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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.
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D.
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8656 Via Mallorca
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Unit G
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La Jolla, CA 92037
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\begin_layout Phone Number
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922-7470
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https://github.com/DarwinAwardWinner
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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:
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name "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"
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Update this link to one in the resume repo when possible
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Advisor:
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LatexCommand href
name "Andrew Su"
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2005—2009
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B.
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S.
in Biology with High Distinction; B.
\begin_inset space \thinspace{}
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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:
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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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\begin_layout Description
Contact: Dr.
Andrew Su,
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LatexCommand href
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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 $^{+}$
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T-cell activation as well as epigenetic convergence between naive and memory
cells after activation
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.
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Links:
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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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,
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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
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, preserving a youthful phenotype at the molecular level
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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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Performed comparative analysis of multiple differential expression statistical
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false positive control.
Presented on theoretical and practical similarities and differences between
methods.
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,
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,
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LatexCommand href
name "Example plot "
target "https://darwinawardwinner.github.io/resume/examples/Salomon/globin/pval-comparisons.pdf"
literal "false"
\end_inset
\end_layout
\begin_layout Itemize
Adapted common normalization methods from RNA-seq to improve performance
in analysis of RASL-seq experiments
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LatexCommand cite
key "Scott2016"
literal "true"
\end_inset
.
\end_layout
\end_inset
\end_layout
\begin_layout Subsection
Summer Internship, Informatics IT, Merck & Co.
\begin_inset space \hfill{}
\end_inset
Boston, MA
\begin_inset space \qquad{}
\end_inset
2011
\end_layout
\begin_layout Description
Contact: Adnan Derti,
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name "[email protected]"
target "[email protected]"
type "mailto:"
literal "false"
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\begin_inset Note Note
status open
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Notify Adnan
\end_layout
\end_inset
\end_layout
\begin_layout Itemize
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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\end_inset
\size small
Link:
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LatexCommand href
name "Presentation Slides"
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\begin_layout Itemize
Assisted in a molecular genetics study to evaluate peformance of two variant
calling algorithms in detection of causal mutations in antibiotic-resistant
bacterial genomes.
\end_layout
\begin_layout Subsection
Gaasterland Lab, UCSD Bioinformatcs
\begin_inset space \hfill{}
\end_inset
La Jolla, CA
\begin_inset space \qquad{}
\end_inset
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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key "VanNieuwerburgh2012"
literal "true"
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.
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Links:
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;
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\end_inset
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Performed a molecular genetics study to find potential causal mutations
for
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name "fatal iron overload disease"
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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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\end_inset
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Link:
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\begin_layout Itemize
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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\end_inset
\size small
Links:
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LatexCommand href
name "Example 1"
target "https://darwinawardwinner.github.io/resume/examples/Gaasterland/neartarget.pdf"
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