resume/ryan_thompson_resume.lyx

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Ryan C.
 Thompson, Ph.
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D.
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\begin_layout CV Name
Ryan C.
 Thompson, Ph.
\begin_inset space \thinspace{}
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D.
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\begin_layout Contact Address
8656 Via Mallorca
\begin_inset Newline newline
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Unit G
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La Jolla, CA 92037
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\begin_layout Phone Number
(908)
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922-7470
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\begin_layout Email
rct@thompsonclan.org
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\begin_layout Website
https://github.com/DarwinAwardWinner
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\begin_layout Section
Summary
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Seeking what kind of job?
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Accomplished, experienced computational biologist with deep knowledge of
 biology, mathematics, statistics, and programming.
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12 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.
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Focus on sound statistical analysis, effective data visualization and communicat
ion, and making expert knowledge and successful analysis methods available
 as re-usable software tools.
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Work in machine learning?
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Supportive team member and experienced mentor with a strong ability to help
 others connect biological, statistical, and computational understanding.
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Education
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2012—2019
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Ph.
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D.
 in Bioinformatics
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, 
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The Scripps Research Institute
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, La Jolla, California 
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Dissertation: 
\emph on

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Update this link to one in the resume repo when possible
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Advisor: 
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2005—2009
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B.
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S.
 in Biology with High Distinction; B.
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A.
 in Mathematics
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University of Virginia
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, Charlottesville, Virginia 
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Undergraduate thesis: 
\emph on

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Advisor: 
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Research Experience
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Salomon & Su Labs, The Scripps Research Institute 
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 La Jolla, CA
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 2012—2019
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Contact: Dr.
 Andrew Su, 
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\begin_layout Itemize
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
\begin_inset Formula $^{+}$
\end_inset

 T-cell activation as well as epigenetic convergence between naive and memory
 cells after activation 
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.
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Significantly improved cross-validated performance of machine learning classifie
r for identifying biomarkers of transplant rejection by developing appropriate
 single-sample microarray normalization procedures 
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, including training a custom set of frozen RMA normalization vectors.
 Classifier is currently being developed into a clinical test for transplant
 dysfunction.
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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 originall
y designed for RNA-seq data.
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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 
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.
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Mentored 3 coworkers from both biology and programming backgrounds in learning
 bioinformatics.
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Investigated effects of life-span-extending drug on worm gene expression
 over time revealing that the drug retards age-related 
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transcriptional drift
\begin_inset Quotes erd
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, preserving a youthful phenotype at the molecular level 
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.
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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.
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\begin_layout Itemize
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.
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, 
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\begin_layout Itemize
Adapted common normalization methods from RNA-seq to improve performance
 in analysis of RASL-seq experiments 
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.
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\begin_layout Subsection
Summer Internship, Informatics IT, Merck & Co.
 
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 Boston, MA
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 2011
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Contact: Adnan Derti, 
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Notify Adnan
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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.
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Assisted in a molecular genetics study to evaluate peformance of two variant
 calling algorithms in detection of causal mutations in antibiotic-resistant
 bacterial genomes.
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Gaasterland Lab, UCSD Bioinformatcs 
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 La Jolla, CA
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 2010—2012
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Contact: Terry Gaasterland, 
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Designed and implemented Deloxer, a critical software step in a new Illumina
 mate-pair sequencing protocol using Cre recombination.
 Deloxer is publishedand now in use in several labs around the world 
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.
 
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Performed a molecular genetics study to find potential causal mutations
 for 
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 in critically endangered black rhinoceros by 
\emph on
de novo
\emph default
 assembly of transcriptomes for black rhino and closely-related white rhino.
 Developed a custom pipeline to match up ortholog gene pairs, discover single-nu
cleotide differences between them, and functionally annotate these differences,
 and delivered a list of potential causal variants to collaborators for
 follow-up.
 
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Helped design & implement one of the first large-scale high-throughput exome
 sequencing pipelines for SNP discovery and functional annotation, including
 QC and validation of on-target coverage depth and reproducibility of coverage.
 
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Analyzed miRNA target predictions using GO & KEGG grouping to identify target
 pathways of autophagy-related miRNAs for biological validation.
 
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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.
 
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\end_inset


\size small
Link: 
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Investigated the binding motif specificity of ZASC1 transcription factor
 in mouse T-cells using Affymetrix expression microarrays in ZASC1 siRNA
 knockdown experiment.
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Timko Lab, U.
 of Virginia Biology 
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 Charlottesville, VA
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 2007—2009
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\begin_layout Description
Advisor: Paul J.
 Rushton
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\begin_layout Itemize
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 
\begin_inset CommandInset citation
LatexCommand cite
key "Thompson2009"
literal "true"

\end_inset

.
\end_layout

\begin_layout Itemize
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.
 
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\end_inset


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Link: 
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Acted as translator between biological researchers and computational analysts
 to help match computational solutions to biological problems.
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\end_inset


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Skills
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\begin_layout Description
Computing
\begin_inset space ~
\end_inset

Skills R/Bioconductor, Python, Perl, Lisp, Java, C#, C++; Git version control;
 Remote UNIX system administration & software compilation, computing cluster
 job management & parallel computation
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\end_inset


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Public code: 
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Stack Overflow profile: 
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Active member of the Bioconductor community since 2012 and contributing
 developer for several packages.
 
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Links: 
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; Packages: 
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, 
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\begin_layout Description
Statistics,
\begin_inset space ~
\end_inset

Machine
\begin_inset space ~
\end_inset

Learning,
\begin_inset space ~
\end_inset

&
\begin_inset space ~
\end_inset

Data
\begin_inset space ~
\end_inset

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 visualizatio
n & presentation, reproducible research practices
\end_layout

\begin_layout Description
Wet
\begin_inset space ~
\end_inset

Lab: PCR, molecular cloning, recombinant protein purification, epitope mapping,
 site-directed mutagenesis, 2D gels, real-time PCR, and associated data
 analysis 
\end_layout

\begin_layout Description
Languages: English: native speaker; German: written and spoken
\end_layout

\begin_layout Section
Other Work Experience
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2005—2007
\end_layout

\end_inset

 Help Desk & Computing Advisor, U.
\begin_inset space \thinspace{}
\end_inset

Va.
 IT Dept.
 
\begin_inset space \hfill{}
\end_inset

 Charlottesville, VA 
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2006—2009
\end_layout

\end_inset

 Summer Sailing Instructor, Raritan Yacht Club 
\begin_inset space \hfill{}
\end_inset

 Perth Amboy, NJ 
\end_layout

\begin_layout Section
Awards & Honors
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2006—2009
\end_layout

\end_inset

 
\begin_inset CommandInset href
LatexCommand href
name "Echols Scholar"
target "http://echols.as.virginia.edu/front"
literal "false"

\end_inset

, University of Virginia
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2006
\end_layout

\end_inset


\begin_inset CommandInset href
LatexCommand href
name "Phi Eta Sigma National Honor Society"
target "https://www.phietasigma.org/"
literal "false"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2006
\end_layout

\end_inset


\begin_inset CommandInset href
LatexCommand href
name "National Society of Collegiate Scholars"
target "https://nscs.org/"
literal "false"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2005
\end_layout

\end_inset

Edward J.
 Bloustein Disguingished Scholar
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
2005
\end_layout

\end_inset


\begin_inset CommandInset href
LatexCommand href
name "National Merit Scholar"
target "https://www.nationalmerit.org/"
literal "false"

\end_inset


\end_layout

\begin_layout Section
Peer-reviewed Publications
\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
The following command suppresses the bibliography's own title, since we
 have one above that's formatted the way we want.
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begingroup 
\end_layout

\begin_layout Plain Layout


\backslash
renewcommand{
\backslash
section}[2]{}%
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset bibtex
LatexCommand bibtex
btprint "btPrintAll"
bibfiles "mypubs-PROCESSED"
options "plainurlyr-rev"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
endgroup
\end_layout

\end_inset


\end_layout

\begin_layout Section
Other Works
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begingroup 
\end_layout

\begin_layout Plain Layout


\backslash
renewcommand{
\backslash
section}[2]{}%
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset bibtex
LatexCommand bibtex
btprint "btPrintAll"
bibfiles "myunpubs-PROCESSED"
options "plainurlyr-rev"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
endgroup
\end_layout

\end_inset


\end_layout

\begin_layout Section
Presentations and Teaching
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
May 8, 2018
\end_layout

\end_inset

 
\series bold
Guest lecturer on RNA-Seq
\series default
 for Advanced Tools and Data Challenges in Bioinformatics course (
\begin_inset CommandInset href
LatexCommand href
name "Lecture"
target "https://darwinawardwinner.github.io/resume/examples/Salomon/Teaching/RNA-Seq%20Lecture.pdf"
literal "false"

\end_inset

 & 
\begin_inset CommandInset href
LatexCommand href
name "Lab"
target "https://darwinawardwinner.github.io/resume/examples/Salomon/Teaching/RNA-Seq%20Lab.html"
literal "false"

\end_inset

).
 University of California, San Diego, CA
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
November 21, 2016
\end_layout

\end_inset

 
\series bold

\begin_inset CommandInset href
LatexCommand href
name "Advanced RNA-Seq Analysis"
target "https://darwinawardwinner.github.io/resume/examples/Salomon/Advanced%20RNA-seq%20Analysis.pdf"
literal "false"

\end_inset

.

\series default
 Schork Lab, J.
 Craig Venter Institute, La Jolla, CA
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
August 15, 2016
\end_layout

\end_inset

 
\series bold
RNA-seq Analysis.

\series default
 Bristol-Myers Squibb, Hopewell, NJ
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
April 29, 2016
\end_layout

\end_inset

 
\series bold
Lecturer on Introductory RNA-seq Analysis
\series default
 for Applied Bioinformatics and Computational Biology course.
 The Scripps Research Institute, La Jolla, CA
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
December 21, 2015
\end_layout

\end_inset

 
\series bold
Advanced RNA-Seq Analysis.

\series default
 Bristol-Myers Squibb, Hopewell, NJ
\end_layout

\begin_layout Standard
\begin_inset Flex Years
status open

\begin_layout Plain Layout
November 13, 2015
\end_layout

\end_inset

 
\series bold
Advanced RNA-Seq Analysis.

\series default
 The Scripps Research Institute, La Jolla, CA
\end_layout

\end_body
\end_document