute
----------
La Jolla, CA; 2012—2019
 
Contact: Dr. Andrew Su, asu@scripps.edu

* Created an open source, reproducible workflow to analyze a large
  multi-omics next-gen sequencing dataset of 220 RNA-seq and ChIP-seq
  samples to reveal coordinated changes in histone marks and gene
  expression during CD4 + T-cell activation as well as epigenetic
  convergence between naive and memory cells after activation [1,3,8].
* Significantly improved cross-validated performance of machine
  learning classifier for identifying biomarkers of transplant
  rejection by developing appropriate single-sample microarray
  normalization procedures [5], including training a custom set of
  frozen RMA normalization vectors. Classifier is currently being
  developed into a clinical test for transplant dysfunction.
* Performed a comprehensive comparative evaluation of over 20 subtly
  different statistical models for differential methylation in
  Illumina 450k arrays, selecting a model that best explained the
  observed sources and trends of variation in the data, including
  cross-domain application of a method originally designed for RNA-seq
  data.
* Evaluated and optimized cost and performance of custom protocol for
  RNA-seq of human and primate blood samples while minimizing nuisance
  globin reads. Increased yield of useful reads nearly 2-fold [7].
* Investigated effects of life-span-extending drug on worm gene
  expression over time revealing that the drug retards age-related
  “transcriptional drift”, preserving a youthful phenotype at the
  molecular level [4].
* Implemented a systems biology tool to analyze and efficiently
  present and summarize differential expression for multiple gene set
  & pathway methods run on multiple pathway databases, as well as
  differential expression of individual genes within each pathway.
* Performed comparative analysis of multiple differential expression
  statistical models to define best practice for optimal sensitivity
  while maintaining false positive control. Presented on theoretical
  and practical similarities and differences between methods.
* Taught basic RNA-seq theory and practical analysis for the
  graduate-level introductory bioinformatics course.
* Adapted common normalization methods from RNA-seq to improve
  performance in analysis of RASL-seq experiments [10].
* Active member of the Bioconductor community since 2012 and
  contributing developer for several Bioconductor packages.
* Mentored 3 coworkers from both biology and programming backgrounds
  in learning bioinformatics.

Summer Internship, Informatics IT, Merck & Co.
----------
Boston, MA; 2011

Contact: Adnan Derti, adnan.derti@gmail.com

* Built a transcriptome assembly and quantification pipeline using
  Cufflinks, including fully-automated cluster job control for
  high-throughput reproducible analysis, and presented a conceptual
  overview of Cufflinks' assembly and quantification algorithms to
  help the team understand Cufflinks.
* Assisted in a molecular genetics study to evaluate peformance of two
  variant calling algorithms in detection of causal mutations in
  antibiotic-resistant bacterial genomes.

Gaasterland Lab, UCSD Bioinformatcs
----------
La Jolla, CA; 2010 - 2012

Contact: Terry Gaasterland, gaasterland@ucsd.edu

* Designed and implemented Deloxer, a critical software step in a new
  Illumina mate-pair sequencing protocol using Cre recombination.
  Deloxer is published [6] and now in use in several labs around the
  world.
* Performed a molecular genetics study to find potential causal
  mutations for fatal iron overload disease in critically endangered
  black rhinoceros by de novo assembly of transcriptomes for black
  rhino and closely-related white rhino. Developed a custom pipeline
  to match up ortholog gene pairs, discover single-nucleotide
  differences between them, and functionally annotate these
  differences, and delivered a list of potential causal variants to
  collaborators for follow-up.
* Helped design & implement a large-scale high-throughput exome
  sequencing pipeline for SNP discovery and functional annotation,
  including QC and validation of on-target coverage depth and
  reproducibility of coverage.
* Created a fully-automated pipeline to produce quality-control
  metrics and plots for Illumina high-throughput sequencing data for
  early identification of failed runs or samples.
* Investigated the binding motif specificity of ZASC1 transcription
  factor in mouse T-cells using Affymetrix expression microarrays in
  ZASC1 siRNA knockdown experiment.
* Analyzed miRNA target predictions using GO & KEGG grouping to
  identify target pathways of autophagy-related miRNAs for biological
  validation.

Timko Lab, U. of Virginia Biology
----------
Charlottesville, VA; 2007—2009

Advisor: Paul J. Rushton

* Undergraduate thesis: Designed and implemented Contig Farmer, an
  algorithm for efficient selective contig assembly starting from
  “seed” sequences of interest, and used Contig Farmer to accelerate
  transcription factor gene discovery in cowpea and tobacco shotgun
  genomic sequence data [11].
* Investigated transcription factors mediating plant stress response
  using expression microarray time-course, and refined the custom
  microarray design using data from previous runs to identify and
  eliminate uninformative probes, yielding an improved design for
  future studies.
* Acted as interpreter to explain complex biological concepts to
  programmers and explain complex computational problems to
  biologists.

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 

* Provided support via phone and on-site for students, faculty, and
  staff having problems with computers, phone system, network access,
  malware, hardware setup, and university web services
* Tasks included support for university-provided software, virus
  removal, iPod recovery, printer setup and repair, diagnosis of
  hardware malfunctions, and data recovery from failing hard disks

Summer Sailing Instructor, Raritan Yacht Club
----------
Perth Amboy, NJ; 2006—2009

* Instructed children ages 8-18 in sailing skills, safety, seamanship,
  knots, rigging & de-rigging boats, navigation, and racing strategy
  and technique, with an emphasis on building character and
  self-reliance
* Ensured safety of students and staff by maintaining boats and
  equipment in good repair, by being vigilant to traffic and hazards
  on a busy waterway, and by communicating and coordinating
  efficiently with other staff
* Helped organize, run, and referee several regattas per season for
  students from RYC and neighboring yacht clubs

Awards & Honors
==========
2006—2009 Echols Scholar, University of Virginia
2006 Phi Eta Sigma National Honor Society
2006 National Society of Collegiate Scholars
2005 Edward J. Bloustein Disguingished Scholar
2005 National Merit Scholar

Peer-reviewed Publications
==========

[1] Sarah A. LaMere, Ryan C. Thompson, Xiangzhi Meng, H. Kiyomi
Komori, Adam Mark, and Daniel R. Salomon. H3K27 Methylation Dynamics
during CD4 T Cell Activation: Regulation of JAK/STAT and IL12RB2
Expression by JMJD3. The Journal of Immunology, 199(9):3158–3175,
November 2017. doi:10/gchc9x.

[2] S. M. Kurian, E. Velazquez, R. Thompson, T. Whisenant, S. Rose, N.
Riley, F. Harrison, T. Gelbart, J. J. Friedewald, J. Charette, S.
Brietigam, J. Peysakhovich, M. R. First, M. M. Abecassis, and D. R.
Salomon. Orthogonal Comparison of Molecular Signatures of Kidney
Transplants With Subclinical and Clinical Acute Rejection: Equivalent
Performance Is Agnostic to Both Technology and Platform. American
Journal of Transplantation, 17(8):2103–2116, August 2017.
doi:10/gbp6vr.

[3] S. A. LaMere, R. C. Thompson, H. K. Komori, A. Mark, and D. R.
Salomon. Promoter H3K4 methylation dynamically reinforces
activation-induced pathways in human CD4 T cells. Genes & Immunity,
17(5):283–297, July 2016. doi:10/f97x85.

[4] 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(December2015):1–39, December 2015.
doi:10/ggcxmg.

[5] S M Kurian, a N Williams, T Gelbart, D Campbell, T S Mondala, S R
Head, S Horvath, L Gaber, R Thompson, T Whisenant, W Lin, P
Langfelder, E H Robison, R L Schaffer, J S Fisher, J Friedewald, S M
Flechner, L K Chan, A C Wiseman, H Shidban, R Mendez, R Heilman, M M
Abecassis, C L Marsh, and D R Salomon. Molecular Classifiers for Acute
Kidney Transplant Rejection in Peripheral Blood by Whole Genome Gene
Expression Profiling. American Journal of Transplantation,
14(5):1164–1172, May 2014. doi:10/f5xswg.

[6] 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, 40(3):e24, February 2012.
doi:10/fmzd3r.

Other Works
==========

[7] 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). (In
preparation). Institution: The Scripps Research Institute, 2019.

[8] Ryan C. Thompson, Sarah A. Lamere, and Daniel R. Salomon.
Reproducible genome-wide epigenetic analysis of H3K4 and H3K27
methylation in naïve and memory CD4+ T-cell activation. (In
preparation). Institution: The Scripps Research Institute, 2019.

[9] Ryan C. Thompson. Bioinformatic Analysis of Complex ,
High-Throughput Genomic and Epigenomic Data in the Context of CD4+
T-Cell Differentiation and Diagnosis and Treatment of Transplant
Rejection. PhD thesis, The Scripps Research Institute, 2019.

[10] 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. bioRxiv, 2016. doi:10/ggcxmn.

[11] Ryan C. Thompson, Paul J. Rushton, Tom W. Laudeman, and Michael
P. Timko. Contig Farmer : A tool for extracting maximal-length
contiguous sequences from a database of short sequence reads
(Undergraduate Thesis), June 2009. Institution: University of
Virginia.
http://darwinawardwinner.github.io/resume/examples/UVa/contigfarmer.pdf

[12] Ryan C. Thompson. The Sources and Limits of Geometric Rigor from
Euclid Through Descartes, May 2008. Institution: University of
Virginia.
 http://darwinawardwinner.github.io/resume/examples/UVa/math-history-paper.pdf

Presentations and Teaching
==========
* May 8, 2018: Guest lecturer on RNA-Seq for Advanced Tools and Data
  Challenges in Bioinformatics course (Lecture & Lab). University of
  California, San Diego, CA
* November 21, 2016: Advanced RNA-Seq Analysis. Schork Lab, J. Craig
  Venter Institute, La Jolla, CA
* August 15, 2016: RNA-seq Analysis. Bristol-Myers Squibb, Hopewell,
  NJ
* April 29, 2016: Lecturer on Introductory RNA-seq Analysis for
  Applied Bioinformatics and Computational Biology course. The Scripps
  Research Institute, La Jolla, CA
* December 21, 2015: Advanced RNA-Seq Analysis. Bristol-Myers Squibb,
  Hopewell, NJ
* November 13, 2015: Advanced RNA-Seq Analysis. The Scripps Research
  Institute, La Jolla, CA

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