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-<div class="standard" id='magicparlabel-1'><span class="flex_cv_image"><img src="headshot-crop.png" width="100"></span></div>
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-<div class="cv_name" id='magicparlabel-6'>Ryan C. Thompson</div>
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-<div class="contact_address" id='magicparlabel-7'><span class="contact_address_label">Contact Address:</span> 8656 Via Mallorca
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-Unit G
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-La Jolla, CA 92037</div>
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-<div class="phone_number" id='magicparlabel-8'><span class="phone_number_label">Phone:</span> (908) 922-7470</div>
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-<div class="email" id='magicparlabel-9'><span class="email_label">Email:</span> rct@thompsonclan.org</div>
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-<div class="website" id='magicparlabel-10'><span class="website_label">Website:</span> https://github.com/DarwinAwardWinner</div>
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-<div class="section" id='magicparlabel-11'><span class="section_label"></span> Summary</div>
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-<ul class="itemize" id='magicparlabel-12'><li class="itemize_item">Well-rounded computational biologist with deep knowledge of biology, mathematics, and programming</li>
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-<li class="itemize_item">10 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 </li>
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-<li class="itemize_item">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</li>
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-<li class="itemize_item">Supportive team member with a strong ability to foster cross-disciplinary literacy by explaining concepts at the right level of abstraction</li>
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-</ul>
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-<div class="section" id='magicparlabel-16'><span class="section_label"></span> Education</div>
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-<dl class='description' id='magicparlabel-17'><dt class="description_label">The Scripps Research Institute</dt>
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-Ph. D. in Bioinformatics, 2019</dd>
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-<dt class="description_label">University of Virginia</dt>
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-<dd class="description_item">
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-B.S. in Biology, B.A. in Mathematics, 2009
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-Echols Scholar</dd>
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-</dl>
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-<div class="section" id='magicparlabel-19'><span class="section_label"></span> Research Experience</div>
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-<div class="subsection" id='magicparlabel-20'><span class="subsection_label"></span> Salomon Lab, The Scripps Research Institute La Jolla, CA   2012 - 2019</div>
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-<dl class='description' id='magicparlabel-21'><dt class="description_label">Contact:</dt>
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-<dd class="description_item"> Dr. Andrew Su, <a href="asu@scripps.edu">asu@scripps.edu</a></dd>
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-<ul class="itemize" id='magicparlabel-22'><li class="itemize_item">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 [<a href='#LyXCite-lamere2016'><span class="bib-label">2</span></a>, <a href='#LyXCite-lamere2017_JMJD3'><span class="bib-label">3</span></a>].
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-Links: <a href="https://github.com/DarwinAwardWinner/CD4-csaw#re-analysis-of-a-combined-chip-seq--rna-seq-data-set">Reproducible workflow</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/CD4/ChIP-Seq%20presentation.pdf">Slides</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/CD4/">Example results and visualizations</a></li>
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-<li class="itemize_item">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. [<a href='#LyXCite-Rangarajue08833'><span class="bib-label">4</span></a>]
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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/mdsplots-multidim.pdf">PCoA Plot</a> </li>
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-<li class="itemize_item">Significantly improved performce of machine learning classifier for identifying transplant rejection by developing appropriate single-sample microarray normalization procedures[<a href='#LyXCite-kurian2014molecular'><span class="bib-label">1</span></a>], 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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-Links: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/fRMA/">fRMA example code & plots</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Classifier%20Math%20Write-up.pdf">Classifier Method Write-up</a></li>
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-<li class="itemize_item">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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-Links: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Pathways/Pathway%20Presentation.pdf">Presentation</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Pathways/Pathway%20Analysis%20Example.html">Example Results</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Pathways/Cyno%20Pathway%20Summary.pdf">Summary</a></li>
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-<li class="itemize_item">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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-Links: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/DGE%20Presentation.pdf">RNA-seq Presentation</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Advanced%20RNA-seq%20Analysis.pdf">Advanced RNA-seq Presentation</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/globin/pval-comparisons.pdf">Example plot </a></li>
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-<li class="itemize_item">Taught basic RNA-seq theory and practical analysis for the graduate-level introductory bioinformatics course.
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-Links: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Teaching/RNA-Seq Lecture.pdf">Lecture Slides</a>, <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/Teaching/RNA-Seq Lab.html">Hands-on lab section</a></li>
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-<li class="itemize_item">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. [<a href='#LyXCite-globin_reduction'><span class="bib-label">6</span></a>]
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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/globin/">Example results</a></li>
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-<li class="itemize_item">Adapted common normalization methods from RNA-seq to improve performance in analysis of RASL-seq experiments. [<a href='#LyXCite-Scott036061'><span class="bib-label">7</span></a>]</li>
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-<li class="itemize_item">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.
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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/450k/">Example diagnostic plots</a></li>
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-<li class="itemize_item">Active member of the Bioconductor community and contributing developer for several Bioconductor packages.
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-Links: <a href="http://bioconductor.org/packages/release/bioc/html/BiocParallel.html">BiocParallel</a>, <a href="http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html">ChIPPeakAnno</a>, <a href="http://bioconductor.org/packages/release/bioc/html/mygene.html">MyGene</a>, <a href="https://support.bioconductor.org/u/5618/">Support Profile</a></li>
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-<li class="itemize_item">Mentored 2 coworkers in learning bioinformatics, one from a programming background and the other from a biology background.</li>
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-</ul>
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-<div class="subsection" id='magicparlabel-33'><span class="subsection_label"></span> Summer Internship, Informatics IT, Merck & Co. Boston, MA   2011</div>
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-<dl class='description' id='magicparlabel-34'><dt class="description_label">Contact:</dt>
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-<dd class="description_item"> Adnan Derti, <a href="adnan.derti@gmail.com">adnan.derti@gmail.com</a> </dd>
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-<ul class="itemize" id='magicparlabel-35'><li class="itemize_item">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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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/cufflinks-presentation.pdf">Presentation Slides</a></li>
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-<li class="itemize_item">Assisted in a molecular genetics study to evaluate peformance of two variant calling algorithms in detection of causal mutations in antibiotic-resistant bacterial genomes.</li>
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-<div class="subsection" id='magicparlabel-37'><span class="subsection_label"></span> Gaasterland Lab, UCSD Bioinformatcs La Jolla, CA   2010 - 2012</div>
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-<dl class='description' id='magicparlabel-38'><dt class="description_label">Contact:</dt>
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-<dd class="description_item"> Terry Gaasterland, <a href="gaasterland@ucsd.edu">gaasterland@ucsd.edu</a> </dd>
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-</dl>
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-<ul class="itemize" id='magicparlabel-39'><li class="itemize_item">Designed and implemented Deloxer, a critical software step in a new Illumina mate-pair sequencing protocol using Cre recombination. Deloxer is published[<a href='#LyXCite-van2011illumina'><span class="bib-label">8</span></a>] and now in use in several labs around the world.
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-Links: <a href="http://genomes.sdsc.edu/downloads/deloxer/index.html">Documentation</a>; <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/delox.R.html">Code</a></li>
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-<li class="itemize_item">Performed a molecular genetics study to find potential causal mutations for <a href="https://en.wikipedia.org/wiki/Black_rhinoceros#Threats">fatal iron overload disease</a> in critically endangered black rhinoceros by <em>de novo</em> 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.
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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/ipi-results-small.txt">Example results</a></li>
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-<li class="itemize_item">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.
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-Links: <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/neartarget.pdf">Example 1</a>; <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/on-off-coverage.pdf">Example 2</a>; <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/depth-consistency.pdf">Example 3</a></li>
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-<li class="itemize_item">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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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/illumina-qc.png">Example results</a></li>
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-<li class="itemize_item">Investigated the binding motif specificity of ZASC1 transcription factor in mouse T-cells using Affymetrix expression microarrays in ZASC1 siRNA knockdown experiment.</li>
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-<li class="itemize_item">Analyzed miRNA target predictions using GO & KEGG grouping to identify target pathways of autophagy-related miRNAs for biological validation.
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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/mirna-results.html">Example results</a></li>
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-</ul>
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-<div class="subsection" id='magicparlabel-45'><span class="subsection_label"></span> Timko Lab, U. of Virginia BiologyCharlottesville, VA   2007 - 2009</div>
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-<dl class='description' id='magicparlabel-46'><dt class="description_label">Contact:</dt>
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-<dd class="description_item"> Paul J. Rushton, <a href="Paul.Rushton@sdstate.edu">Paul.Rushton@sdstate.edu</a></dd>
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-<ul class="itemize" id='magicparlabel-47'><li class="itemize_item">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[<a href='#LyXCite-cfarmer'><span class="bib-label">5</span></a>].</li>
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-<li class="itemize_item">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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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/UVa/probe-selection.R.html">Code</a></li>
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-<li class="itemize_item">Acted as interpreter to explain complex biological concepts to programmers and explain complex computational problems to biologists.
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-Link: <a href="https://darwinawardwinner.github.io/resume/examples/UVa/blast-slides.pdf">Presentation Slides</a> </li>
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-<div class="section" id='magicparlabel-50'><span class="section_label"></span> Skills</div>
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-<dl class='description' id='magicparlabel-51'><dt class="description_label">Computing Skills</dt>
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-<dd class="description_item"> 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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-Public code: <a href="https://github.com/DarwinAwardWinner">https://github.com/DarwinAwardWinner</a>
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-StackOverflow Profile: <a href="http://stackoverflow.com/users/125921">http://stackoverflow.com/users/125921</a> </dd>
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-<dt class="description_label">Statistics & Data Analysis</dt>
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-<dd class="description_item"> 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</dd>
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-<dt class="description_label">Wet Lab:</dt>
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-<dd class="description_item"> PCR, molecular cloning, recombinant protein purification, epitope mapping, site-directed mutagenesis, 2D gels, real-time PCR, and associated data analysis </dd>
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-<dt class="description_label">Languages:</dt>
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-<dd class="description_item"> English: native speaker; German: written and spoken</dd>
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-<div class="section" id='magicparlabel-55'><span class="section_label"></span> Other Work Experience</div>
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-<div class="subsection" id='magicparlabel-56'><span class="subsection_label"></span> Computing Advisor & Help Desk, U. Va. IT Dept. Charlottesville, VA    2005 - 2007 </div>
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-<ul class="itemize" id='magicparlabel-57'><li class="itemize_item">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</li>
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-<li class="itemize_item">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</li>
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-<div class="subsection" id='magicparlabel-59'><span class="subsection_label"></span> Summer Sailing Instructor, Raritan Yacht Club Perth Amboy, NJ    2006 - 2009 </div>
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-<ul class="itemize" id='magicparlabel-60'><li class="itemize_item">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</li>
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-<li class="itemize_item">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</li>
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-<li class="itemize_item">Helped organize, run, and referee several regattas per season for students from RYC and neighboring yacht clubs</li>
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-</ul>
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-<div class="standard" id='magicparlabel-73'><h2 class='bibtex'>References</h2><div class='bibtex'><div class='bibtexentry' id='LyXCite-cfarmer'><span class='bibtexinfo'><span class="bib-fullnames:author"> Ryan C. Thompson, Paul J. Rushton, Tom W. Laudeman, and Michael P. Timko</span>, "<span class="bib-title">http://darwinawardwinner.github.io/resume/examples/UVa/contigfarmer.pdfContig Farmer: a tool for extracting maximal-length contiguous sequences from a database of short sequence reads (Undergraduate Thesis)</span>" (<span class="bib-year">2009</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-eiv_2017'><span class='bibtexinfo'><span class="bib-fullnames:author">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</span>, "<span class="bib-title">Orthogonal Comparison of Molecular Signatures of Kidney Transplants with Subclinical and Clinical Acute Rejection -- Equivalent Performance is Agnostic to either Technology or Platform</span>", <i><span class="bib-journal">American Journal of Transplantation</span></i> (<span class="bib-year">2017</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-globin_reduction'><span class='bibtexinfo'><span class="bib-fullnames:author"> 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</span>, "<span class="bib-title">Optimizing yield of deep RNA sequencing for gene expression profiling of peripheral blood samples from cynomolgus monkeys (Macaca fascicularis)</span>", <i><span class="bib-journal">Journal of Biological Methods (in review)</span></i> (<span class="bib-year">2016</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-kurian2014molecular'><span class='bibtexinfo'><span class="bib-fullnames:author">SM Kurian, AN Williams, T Gelbart, D Campbell, TS Mondala, SR Head, S Horvath, L Gaber, R Thompson, T Whisenant</span>, "<span class="bib-title">Molecular Classifiers for Acute Kidney Transplant Rejection in Peripheral Blood by Whole Genome Gene Expression Profiling</span>", <i><span class="bib-journal">American Journal of Transplantation</span></i> <span class="bib-volume">14</span>, <span class="bib-number">5</span> (<span class="bib-year">2014</span>), pp. <span class="bib-pages">1164--1172</span>.</span></div>
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-<div class='bibtexentry' id='LyXCite-lamere2016'><span class='bibtexinfo'><span class="bib-fullnames:author">Sarah LaMere, Ryan C. Thompson, H. Kiyomi Komori, Adam Mark, and Daniel R. Salomon</span>, "<span class="bib-title">Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells</span>", <i><span class="bib-journal">Genes & Immunity</span></i> (<span class="bib-year">2016</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-lamere2017_JMJD3'><span class='bibtexinfo'><span class="bib-fullnames:author">Sarah LaMere, Ryan C. Thompson, Xiangzhi Meng, H. Kiyomi Komori, A. Mark, and Daniel R. Salomon</span>, "<span class="bib-title">H3K27 methylation dynamics during CD4 T cell activation: regulation of JAK/STAT and IL12RB2 expression by JMJD3</span>", <i><span class="bib-journal">Journal of Immunology (accepted)</span></i> (<span class="bib-year">2017</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-math_history_paper'><span class='bibtexinfo'><span class="bib-fullnames:author"> Ryan C. Thompson</span>, "<span class="bib-title">http://darwinawardwinner.github.io/resume/examples/UVa/math-history-paper.pdfThe sources and limits of geometric rigor from Euclid through Descartes</span>" (<span class="bib-year">2008</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-Rangarajue08833'><span class='bibtexinfo'><span class="bib-fullnames:author">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</span>, "<span class="bib-title">Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality</span>", <i><span class="bib-journal">eLife</span></i> <span class="bib-volume">4</span> (<span class="bib-year">2015</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-Scott036061'><span class='bibtexinfo'><span class="bib-fullnames:author">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</span>, "<span class="bib-title">RASLseqTools: open-source methods for designing and analyzing RNA-mediated oligonucleotide Annealing, Selection, and, Ligation sequencing (RASL-seq) experiments</span>", <i><span class="bib-journal">Nucleic Acids Research (in review)</span></i> (<span class="bib-year">2016</span>).</span></div>
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-<div class='bibtexentry' id='LyXCite-van2011illumina'><span class='bibtexinfo'><span class="bib-fullnames:author">Filip Van Nieuwerburgh, Ryan C. Thompson, Jessica Ledesma, Dieter Deforce, Terry Gaasterland, Phillip Ordoukhanian, and Steven R Head</span>, "<span class="bib-title">Illumina Mate-Paired DNA Sequencing Library Preparation Using Cre-Lox Recombination</span>", <i><span class="bib-journal">Nucleic Acids Research</span></i> (<span class="bib-year">2011</span>), pp. <span class="bib-pages">gkr1000</span>.</span></div>
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