Add text-only version of resume

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ryan_thompson_resume.mkdn

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+Ryan C. Thompson
+
+Contact Address:
+
+    8656 Via Mallorca
+    Unit G
+    La Jolla, CA 92037
+
+Phone: (908) 922-7470
+Email: rct@thompsonclan.org
+Website: https://github.com/DarwinAwardWinner
+
+Summary
+=======
+
+* Well-rounded computational biologist with deep knowledge of biology,
+  mathematics, and programming
+* 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
+* 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
+* Supportive team member with a strong ability to foster
+  cross-disciplinary literacy by explaining concepts at the right
+  level of abstraction
+
+Education
+=========
+
+The Scripps Research Institute
+
+* Ph. D. in Bioinformatics, expected 2017
+
+University of Virginia
+
+* B.S. in Biology, B.A. in Mathematics, 2009
+* Echols Scholar
+
+Research Experience
+===================
+
+Salomon Lab, The Scripps Research Institute
+-------------------------------------------
+La Jolla, CA   2012 - 2017
+
+Contact: Dr. Andrew Su, asu@scripps.edu
+
+* 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 [2, 3].
+* 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. [4]
+* Significantly improved performce of machine learning classifier for
+  identifying transplant rejection by developing appropriate
+  single-sample microarray normalization procedures[1], including
+  training a custom set of frozen RMA normalization vectors.
+  Classifier is currently being developed into a clinical test for
+  transplant dysfunction.
+* 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.
+* 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.
+* Taught basic RNA-seq theory and practical analysis for the
+  graduate-level introductory bioinformatics course.
+* 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. [7]
+* Adapted common normalization methods from RNA-seq to improve
+  performance in analysis of RASL-seq experiments. [5]
+* 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.
+* Active member of the Bioconductor community and contributing
+  developer for several Bioconductor packages.
+* Mentored 2 coworkers in learning bioinformatics.
+
+Summer Internship, Informatics IT, Merck & Co.
+----------------------------------------------
+Boston, MA   2011
+
+Contact:
+    Adnan Derti, adnan.derti@gmail.com 
+
+* 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.
+* Assisted in a molecular genetics study to evaluate peformance of two
+  variant calling algorithms in detection of causal mutations in
+  antibiotic-resistant bacterial genomes.
+
+Gaasterland Lab, UCSD Bioinformatcs
+-----------------------------------
+La Jolla, CA   2010 - 2012
+
+Contact: Terry Gaasterland, gaasterland@ucsd.edu 
+
+* Designed and implemented Deloxer, a critical software step in a new
+  Illumina mate-pair sequencing protocol using Cre recombination.
+  Deloxer is published[8] and now in use in several labs around the
+  world.
+* Performed a molecular genetics study to find potential causal
+  mutations for fatal iron overload disease in critically endangered
+  black rhinoceros by de novo assembly of black rhino transcriptome
+  using Trinity and comparison to closely-related white rhino
+  transcriptome. 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.
+* 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.
+* 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.
+* Investigated the binding motif specificity of ZASC1 transcription
+  factor in mouse T-cells using Affymetrix expression microarrays in
+  ZASC1 siRNA knockdown experiment.
+* Analyzed miRNA target predictions using GO & KEGG grouping to
+  identify target pathways of autophagy-related miRNAs for biological validation.
+
+Timko Lab, U. of Virginia Biology
+---------------------------------
+Charlottesville, VA   2007 - 2009
+
+Contact: Paul J. Rushton, Paul.Rushton@sdstate.edu
+
+* 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[6].
+* 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.
+* Acted as interpreter to explain complex biological concepts to
+  programmers and explain complex computational problems to
+  biologists.
+
+Skills
+======
+
+Computing Skills: R/BioConductor, Python, Perl, Lisp, Java, C#, C++;
+Git version control; Remote UNIX system administration & software
+compilation, computing cluster job management & parallel computation
+
+* Public code: https://github.com/DarwinAwardWinner
+* StackOverflow Profile: http://stackoverflow.com/users/125921
+
+Statistics & Data 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 visualization & presentation,
+reproducible research practices
+  
+Wet Lab: PCR, molecular cloning, recombinant protein purification,
+epitope mapping, site-directed mutagenesis, 2D gels, real-time PCR,
+and associated data analysis
+  
+Languages: English: native speaker; German: written and spoken
+
+Other Work Experience
+=====================
+
+Computing Advisor & Help Desk, U. Va. IT Dept. Charlottesville, VA    2005 - 2007
+
+* 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
+* 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
+
+Summer Sailing Instructor, Raritan Yacht Club Perth Amboy, NJ    2006 - 2009
+
+* 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
+* 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
+* Helped organize, run, and referee several regattas per season for
+  students from RYC and neighboring yacht clubs
+
+Writings and Publications
+=========================
+
+[1] 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.
+Orthogonal comparison of molecular signatures of kidney transplants
+with subclinical and clinical acute rejection – equivalent performance
+is agnostic to either technology or platform. American Journal of
+Transplantation, 2017.
+
+[2] Sarah LaMere, Ryan C. Thompson, Xiangzhi Meng, H. Kiyomi Komori,
+A. Mark, and Daniel R. Salomon. H3K27 methylation dynamics during CD4
+T cell activation: regulation of JAK/STAT and IL12RB2 expression by
+JMJD3. Journal of Immunology (in review), 2017.
+
+[3] Sarah LaMere, Ryan C. Thompson, H. Kiyomi Komori, Adam Mark, and
+Daniel R. Salomon. Promoter H3K4 methylation dynamically reinforces
+activation-induced pathways in human CD4 T cells. Genes & Immunity,
+May 2016.
+
+[4] 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. Optimizing yield
+of deep RNA sequencing for gene expression profiling of peripheral
+blood samples from cynomolgus monkeys (Macaca fascicularis). Journal
+of Biological Methods (in review), 2016.
+
+[5] 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.
+RASLseqTools: opensource methods for designing and analyzing
+RNA-mediated oligonucleotide Annealing, Selection, and, Ligation
+sequencing (RASL-seq) experiments. Nucleic Acids Research (in review),
+2016.
+
+[6] 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. Suppression of
+transcriptional drift extends C. elegans lifespan by postponing the
+onset of mortality. eLife, 4, 2015.
+
+[7] SM Kurian, AN Williams, T Gelbart, D Campbell, TS Mondala, SR
+Head, S Horvath, L Gaber, R Thompson, T Whisenant, et al. Molecular
+Classifiers for Acute Kidney Transplant Rejection in Peripheral Blood
+by Whole Genome Gene Expression Profiling. American Journal of
+Transplantation, 14(5):1164–1172, 2014.
+
+[8] Filip Van Nieuwerburgh, Ryan C. Thompson, Jessica Ledesma, Dieter
+Deforce, Terry Gaasterland, Phillip Ordoukhanian, and Steven R Head.
+Illumina Mate-Paired DNA Sequencing Library Preparation Using Cre-Lox
+Recombination. Nucleic Acids Research, page gkr1000, 2011.
+
+[9] Ryan C. Thompson, Paul J. Rushton, Tom W. Laudeman, and Michael P.
+Timko. Contig Farmer: a tool for extracting maximal-length contiguous
+sequences from a database of short sequence reads (Undergraduate
+Thesis). June 2009.
+http://darwinawardwinner.github.io/resume/examples/UVa/contigfarmer.pdf
+
+[10] Ryan C. Thompson. The sources and limits of geometric rigor from
+Euclid through Descartes. May 2008.
+http://darwinawardwinner.github.io/resume/examples/UVa/math-history-paper.pdf