Frederick A. "Erick" Matsen

Professor, Fred Hutchinson Cancer Research Center;

Affiliate Professor, Genome Sciences & Statistics, University of Washington;

Investigator, Howard Hughes Medical Institute


CV           

Research statement: I'm interested in developing Bayesian phylogenetics as an optimization problem, and in understanding the process by which the adaptive immune system learns to recognize foreign antigen.

Personal interests: Historically I've loved climbing, backcountry skiing and kayaking; right now I'm raising two kids.

Hometown: Seattle, WA

Duncan Ralph

Staff scientist


  

Research statement: I develop computational methods for inference on B cell receptor deep sequencing data, and apply these methods to data from wet lab collaborators at the Hutch and elsewhere. Recent projects include recapitulating the development of broadly-neutralizing anti-HIV antibodies, and choosing antibodies from deep sequencing data for synthesis and testing against dengue virus.

Personal interests: In town I run and gym climb; out of town I climb and ski in the mountains.

Hometown: Arcata, CA

Thayer Fisher

Biostatistics PhD student


     

Research statement: I am interested in how we can model and simulate how B cells mutate at the mechanistic level.

Personal interests: In my spare time I enjoy watching and playing soccer, rock climbing, and playing chess.

Hometown: Seattle, WA

Jared G. Galloway

Programmer


     

Research statement: I’m fascinated by all facets of biology. Recently, I’ve focused my energy on protein-antibody interaction studies where high throughput protocols, big data, and statistics intersect.

Personal interests: My time is primarily spent cycling, listening to podcasts of a wide variety, reading, skiing, and annoying my cat.

Hometown: Bozeman, MT

Zorian Thornton

Genome Sciences PhD student


     

Research statement: I am interested in studying how mutations impact the biophysical properties of antibodies and quickly evolving viral proteins using interpretable deep neural networks.

Personal interests: In my free time I enjoy watching history documentaries, blogging, making YouTube videos, baking sweets, playing and watching sports and powerlifting.

Hometown: Goochland, VA

Magdalena "Maggie" Russell

Molecular and Cellular Biology PhD student


  

Research statement: I’m interested in identifying and understanding genetic biases during the T cell receptor generation process, and how they lead to repertoire variability across individuals and in the context of disease.

Personal interests: I enjoy hiking, cross country and downhill skiing, baking, painting, and crocheting!

Hometown: Bozeman, MT

Kevin Sung

Postdoc (joint with Julie Overbaugh)


  

Research statement: I’m interested in applying mathematical and statistical methods to a variety of topics in immunology.

Personal interests: Sports and food! Particularly basketball and tiramisu...

Hometown: Toronto, ON, Canada

Hassan Nasif

Statistics PhD student


  

Research statement: I’m interested in developing fast and statistically rigorous algorithms for Bayesian phylogenetic inference, with a focus on variational inference and optimization.

Personal interests: I love to hike, weightlift, read science fiction, play board games, and enjoy good coffee/tea/food with friends.

Hometown: Raleigh, NC

Will Dumm

Programmer


  

Research statement: I’m interested in using math to develop new algorithms for phylogenetic inference.

Personal interests: I enjoy hiking, swimming, flying, kayaking, playing violin, and searching for abandoned and unpicked fruit trees.

Hometown: Kodiak, AK

David Rich

Programmer


  

Research statement: I’m interested in using my knowledge in computer science and bioinformatics to help research and develop new methods for Bayesian phylogenetic inference.

Personal interests: I enjoy hiking, fly fishing, horseback riding, playing guitar, and gaming.

Hometown: Seeley Lake, MT

Thien Tran

Undergraduate research assistant


     

Research statement: I’m interested in applying computer science to a variety of problems from different branches of biology.

Personal interests: I enjoy hiking, skiing, and visiting new places with my friends and family. In my free time, I love baking bagels, watching sunsets, and taking care of my plants.

Hometown: Everett, WA

Ognian Milanov

Programmer


  

Research statement: I'm passionate about finding elegant C++ designs and implementations for complex real-world and theoretical problems.

Personal interests: Raising kids, off roading, homesteading.

Hometown: Novachene, Bulgaria

Assya Trofimov

Postdoc (joint with Armita Nourmohammad and Phil Bradley)


  

Research statement: First trained in biochemistry, then computational biology, I will be attempting to model the relationship between an individual's genetic background and their TCR repertoire.

Personal interests: I really enjoy strategy, worker placement and resource management board games - I play every week. I also love videogames, but I’m now great at them. I am a baker - I particularly enjoy trying out new techniques.

Hometown: Montreal, Quebec, Canada

Chris Jennings-Shaffer

Postdoc


     

Research statement: While I was trained as a number theorist (you can find my articles on arxiv.org), my work has always been computational and now I focus on data science. I am interested in how mathematics applies to solving problems in biology.

Personal interests: I enjoy the occasional hike when the weather is nice, but really I like sitting at home with food and drinks. I should get a cat.

Hometown: Seattle, WA

Hugh Haddox

Project manager


  

Research statement: Viruses rapidly evolve. So do the immune responses that combat them. I'm interested in tying together high-throughput experimental data and biophysical models to better understand how these processes work.

Personal interests: I love playing soccer, climbing, and trail running. I also love cooking and listening to audiobooks.

Hometown: Denver, CO

Nico Courts

Postdoc


     

Research statement: My first loves will always be mathematics and computer science, but I am passionate about finding ways to leverage my interests into creating positive change in the world around me through creative problem solving and the application of technology.

Personal interests: I am a fan of hiking, sailing, and wandering when I am out and about in the world and video games and Chinese tea (pu'er and wulong in particular) when I am at home. Oh, and cuddling with my cat, Emmy!

Hometown: Glendora, CA

Mary Barker

Postdoc


     

Research statement: (This will probably change once I am there and starting work) I am interested in computational math, in both pure and applied settings. My favorite problems so far are in gerrymandering, moduli theory, and finite element exterior calculus.

Personal interests: I enjoy long hikes, playing and repairing violins, and making new food with people.

Hometown: St. Louis, MO

Jiansi Gao

Postdoc


  

Research statement: I'm interested in developing Bayesian phylogenetic methods to model the evolution of rapidly evolving pathogens, and efficient numerical algorithms to enable computationally intensive phylogenetic analyses with large datasets.

Personal interests: I enjoy reading about history and staring at maps. I like playing all sorts of sports (not very good at any of them though) and watching some of them (e.g., basketball and F1).

Hometown: Tianjin, China

Claris Winston

Undergraduate research assistant


  

Research statement: I'm fascinated by the various applications of computer science in several real world scenarios. I'm interested in exploring the intersection of computer science and biological sciences, and applying statistical analysis/machine learning.

Personal interests: I enjoy drawing, gymnastics, and composing music! I also love baking sweet treats and cake decorating.

Hometown: Vienna, VA

Yoonseo Song

Undergraduate research assistant


  

Personal interests: I love traveling, spending time with family and friends, cooking and baking, and exploring enw food/coffee places!

Hometown: Camas, WA / Seoul, South Korea

Mackenzie Johnson

Postdoc (starting Jan 2023)


     

Research statement: I am interested in improving methods for evolutionary inference on biological sequence data using statistics and deep learning.

Personal interests: I enjoy climbing, hiking, seeing live music, and watching reality TV.

Hometown: Overland Park, KS

Thanasi Bakis

Statistics PhD student (UC Irvine, with Vladimir Minin)


  

Research statement: My interests revolve around computational statistics and Bayesian inference, and I am currently exploring their applications to phylogenetic inference.

Personal interests: I enjoy music (listening, and playing saxophone) and love to explore boba shops!

Hometown: La Habra, CA


Student/Postdoc Alumni

Vu Dinh

Completed postdoc in 2017;

Assistant professor, U. Delaware Mathematical Sciences



     

Julia Fukuyama

Completed postdoc in 2018;

Assistant professor, Indiana University Bloomington Statistics



     

David Shaw

Completed postdoc in 2018;

Data Scientist, Mighty AI



  

Chris Whidden

Completed postdoc in 2018;

Assistant Professor, Dalhousie University Computer Science



        

Kristian Davidsen

Completed masters/programmer position in 2018;

PhD student, Lucas Sullivan lab



  

Amrit Dhar

Completed Statistics PhD in 2019;

Data Scientist, Google



  

Cheng Zhang (张成)

Completed postdoc in 2019;

Assistant professor, Peking University Mathematical Sciences



     

Jean Feng

Completed Biostatistics PhD in 2020;

Assistant Professor, UCSF Biostatistics and Epidemiology



     

Branden Olson

Completed Statistics PhD in 2020;

Data Scientist, Workday



     

Seong-Hwan Jun

Completed postdoc in 2020;

Postdoc with Raphael Gottardo



  

Andy Magee

Completed Biology PhD in 2021 (joint with Vladimir Minin);

Postdoc with Marc Suchard



     

Anna Kooperberg

Undergraduate intern 2021 (CS at MIT);

Hedge fund quant



  

Michael Karcher

Completed postdoc in 2021;

Assistant Professor, Muhlenberg College



  

Shosuke Kiami

Undergraduate intern 2021 (CS at UW);



  

Lucy Yang

Undergraduate intern 2021 (CS at UC Berkeley);



  

Will DeWitt

Genome Sciences PhD student (joint with Kelley Harris);

Postdoc, Yun Song lab, UC Berkeley



     

Research statement: I’m broadly interested in computational and mathematical biology, and focus on both quantitative immunology and evolutionary genomics.

Personal interests: I enjoy playing in the snow, cooking, gazing at sunsets, photographing birds, and playing guitar and ukulele.

Hometown: Bradford, VT

Tanvi Ganapathy

High school intern 2021, 2022



  

Research statement: I’m interested in the applications of computer science to solve biological problems and hopefully make these solutions more accessible.

Personal interests: I like skiing, baking, reading science fiction, and playing board games.

Hometown: Bellevue, WA

Alyssa Pratt

SURP intern



  

Research statement: I’m interested in creating computational tools and algorithms that can be used to model experimental data, especially in the areas of evolutionary and molecular biology.

Personal interests: I like practicing archery, going hiking, cooking, and reading science fiction in my free time!

Hometown: Portland, OR

William Howard-Snyder

Undergraduate research assistant



     

Research statement: I'm excited about applying techniques from computer science to problems in biology and medicine.

Personal interests: Outdoors, I enjoy hiking, snowboarding, and playing tennis. Indoors, I like to play board games like Catan, Chess, and Avalon.

Hometown: Bellingham, WA