RGLab
Raphael Gottardo's Research Lab
About us
We are part of the Vaccine and Infectious Disease Division of Fred Hutch in Seattle. We develop statistical methods and software tools for the analysis of high throughput biological data with an emphasis on immunology and vaccine research. We work with bench scientists and clinicians to understand and ultimately help develop vaccines and/or cure severe diseases such HIV, malaria and cancer.
Members
| Name | Position | Links |
|---|---|---|
| Raphael Gottardo | Principal Investigator | Github, Twitter |
| Robert Amezquita | Postdoctoral Fellow | Github, Twitter |
| Dror Berel | Bioinformatics Analyst | Github |
| Lev "Leo" Dashevskiy | Software Dev Engineer | Github |
| Greg Finak | Senior Staff Scientist | Github, Twitter |
| Evan Greene | Postdoctoral Fellow | Github |
| Gil Guday | Undergraduate Intern | Github |
| Evan Henrich | Software Dev Engineer | Github |
| Greg Imholte | PhD Student | Github |
| Mike Jiang | Software Dev Engineer | Github |
| Ju Yeong Kim | Software Dev Engineer | Github, Twitter |
| Sam Koelle | PhD Student | Github |
| Amit Meir | PhD Student | Github |
| Carl Murie | Bioinformatics Analyst | Github |
| Lindsey Mwoga | Executive Assistant | |
| Jason Taylor | Systems Analyst/Programmer | Github |
| Phu Van | Bioinformatics Analyst | Github |
| Valentin Voillet | Postdoctoral Fellow | Github, Twitter |
| Lauren Wolfe | Software Dev Engineer | Github, Twitter |
| Chad Young | Data Scientist | Github |
From left to right: Jingyuan, Lynn, Mike, Sangsoon, Phu, Renan, Jacob, Leo, Raphael, Greg F., and Masanao.
Selected Publications
The contribution of cell cycle to heterogeneity in single-cell RNA-seq data
McDavid, A. et al.
Nat. Biotechnol. 2016; 34:591–593.
PMID: 27281413
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Finak, G. et al.
Genome Biol. 2015; 16:278.
PMID: 26653891
COMPASS identifies T-cell subsets correlated with clinical outcomes
Lin, L. et al.
Nat Biotechnol. 2015; 33:610-616.
PMID: 26006008
Orchestrating high-throughput genomic analysis with Bioconductor
Huber, W. et al.
Nat Methods. 2015; 12:115-121.
PMID: 25633503
Critical assessment of automated flow cytometry data analysis techniques
Aghaeepour, N. et al.
Nat. Methods. 2013; 10:228-238.
PMID: 23396282
Alumni
| Name | Current Position |
|---|---|
| Luke Bornn | Assistant Professor, Simon Fraser University and Vice President, Strategy and Analytics Sacramento Kings |
| Francois Caron | Associate Professor, Oxford University |
| Xiaohui Chen | Assistant Professor, University of Illinois at Urbana-Champaign |
| Jingyuan Deng | Data Scientist, Expedia |
| Arnaud Droit | Associate Professor, Université Laval |
| Mukta Dutta | |
| Jacob Frelinger | Site Reliability Engineer, Google |
| Lynn Lin | Assistant Professor, Pennsylvania State University |
| Kenneth Lo | Data Scientist, Apple |
| Andrew McDavid | Assistant Professor, University of Rochester |
| Kaida Ning | Biostatistician, Yale University |
| Eloi Mercier | Computational Biologist, BC Cancer Agency |
| John Ramey | Principal Data Scientist, Novilabs |
| Renan Sauteraud | PhD Student, Pennsylvania State University |
| Marie-Pier Scott-Boyer | Postdoctoral Fellow, University of Trent |
| Kevin Ushey | Software Engineer, RStudio |
| Sangsoon Woo | Statistical Geneticist, Axio Research |
| Masanao Yajima | Associate Professor of Practice, Boston University |
| Xuekui Zhang | Assistant Professor and Canada Research Chair, University of Victoria |