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.


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


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