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ryan_thompson_resume.html

@@ -113,13 +113,12 @@ La Jolla, CA 92037</div>
 
 <ul class="itemize"><a id='magicparlabel-12' /><li class="itemize_item">Well-rounded computational biologist with deep knowledge of biology, mathematics, and programming</li>
 <li class="itemize_item">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 </li>
-<li class="itemize_item">Strong focus on sound statistical analysis and effective data visualization and presentation</li>
+<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>
 <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>
-<li class="itemize_item">Focus on packaging expert knowledge and successful analysis methods into re-usable software tools to share best practices and improve team efficiency over time</li>
 </ul>
-<div class="section"><a id='magicparlabel-17' /><span class="section_label"></span> Education</div>
+<div class="section"><a id='magicparlabel-16' /><span class="section_label"></span> Education</div>
 
-<dl class='description'><a id='magicparlabel-18' /><dt class="description_label">The Scripps Research Institute</dt>
+<dl class='description'><a id='magicparlabel-17' /><dt class="description_label">The Scripps Research Institute</dt>
 <dd class="description_item">  
 <br />
 
@@ -133,18 +132,18 @@ B.S. in Biology, B.A. in Mathematics, 2009
 
 Echols Scholar</dd>
 </dl>
-<div class="section"><a id='magicparlabel-20' /><span class="section_label"></span> Research Experience</div>
-<div class="subsection"><a id='magicparlabel-21' /><span class="subsection_label"></span> Salomon Lab, The Scripps Research Institute  La Jolla, CA&emsp;&emsp; 2012 - 2017</div>
+<div class="section"><a id='magicparlabel-19' /><span class="section_label"></span> Research Experience</div>
+<div class="subsection"><a id='magicparlabel-20' /><span class="subsection_label"></span> Salomon Lab, The Scripps Research Institute  La Jolla, CA&emsp;&emsp; 2012 - 2017</div>
 
-<dl class='description'><a id='magicparlabel-22' /><dt class="description_label">Contact:</dt>
+<dl class='description'><a id='magicparlabel-21' /><dt class="description_label">Contact:</dt>
 <dd class="description_item"> Dr. Andrew Su, <a href="asu@scripps.edu">asu@scripps.edu</a></dd>
 </dl>
 
-<ul class="itemize"><a id='magicparlabel-23' /><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-lamere2016_JMJD3'>#<span class="bib-key">lamere2016-JMJD3</span></a>].
+<ul class="itemize"><a 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>].
 <br />
 
 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>
-<li class="itemize_item">Investigated effects of life-span-extending drug on worm gene expression over time revealing that the drug retards age-related &ldquo;transcriptional drift&rdquo;, preserving a youthful phenotype at the molecular level. [<a href='#LyXCite-Rangarajue08833'><span class="bib-label">3</span></a>] 
+<li class="itemize_item">Investigated effects of life-span-extending drug on worm gene expression over time revealing that the drug retards age-related &ldquo;transcriptional drift&rdquo;, preserving a youthful phenotype at the molecular level. [<a href='#LyXCite-Rangarajue08833'><span class="bib-label">4</span></a>] 
 <br />
 
 Link: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/mdsplots-multidim.pdf">PCoA Plot</a> </li>
@@ -164,11 +163,11 @@ Links: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/DGE%
 <br />
 
 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>
-<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>]
+<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">7</span></a>]
 <br />
 
 Link: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/globin/">Example results</a></li>
-<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">4</span></a>]</li>
+<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">5</span></a>]</li>
 <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.
 <br />
 
@@ -179,25 +178,25 @@ Link: <a href="https://darwinawardwinner.github.io/resume/examples/Salomon/450k/
 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>
 <li class="itemize_item">Mentored 2 coworkers in learning bioinformatics.</li>
 </ul>
-<div class="subsection"><a id='magicparlabel-34' /><span class="subsection_label"></span> Summer Internship, Informatics IT, Merck &amp; Co. Boston, MA&emsp;&emsp; 2011</div>
+<div class="subsection"><a id='magicparlabel-33' /><span class="subsection_label"></span> Summer Internship, Informatics IT, Merck &amp; Co. Boston, MA&emsp;&emsp; 2011</div>
 
-<dl class='description'><a id='magicparlabel-35' /><dt class="description_label">Contact:</dt>
+<dl class='description'><a id='magicparlabel-34' /><dt class="description_label">Contact:</dt>
 <dd class="description_item"> Adnan Derti, <a href="adnan.derti@gmail.com">adnan.derti@gmail.com</a> </dd>
 </dl>
 
-<ul class="itemize"><a id='magicparlabel-36' /><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.
+<ul class="itemize"><a 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.
 <br />
 
 Link: <a href="https://darwinawardwinner.github.io/resume/examples/cufflinks-presentation.pdf">Presentation Slides</a></li>
 <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>
 </ul>
-<div class="subsection"><a id='magicparlabel-38' /><span class="subsection_label"></span> Gaasterland Lab, UCSD Bioinformatcs La Jolla, CA&emsp;&emsp; 2010 - 2012</div>
+<div class="subsection"><a id='magicparlabel-37' /><span class="subsection_label"></span> Gaasterland Lab, UCSD Bioinformatcs La Jolla, CA&emsp;&emsp; 2010 - 2012</div>
 
-<dl class='description'><a id='magicparlabel-39' /><dt class="description_label">Contact:</dt>
+<dl class='description'><a id='magicparlabel-38' /><dt class="description_label">Contact:</dt>
 <dd class="description_item"> Terry Gaasterland, <a href="gaasterland@ucsd.edu">gaasterland@ucsd.edu</a> </dd>
 </dl>
 
-<ul class="itemize"><a id='magicparlabel-40' /><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">7</span></a>] and now in use in several labs around the world. 
+<ul class="itemize"><a 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. 
 <br />
 
 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>
@@ -219,13 +218,13 @@ Link: <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/i
 
 Link: <a href="https://darwinawardwinner.github.io/resume/examples/Gaasterland/mirna-results.html">Example results</a></li>
 </ul>
-<div class="subsection"><a id='magicparlabel-46' /><span class="subsection_label"></span> Timko Lab, U. of Virginia BiologyCharlottesville, VA&emsp;&emsp; 2007 - 2009</div>
+<div class="subsection"><a id='magicparlabel-45' /><span class="subsection_label"></span> Timko Lab, U. of Virginia BiologyCharlottesville, VA&emsp;&emsp; 2007 - 2009</div>
 
-<dl class='description'><a id='magicparlabel-47' /><dt class="description_label">Contact:</dt>
+<dl class='description'><a id='magicparlabel-46' /><dt class="description_label">Contact:</dt>
 <dd class="description_item"> Paul J. Rushton, <a href="Paul.Rushton@sdstate.edu">Paul.Rushton@sdstate.edu</a></dd>
 </dl>
 
-<ul class="itemize"><a id='magicparlabel-48' /><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>
+<ul class="itemize"><a 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">6</span></a>].</li>
 <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. 
 <br />
 
@@ -235,9 +234,9 @@ Link: <a href="https://darwinawardwinner.github.io/resume/examples/UVa/probe-sel
 
 Link: <a href="https://darwinawardwinner.github.io/resume/examples/UVa/blast-slides.pdf">Presentation Slides</a> </li>
 </ul>
-<div class="section"><a id='magicparlabel-51' /><span class="section_label"></span> Skills</div>
+<div class="section"><a id='magicparlabel-50' /><span class="section_label"></span> Skills</div>
 
-<dl class='description'><a id='magicparlabel-52' /><dt class="description_label">Computing&nbsp;Skills</dt>
+<dl class='description'><a id='magicparlabel-51' /><dt class="description_label">Computing&nbsp;Skills</dt>
 <dd class="description_item"> R/BioConductor, Python, Perl, Lisp, Java, C#, C++; Git version control; Remote UNIX system administration &amp; software compilation, computing cluster job management &amp; parallel computation
 <br />
 
@@ -252,15 +251,15 @@ StackOverflow Profile: <a href="http://stackoverflow.com/users/125921">http://st
 <dt class="description_label">Languages:</dt>
 <dd class="description_item"> English: native; German: written and spoken</dd>
 </dl>
-<div class="section"><a id='magicparlabel-56' /><span class="section_label"></span> Other Work Experience</div>
-<div class="subsection"><a id='magicparlabel-57' /><span class="subsection_label"></span> Computing Advisor &amp; Help Desk, U.&thinsp;Va. IT Dept.  Charlottesville, VA &emsp;&emsp; 2005 - 2007 </div>
+<div class="section"><a id='magicparlabel-55' /><span class="section_label"></span> Other Work Experience</div>
+<div class="subsection"><a id='magicparlabel-56' /><span class="subsection_label"></span> Computing Advisor &amp; Help Desk, U.&thinsp;Va. IT Dept.  Charlottesville, VA &emsp;&emsp; 2005 - 2007 </div>
 
-<ul class="itemize"><a id='magicparlabel-58' /><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>
+<ul class="itemize"><a 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>
 <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>
 </ul>
-<div class="subsection"><a id='magicparlabel-60' /><span class="subsection_label"></span> Summer Sailing Instructor, Raritan Yacht Club  Perth Amboy, NJ &emsp;&emsp; 2006 - 2009 </div>
+<div class="subsection"><a id='magicparlabel-59' /><span class="subsection_label"></span> Summer Sailing Instructor, Raritan Yacht Club  Perth Amboy, NJ &emsp;&emsp; 2006 - 2009 </div>
 
-<ul class="itemize"><a id='magicparlabel-61' /><li class="itemize_item">Instructed children ages 8-18 in sailing skills, safety, seamanship, knots, rigging &amp; de-rigging boats, navigation, and racing strategy and technique, with an emphasis on building character and self-reliance</li>
+<ul class="itemize"><a id='magicparlabel-60' /><li class="itemize_item">Instructed children ages 8-18 in sailing skills, safety, seamanship, knots, rigging &amp; de-rigging boats, navigation, and racing strategy and technique, with an emphasis on building character and self-reliance</li>
 <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>
 <li class="itemize_item">Helped organize, run, and referee several regattas per season for students from RYC and neighboring yacht clubs</li>
 </ul>
@@ -268,7 +267,7 @@ StackOverflow Profile: <a href="http://stackoverflow.com/users/125921">http://st
 
 
 
-<div class="standard"><a id='magicparlabel-74' /><h2 class='bibtex'>References</h2><div class='bibtex'><div class='bibtexentry' id='LyXCite-cfarmer'><span class='bibtexinfo'><span class="bib-author">Ryan C. Thompson and Rushton, Paul J. and Laudeman, Tom W. and Timko, Michael P.</span>, "<span class="bib-title">http://mneme.homenet.org/~ryan/resume/examples/UVa/contigfarmer.pdfContig Farmer: a tool for extracting maximal-le…</span>" (<span class="bib-year">2009</span>).</span></div>
+<div class="standard"><a id='magicparlabel-73' /><h2 class='bibtex'>References</h2><div class='bibtex'><div class='bibtexentry' id='LyXCite-cfarmer'><span class='bibtexinfo'><span class="bib-author">Ryan C. Thompson and Rushton, Paul J. and Laudeman, Tom W. and Timko, Michael P.</span>, "<span class="bib-title">http://mneme.homenet.org/~ryan/resume/examples/UVa/contigfarmer.pdfContig Farmer: a tool for extracting maximal-le…</span>" (<span class="bib-year">2009</span>).</span></div>
 <div class='bibtexentry' id='LyXCite-eiv_2017'><span class='bibtexinfo'><span class="bib-author">Kurian, Sunil and Velazquez, Enrique and Ryan Thompson and Whisenant, Thomas and Rose, Stanley and Riley, Nicole and H…</span>, "<span class="bib-title">Orthogonal Comparison of Molecular Signatures of Kidney Transplants with Subclinical and Clinical Acute Rejection -- Equivalent…</span>", <i><span class="bib-journal">American Journal of Transplantation</span></i> (<span class="bib-year">2017</span>).</span></div>
 <div class='bibtexentry' id='LyXCite-globin_reduction'><span class='bibtexinfo'><span class="bib-author">Ryan C. Thompson and Gelbart, Terri and Head, Steven R. and Ordoukhanian, Phillip and Mullen, Courtney and Han, Dong…</span>, "<span class="bib-title">Optimizing yield of deep RNA sequencing for gene expression profiling of peripheral blood samples from cynomolgus monkeys (…</span>", <i><span class="bib-journal">Journal of Biological Methods (in review)</span></i> (<span class="bib-year">2016</span>).</span></div>
 <div class='bibtexentry' id='LyXCite-kurian2014molecular'><span class='bibtexinfo'><span class="bib-author">Kurian, SM and Williams, AN and Gelbart, T and Campbell, D and Mondala, TS and Head, SR and Horvath, S and Gaber, L and …</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-year">2014</span>), <span class="bib-pages">1164--1172</span>.</span></div>
@@ -279,11 +278,5 @@ StackOverflow Profile: <a href="http://stackoverflow.com/users/125921">http://st
 <div class='bibtexentry' id='LyXCite-Scott036061'><span class='bibtexinfo'><span class="bib-author">Scott, Erick R. and Larman, H. Benjamin and Torkamani, Ali and Schork, Nicholas J. and Wineinger, Nathan and Nanis, Max and ͡…</span>, "<span class="bib-title">RASLseqTools: open-source methods for designing and analyzing RNA-mediated oligonucleotide Annealing, Selection, and, Liga…</span>", <i><span class="bib-journal">Nucleic Acids Research (in review)</span></i> (<span class="bib-year">2016</span>).</span></div>
 <div class='bibtexentry' id='LyXCite-van2011illumina'><span class='bibtexinfo'><span class="bib-author">Van Nieuwerburgh, Filip and Ryan C. Thompson and Ledesma, Jessica and Deforce, Dieter and Gaasterland, Terry and O…</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>), <span class="bib-pages">gkr1000</span>.</span></div>
 </div></div>
-
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-<div class="standard"><a id='magicparlabel-80' /><div style='height:1em'></div></div>
-
-<div class="standard"><a id='magicparlabel-81' />Online version (with links): <a href="https://darwinawardwinner.github.io/resume/ryan_thompson_resume.pdf">https://darwinawardwinner.github.io/resume/ryan_thompson_resume.pdf</a></div>
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ryan_thompson_resume.lyx

@@ -5,6 +5,17 @@
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