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Ryan C. Thompson, Ph.D.
Contact Address:
8656 Via Mallorca
Unit G
La Jolla, CA 92037
Phone: (908) 922-7470
Email: [email protected]
Website: https://github.com/DarwinAwardWinner
Summary
==========
* Accomplished, experienced computational biologist with deep
knowledge of biology, mathematics, statistics, and programming.
* 11 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.
* 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 and experienced mentor with a strong ability
to help others connect biological, statistical, and computational
understanding.
Education
==========
2012—2019: Ph.D. in Bioinformatics, Skaggs Graduate School of Chemical and Biological Sciences
The Scripps Research Institute, La Jolla, California
Advisor: Andrew Su
2005—2009: B.S. in Biology with High Distinction; B.A. in Mathematics
University of Virginia, Charlottesville, Virginia
Advisor: Paul J. Rushton
Research Experience
==========
Salomon & Su Labs, The Scripps Research Institute
----------
La Jolla, CA; 2012—2019
Contact: Dr. Andrew Su, [email protected]
* 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 + T-cell activation as well as epigenetic
convergence between naive and memory cells after activation [1,3,8].
* Significantly improved cross-validated performance of machine
learning classifier for identifying biomarkers of transplant
rejection by developing appropriate single-sample microarray
normalization procedures [5], including training a custom set of
frozen RMA normalization vectors. Classifier is currently being
developed into a clinical test for transplant dysfunction.
* 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.
* 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].
* 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].
* 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.
* Adapted common normalization methods from RNA-seq to improve
performance in analysis of RASL-seq experiments [10].
* Active member of the Bioconductor community since 2012 and
contributing developer for several Bioconductor packages.
* Mentored 3 coworkers from both biology and programming backgrounds
in learning bioinformatics.
Summer Internship, Informatics IT, Merck & Co.
----------
Boston, MA; 2011
Contact: Adnan Derti, [email protected]
* 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, [email protected]
* Designed and implemented Deloxer, a critical software step in a new
Illumina mate-pair sequencing protocol using Cre recombination.
Deloxer is published and now in use in several labs around the world
[6].
* 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 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.
* 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
Advisor: Paul J. Rushton
* 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 [11].
* 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
Awards & Honors
==========
2006—2009 Echols Scholar, University of Virginia
2006 Phi Eta Sigma National Honor Society
2006 National Society of Collegiate Scholars
2005 Edward J. Bloustein Disguingished Scholar
2005 National Merit Scholar
Peer-reviewed Publications
==========
[1] Sarah A. LaMere, Ryan C. Thompson, Xiangzhi Meng, H. Kiyomi
Komori, Adam Mark, and Daniel R. Salomon. H3K27 Methylation Dynamics
during CD4 T Cell Activation: Regulation of JAK/STAT and IL12RB2
Expression by JMJD3. The Journal of Immunology, 199(9):3158–3175,
November 2017. doi:10/gchc9x.
[2] S. M. Kurian, E. Velazquez, R. Thompson, T. Whisenant, S. Rose, N.
Riley, F. Harrison, T. Gelbart, J. J. Friedewald, J. Charette, S.
Brietigam, J. Peysakhovich, M. R. First, M. M. Abecassis, and D. R.
Salomon. Orthogonal Comparison of Molecular Signatures of Kidney
Transplants With Subclinical and Clinical Acute Rejection: Equivalent
Performance Is Agnostic to Both Technology and Platform. American
Journal of Transplantation, 17(8):2103–2116, August 2017.
doi:10/gbp6vr.
[3] S. A. LaMere, R. C. Thompson, H. K. Komori, A. Mark, and D. R.
Salomon. Promoter H3K4 methylation dynamically reinforces
activation-induced pathways in human CD4 T cells. Genes & Immunity,
17(5):283–297, July 2016. doi:10/f97x85.
[4] 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(December2015):1–39, December 2015.
doi:10/ggcxmg.
[5] S M Kurian, a N Williams, T Gelbart, D Campbell, T S Mondala, S R
Head, S Horvath, L Gaber, R Thompson, T Whisenant, W Lin, P
Langfelder, E H Robison, R L Schaffer, J S Fisher, J Friedewald, S M
Flechner, L K Chan, A C Wiseman, H Shidban, R Mendez, R Heilman, M M
Abecassis, C L Marsh, and D R Salomon. Molecular Classifiers for Acute
Kidney Transplant Rejection in Peripheral Blood by Whole Genome Gene
Expression Profiling. American Journal of Transplantation,
14(5):1164–1172, May 2014. doi:10/f5xswg.
[6] 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, 40(3):e24, February 2012.
doi:10/fmzd3r.
Other Works
==========
[7] 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). (In
preparation). Institution: The Scripps Research Institute, 2019.
[8] Ryan C. Thompson, Sarah A. Lamere, and Daniel R. Salomon.
Reproducible genome-wide epigenetic analysis of H3K4 and H3K27
methylation in naïve and memory CD4+ T-cell activation. (In
preparation). Institution: The Scripps Research Institute, 2019.
[9] Ryan C. Thompson. 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. PhD thesis, The Scripps Research Institute, 2019.
[10] 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: Open- source methods for designing and analyzing
RNA-mediated oligonucleotide Annealing, Selection, and, Ligation
sequencing (RASL-seq) experiments. bioRxiv, 2016. doi:10/ggcxmn.
[11] 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. Institution: University of
Virginia.
http://darwinawardwinner.github.io/resume/examples/UVa/contigfarmer.pdf
[12] Ryan C. Thompson. The Sources and Limits of Geometric Rigor from
Euclid Through Descartes, May 2008. Institution: University of
Virginia.
http://darwinawardwinner.github.io/resume/examples/UVa/math-history-paper.pdf
Presentations and Teaching
==========
* May 8, 2018: Guest lecturer on RNA-Seq for Advanced Tools and Data
Challenges in Bioinformatics course (Lecture & Lab). University of
California, San Diego, CA
* November 21, 2016: Advanced RNA-Seq Analysis. Schork Lab, J. Craig
Venter Institute, La Jolla, CA
* August 15, 2016: RNA-seq Analysis. Bristol-Myers Squibb, Hopewell,
NJ
* April 29, 2016: Lecturer on Introductory RNA-seq Analysis for
Applied Bioinformatics and Computational Biology course. The Scripps
Research Institute, La Jolla, CA
* December 21, 2015: Advanced RNA-Seq Analysis. Bristol-Myers Squibb,
Hopewell, NJ
* November 13, 2015: Advanced RNA-Seq Analysis. The Scripps Research
Institute, La Jolla, CA
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