resume/ryan_thompson_resume.lyx

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\begin_body

\begin_layout Standard
\begin_inset Flex CV Image
status open

\begin_layout Plain Layout
headshot-crop.jpg
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\begin_layout CV Name
Ryan C.
 Thompson
\end_layout

\begin_layout Contact Address
8656 Via Mallorca G
\begin_inset Newline newline
\end_inset

La Jolla, CA 92037
\end_layout

\begin_layout Phone Number
(908) 922-7470
\end_layout

\begin_layout Email
rct@thompsonclan.org
\end_layout

\begin_layout Website
https://github.com/DarwinAwardWinner
\end_layout

\begin_layout Section
Summary
\end_layout

\begin_layout Itemize
Well-rounded computational biologist with deep knowledge of biology, mathematics
, and programming
\end_layout

\begin_layout Itemize
9 years of bioinformatics experience answering a wide range of complex biologica
l questions through analysis of large NGS- and microarray-based whole transcript
ome and epigenetic data sets with a strong focus on sound statistical analysis
 and effective data visualization and presentation
\end_layout

\begin_layout Itemize
Supportive team member with a strong ability to foster cross-disciplinary
 literacy by explaining concepts at the right level of abstraction
\end_layout

\begin_layout Itemize
Focus on packaging expert knowledge and successful analysis methods into
 re-usable software tools to share best practices and improve team efficiency
 over time
\end_layout

\begin_layout Section
Education
\end_layout

\begin_layout Description
The
\begin_inset space \space{}
\end_inset

Scripps
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\end_inset

Research
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\end_inset

Institute 
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\end_inset

 
\begin_inset Newline newline
\end_inset

Ph.
 D.
 in Bioinformatics, expected Fall 2016
\end_layout

\begin_layout Description
University
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\end_inset

of
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\end_inset

Virginia 
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\end_inset

 
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\end_inset

B.S.
 in Biology, B.A.
 in Mathematics, 2009
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\end_inset

Echols Scholar
\end_layout

\begin_layout Section
Research Experience
\end_layout

\begin_layout Subsection
Salomon Lab, The Scripps Research Institute 
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\end_inset

 La Jolla, CA
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\end_inset

 2012 - 2016
\end_layout

\begin_layout Itemize
Significantly improved machine learning classifier performance in cross-validati
on and independent validation by developing appropriate single-sample microarray
 normalization procedures
\begin_inset CommandInset citation
LatexCommand cite
key "kurian2014molecular"

\end_inset

, including training a custom set of frozen RMA normalization vectors.
 Classifier is currently being developed into a clinical test for transplant
 dysfunction.
\begin_inset Newline newline
\end_inset

Links: 
\begin_inset CommandInset href
LatexCommand href
name "fRMA example code & plots"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/fRMA/"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "Classifier Method Write-up"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/Classifier%20Math%20Write-up.pdf"

\end_inset


\end_layout

\begin_layout Itemize
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.
\begin_inset Newline newline
\end_inset

Links: 
\begin_inset CommandInset href
LatexCommand href
name "Presentation"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/Pathways/Pathway%20Presentation.pdf"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "Example Results"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/Pathways/Pathway%20Analysis%20Example.html"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "Summary"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/Pathways/Cyno%20Pathway%20Summary.pdf"

\end_inset


\end_layout

\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 in lab meeting and in seminars at Merck and BMS bioinformatics
 departments.
\begin_inset Newline newline
\end_inset

Links: 
\begin_inset CommandInset href
LatexCommand href
name "RNA-seq Presentation"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/DGE%20Presentation.pdf"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "Advanced RNA-seq Presentation"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/Advanced%20RNA-seq%20Analysis.pdf"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "Example plot "
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/globin/pval-comparisons.pdf"

\end_inset


\end_layout

\begin_layout Itemize
Analyzed large multi-omics next-gen sequencing dataset of 220 RNA-seq and
 ChIP-seq samples to reveal interactions between differential histone methylatio
n and differential gene expression during T-cell activation, as well as
 key differences in activation between naïve and memory cells 
\begin_inset CommandInset citation
LatexCommand cite
key "lamere2016"

\end_inset

.
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Example results and visualizations"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/CD4/"

\end_inset

 
\end_layout

\begin_layout Itemize
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 from 20% to 75%.
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Example results"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/globin/"

\end_inset


\end_layout

\begin_layout Itemize
Investigated effects of life-span-extending drug on worm gene expression
 over time revealing that the drug retards age-related 
\begin_inset Quotes eld
\end_inset

transcriptional drift
\begin_inset Quotes erd
\end_inset

, preserving youthful phenotype at the molecular level.
 
\begin_inset CommandInset citation
LatexCommand cite
key "Rangarajue08833"

\end_inset

 
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "PCoA Plot"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/mdsplots-multidim.pdf"

\end_inset

 
\end_layout

\begin_layout Itemize
Identified normalization methods from other problem domains that improved
 performance in analysis of RASL-seq experiments.
 
\begin_inset CommandInset citation
LatexCommand cite
key "Scott036061"

\end_inset


\end_layout

\begin_layout Itemize
Performed a comprehensive comparitive 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.
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Example diagnostic plots"
target "http://mneme.homenet.org/~ryan/resume/examples/Salomon/450k/"

\end_inset


\end_layout

\begin_layout Itemize
Contributing developer for several Bioconductor packages and active member
 of the Bioconductor community 
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\end_inset

Links: 
\begin_inset CommandInset href
LatexCommand href
name "BiocParallel"
target "http://bioconductor.org/packages/release/bioc/html/BiocParallel.html"

\end_inset

, 
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LatexCommand href
name "ChIPPeakAnno"
target "http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "MyGene"
target "http://bioconductor.org/packages/release/bioc/html/mygene.html"

\end_inset

, 
\begin_inset CommandInset href
LatexCommand href
name "Support Profile"
target "https://support.bioconductor.org/u/5618/"

\end_inset


\end_layout

\begin_layout Itemize
Reference: Dr.
 Daniel Salomon, 
\begin_inset CommandInset href
LatexCommand href
name "dsalomon@scripps.edu"
target "dsalomon@scripps.edu"
type "mailto:"

\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 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.
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Presentation Slides"
target "http://mneme.homenet.org/~ryan/resume/examples/cufflinks-presentation.pdf"

\end_inset


\end_layout

\begin_layout Itemize
Assisted in a molecular genetics study to evaluate peformance of two variant
 calling algorithms in detecting causal mutations in antibiotic-resistant
 bacterial genomes.
 
\end_layout

\begin_layout Itemize
Reference: Adnan Derti, 
\begin_inset CommandInset href
LatexCommand href
name "adnan.derti@gmail.com"
target "adnan.derti@gmail.com"
type "mailto:"

\end_inset

 
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\begin_layout Subsection
Gaasterland Lab, UCSD Bioinformatcs 
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La Jolla, CA
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\end_inset

 2010 - 2012
\end_layout

\begin_layout Itemize
Designed and implemented Deloxer, a critical software step in a new Illumina
 mate-pair sequencing protocol using Cre recombination.
 Deloxer is published
\begin_inset CommandInset citation
LatexCommand cite
key "van2011illumina"

\end_inset

 and now in use in several labs around the world.
 
\begin_inset Newline newline
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Links: 
\begin_inset CommandInset href
LatexCommand href
name "Documentation"
target "http://genomes.sdsc.edu/downloads/deloxer/index.html"

\end_inset

; 
\begin_inset CommandInset href
LatexCommand href
name "Code"
target "http://genomes.sdsc.edu/downloads/deloxer/delox.R"

\end_inset


\end_layout

\begin_layout Itemize
Performed a molecular genetics study to find potential causal mutations
 for 
\begin_inset CommandInset href
LatexCommand href
name "fatal iron overload disease"
target "https://en.wikipedia.org/wiki/Black_rhinoceros#Threats"

\end_inset

 in critically endangered black rhinoceros by 
\emph on
de novo
\emph default
 assembly of black rhino transcriptomes and comparison with closely-related
 white rhino transcriptomes using Trinity.
 Developed a custom pipeline to match up ortholog gene pairs and discover
 and functionally annotate single-nucleotide differences between them, and
 delivered a list of potential variants to collaborators for follow-up.
 
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Example results"
target "http://mneme.homenet.org/~ryan/resume/examples/Gaasterland/ipi-results-small.txt"

\end_inset


\end_layout

\begin_layout Itemize
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.
 
\begin_inset Newline newline
\end_inset

Links: 
\begin_inset CommandInset href
LatexCommand href
name "Example 1"
target "http://mneme.homenet.org/~ryan/resume/examples/Gaasterland/neartarget.pdf"

\end_inset

; 
\begin_inset CommandInset href
LatexCommand href
name "Example 2"
target "http://mneme.homenet.org/~ryan/resume/examples/Gaasterland/on-off-coverage.pdf"

\end_inset

; 
\begin_inset CommandInset href
LatexCommand href
name "Example 3"
target "http://mneme.homenet.org/~ryan/resume/examples/Gaasterland/depth-consistency.pdf"

\end_inset


\end_layout

\begin_layout Itemize
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.
 
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Example results"
target "http://mneme.homenet.org/~ryan/resume/examples/Gaasterland/illumina-qc.html"

\end_inset


\end_layout

\begin_layout Itemize
Investigated the binding motif specificity of ZASC1 transcription factor
 in mouse T-cells using Affymetrix expression microarrays in ZASC1 siRNA
 knockdown experiment.
\end_layout

\begin_layout Itemize
Analyzed miRNA target predictions using GO & KEGG grouping to identify target
 pathways of autophagy-related miRNAs for biological validation.
 
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Example results"
target "http://mneme.homenet.org/~ryan/resume/examples/Gaasterland/mirna-results.html"

\end_inset


\end_layout

\begin_layout Itemize
Reference: Terry Gaasterland, 
\begin_inset CommandInset href
LatexCommand href
name "gaasterland@ucsd.edu"
target "gaasterland@ucsd.edu"
type "mailto:"

\end_inset

 
\end_layout

\begin_layout Subsection
Timko Lab, U.
 of Virginia Biology
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\end_inset

Charlottesville, VA
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\end_inset

 2007 - 2009
\end_layout

\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 "cfarmer"

\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.
 
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Code"
target "http://mneme.homenet.org/~ryan/resume/examples/UVa/probe-selection.R"

\end_inset


\end_layout

\begin_layout Itemize
Acted as interpreter to explain complex biological concepts to programmers
 and explain complex computational problems to biologists.
\begin_inset Newline newline
\end_inset

Link: 
\begin_inset CommandInset href
LatexCommand href
name "Presentation Slides"
target "http://mneme.homenet.org/~ryan/resume/examples/UVa/blast-slides.pdf"

\end_inset

 
\end_layout

\begin_layout Itemize
Reference: Paul J.
 Rushton, 
\begin_inset CommandInset href
LatexCommand href
name "Paul.Rushton@sdstate.edu"
target "Paul.Rushton@sdstate.edu"
type "mailto:"

\end_inset


\end_layout

\begin_layout Section
Skills
\end_layout

\begin_layout Description
Computing
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\end_inset

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

Public code: 
\begin_inset CommandInset href
LatexCommand href
target "https://github.com/DarwinAwardWinner"

\end_inset

 
\begin_inset Newline newline
\end_inset

StackOverflow Profile: 
\begin_inset CommandInset href
LatexCommand href
target "http://stackoverflow.com/users/125921"

\end_inset

 
\end_layout

\begin_layout Description
Statistics
\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; German: written and spoken
\end_layout

\begin_layout Section
Other Work Experience
\end_layout

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

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

 Charlottesville, VA 
\begin_inset space \qquad{}
\end_inset

 2005 - 2007 
\end_layout

\begin_layout Itemize
Provided support via phone and in person for students, faculty, and staff
 having problems with computers, phone system, network access, malware,
 hardware setup, and university web services
\end_layout

\begin_layout Itemize
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
\end_layout

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

 Perth Amboy, NJ 
\begin_inset space \qquad{}
\end_inset

 2006 - 2009 
\end_layout

\begin_layout Itemize
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
\end_layout

\begin_layout Itemize
Ensured safety of students and staff by maintaining boats and equipment
 in good repair, being vigilant to traffic and hazards on a busy waterway,
 and communicating and coordinating efficiently with other staff
\end_layout

\begin_layout Itemize
Helped organize, run, and referee several regattas per season for students
 from RYC and neighboring yacht clubs
\end_layout

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The following command changes the title of the bibliography and also un-does
 the indentation of it
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\backslash
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hspace{-116pt}Writings and Publications}
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\begin_layout Standard
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LatexCommand bibtex
btprint "btPrintAll"
bibfiles "citations"
options "plainyr-rev"

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Online version (with links): 
\begin_inset CommandInset href
LatexCommand href
target "http://mneme.homenet.org/~ryan/resume/ryan_thompson_resume.pdf"

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