Update text resume

ryan_thompson_resume.txt

@@ -1,4 +1,4 @@
-Ryan C. Thompson
+Ryan C. Thompson, Ph.D.
 
 Contact Address:
 
@@ -13,55 +13,62 @@ 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
+* 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
-* 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
+  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
 ==========
 
-The Scripps Research Institute
+2012—2019: Ph.D. in Bioinformatics, Skaggs Graduate School of Chemical and Biological Sciences
+The Scripps Research Institute, La Jolla, California
+Advisor: Andrew Su
 
-* Ph. D. in Bioinformatics, expected 2018
-
-University of Virginia
-
-* B.S. in Biology, B.A. in Mathematics, 2009
-* Echols Scholar
+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 Lab, The Scripps Research Institute
+Salomon & Su Labs, The Scripps Research Institute
 ----------
-La Jolla, CA; 2012 - 2018
+La Jolla, CA; 2012—2019
  
 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].
+  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]
-* 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.
+  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
@@ -72,21 +79,12 @@ Contact: Dr. Andrew Su, asu@scripps.edu
   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, one from a
-  programming background and the other from a biology background.
+  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.
 ----------
@@ -111,7 +109,7 @@ 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
+  Deloxer is published [6] 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
@@ -132,19 +130,20 @@ Contact: Terry Gaasterland, gaasterland@ucsd.edu
   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.
+  identify target pathways of autophagy-related miRNAs for biological
+  validation.
 
 Timko Lab, U. of Virginia Biology
 ----------
-Charlottesville, VA; 2007 - 2009
+Charlottesville, VA; 2007—2009
 
-Contact: Paul J. Rushton, Paul.Rushton@sdstate.edu
+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[6].
+  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
@@ -180,7 +179,9 @@ Languages: English: native speaker; German: written and spoken
 Other Work Experience
 ==========
 
-Computing Advisor & Help Desk, U. Va. IT Dept. Charlottesville, VA; 2005 - 2007
+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,
@@ -189,7 +190,9 @@ Computing Advisor & Help Desk, U. Va. IT Dept. Charlottesville, VA; 2005 - 200
   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
+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
@@ -202,68 +205,114 @@ Summer Sailing Instructor, Raritan Yacht Club Perth Amboy, NJ; 2006 - 2009
 * Helped organize, run, and referee several regattas per season for
   students from RYC and neighboring yacht clubs
 
-Writings and Publications
+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] 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
+[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,
-May 2016.
+17(5):283–297, July 2016. doi:10/f97x85.
 
-[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.
+[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.
 
-[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.
+Other Works
+==========
 
-[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] 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.
 
-[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] 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.
 
-[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. 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.
 
-[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.
+[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
 
-[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
+[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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