resume/ryan_thompson_resume.txt

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
==========

* Well-rounded computational biologist with deep knowledge of biology,
  mathematics, and programming
* 9 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
* Strong 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 with a strong ability to foster
  cross-disciplinary literacy by explaining concepts at the right
  level of abstraction

Education
==========

The Scripps Research Institute

* Ph. D. in Bioinformatics, expected 2017

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 - 2017
 
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 interactions between differential histone
  methylation and differential gene expression during T-cell
  activation, as well as key differences in activation between naïve
  and memory cells [2, 3].
* 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]
* Significantly improved performce of machine learning classifier for
  identifying transplant rejection by developing appropriate
  single-sample microarray normalization procedures[1], including
  training a custom set of frozen RMA normalization vectors.
  Classifier is currently being developed into a clinical test for
  transplant dysfunction.
* 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.
* 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]
* Adapted common normalization methods from RNA-seq to improve
  performance in analysis of RASL-seq experiments. [5]
* 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.
* Active member of the Bioconductor community and contributing
  developer for several Bioconductor packages.
* Mentored 2 coworkers 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[8] 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 black rhino transcriptome
  using Trinity and comparison to closely-related white rhino
  transcriptome. 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

Contact: Paul J. Rushton, Paul.Rushton@sdstate.edu

* 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[6].
* 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

Writings and Publications
==========

[1] 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.

[2] 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 (in review), 2017.

[3] 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,
May 2016.

[4] 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.

[5] 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: opensource methods for designing and analyzing
RNA-mediated oligonucleotide Annealing, Selection, and, Ligation
sequencing (RASL-seq) experiments. Nucleic Acids Research (in review),
2016.

[6] 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.

[7] SM Kurian, AN Williams, T Gelbart, D Campbell, TS Mondala, SR
Head, S Horvath, L Gaber, R Thompson, T Whisenant, et al. Molecular
Classifiers for Acute Kidney Transplant Rejection in Peripheral Blood
by Whole Genome Gene Expression Profiling. American Journal of
Transplantation, 14(5):1164–1172, 2014.

[8] 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, page gkr1000, 2011.

[9] 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.
http://darwinawardwinner.github.io/resume/examples/UVa/contigfarmer.pdf

[10] Ryan C. Thompson. The sources and limits of geometric rigor from
Euclid through Descartes. May 2008.
http://darwinawardwinner.github.io/resume/examples/UVa/math-history-paper.pdf

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