Education

• Ph.D., Molecular and Cellular Biology, University of Washington, 2020.
• Master of Science, Biology, Western Washington University, 2013.
• Master of Science, Computer Science, Western Washington University, 2007.
• Bachelor of Science, Computer Science, Western Washington University, 2006.

Professional experience

Staff Scientist December 2020 - present

Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA

Graduate Research Assistant September 2016 - December 2020

University of Washington (UW) / Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA

• Design, implement, and draft manuscripts for independent research projects
• Contribute computational analyses for internal and external collaborations
• Present research progress through quarterly lab meetings, annual UW/FHCRC Virus Group meetings, and related conferences
• Write grant proposals for viable funding opportunities and participate in FHCRC mock study sections with fellow trainees
• Contribute to monthly meetings with the CDC Influenza Division about evolution of seasonal influenza populations
• Contribute forecasts of seasonal influenza evolution biannually to the World Health Organization for Vaccine Composition Meetings
• Co-design, implement, and maintain Nextstrain, an open source toolkit for real-time pathogen analysis (http://nextstrain.org)
• Mentor and support rotating graduate students, visiting undergraduates, and interning high school students
• Enhance skills in biology, statistics, data visualization through relevant class work

Bioinformatics Specialist June 2011 - September 2016

University of Washington / Howard Hughes Medical Institute, Seattle, WA

• Contributed computational methods and analyses to resolve sequences of previously incomplete regions of human and non-human primate genomes
• Developed flexible, automated, and user-friendly computational pipelines while maintaining existing software
• Created a central, collaborative documentation database for computational and experimental protocols
• Designed, implemented, and drafted manuscripts for independent research projects
• Performed duplication analyses as part of genome sequencing consortiums
• Prepared job descriptions, led interviews, and reviewed applications for new bioinformatics staff
• Trained bioinformatics staff on computational pipelines
• Maintained internal and public online resources including lab website and genome browsers
• Supervised the lab’s computational cluster resources in collaboration with IT staff
• Developed informatics framework and website for the lab’s Pacific Biosciences sequencing service center
• Presented research progress through regular lab meetings

Graduate Teaching Assistant September 2010 - June 2011

Western Washington University, Bellingham, WA

• Communicated introductory biological concepts to undergraduate students
• Presented original material to supplement regular lecture material
• Supported students during lab exercises
• Graded research papers and other assignments
• Created new practical exams in collaboration with fellow teaching assistants
• Oversaw preparation of lab equipment and specimens
• Led discussions about organ systems in prepared dissections

Research Technician, Biology Department December 2009 - September 2010

Western Washington University, Bellingham, WA

• Developed and managed information architecture for the Pacific Northwest Moths biodiversity website (http://pnwmoths.biol.wwu.edu)
• Redesigned existing website for improved usability and accessibility
• Sanitized thousands of inconsistent and duplicate specimen records from spreadsheets into a standard database
• Configured, maintained, and augmented content management system for website
• Created browser-based tools for visualization of species collection data
• Administered web server and database configuration
• Coordinated and supported students working in the lab
• Imaged over 2000 moth specimens using a state-of-the-art biological imaging system
• Post-processed specimen images with Adobe Photoshop using custom macros

Software Developer, University Residences November 2006 - September 2010

Western Washington University, Bellingham, WA

• Designed, implemented, and deployed web applications in conjunction with a team of developers
• Collaborated with stakeholders to develop project goals, requirements, and timelines
• Supervised and supported student programmers with technical goals, methodology, and evaluation
• Created, updated, and maintained shared class libraries
• Developed interface layers to access campus-wide databases on Oracle, Sybase, and MySQL systems
• Optimized high-use applications through profiling and algorithm analysis
• Documented new and existing processes and applications
• Promoted user-centered design and the practice of usability testing
• Built comprehensive unit tests for new and existing applications
• Established pair programming and code review as common practices
• Contributed to open source projects such as SQLAlchemy and Django
• Updated and maintained organizational coding standards
• Assisted in prioritizing department-wide projects

Technical experience

Expert

• Python and its scientific computing and data science tools (numpy, scipy, scikit-learn, pandas, matplotlib, seaborn, et al.)
• UNIX-style command line environments, tools, and scripting
• high performance computing clusters
• version control with Git and GitHub
• machine learning concepts and implementations
• bioinformatics workflow management systems (e.g., Snakemake, GNU Make, etc.)
• genomics tools for quality control, alignment, variant calling, and visualization

Competent practitioner

• SQL, R, Javascript, C, Java, Perl, and PHP
• design and maintenance of relational and non-relational database systems
• data science tools for R (tidyverse)
• interactive visualizations with D3 and altair

Publications

See all publications on Google Scholar. * indicates shared first authorship.

Senior-author publications

• J. Lee*, J. Hadfield*, A. Black, T. R. Sibley, R. A. Neher, T. Bedford, J. Huddleston. Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. Front. Bioinform., Volume 3, Mar 2023.

First-author publications

• J. Huddleston, J. Hadfield, T. R. Sibley, J. Lee, K. Fay, M. Ilcisin, E. Harkins, T. Bedford, R. A. Neher, and E. B. Hodcroft. Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57):2906, Jan 2021.

• J. Huddleston, J. R. Barnes, T. Rowe, X. Xu, R. Kondor, D. E. Wentworth, L. Whittaker, B. Ermetal, R. S. Daniels, J. W. McCauley, S. Fujisaki, K. Nakamura, N. Kishida, S. Watanabe, H. Hasegawa, I. Barr, K. Subbarao, P. Barrat-Charlaix, R. A. Neher, and T. Bedford. Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution. eLife, 9:e60067, Sep 2020.

• S. K. Hilton*, J. Huddleston*, A. Black, K. North, A. S. Dingens, T. Bedford, and J. D. Bloom. dms-view: Interactive visualization tool for deep mutational scanning data. Journal of Open Source Software, 5(52):2353, 2020.

• J. M. Lee*, J. Huddleston*, et al. Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proc. Natl. Acad. Sci. U.S.A., 115(35):E8276-E8285, Aug 2018.

• J. Huddleston, et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res., 27(5):677-685, May 2017.

• D. Gordon*, J. Huddleston*, M. J. Chaisson*, C. M. Hill*, Z. N. Kronenberg*, et al. Long-read sequence assembly of the gorilla genome. Science, 352(6281):aae0344, Apr 2016.

• P. H. Sudmant*, T. Rausch*, E. J. Gardner*, R. E. Handsaker*, A. Abyzov*, J. Huddleston*, Y. Zhang*, K. Ye*, et al. An integrated map of structural variation in 2,504 human genomes. Nature, 526(7571):75-81, Oct 2015.

• J. Huddleston, et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res., 24(4):688-696, Apr 2014.

• J. Huddleston and J. Zhang. Evolutionary rhythm composition with trajectory-based fitness evaluation. In Proceedings of the Twenty-Second AAAI Conference on Artificial Intelligence, pages 1868-1869. AAAI Press, July 2007.

• J. Huddleston and J. Zhang. Effects of musically meaningful operators in evolutionary composition. In Proceedings of the International Computer Music Conference, volume 1, pages 220-223. International Computer Music Association, 2007.

Selected co-author publications

• K. E. Kistler, J. Huddleston, and T. Bedford. Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2. Cell Host Microbe, 30(4):545–555, 04 2022.

• P. Barrat-Charlaix, J. Huddleston, T. Bedford, and R. A. Neher. Limited predictability of amino acid substitutions in seasonal influenza viruses. Mol Biol Evol, 38(7):2767–2777, Jun 2021.

• T. Bedford, A. L. Greninger, P. Roychoudhury, L. M. Starita, M. Famulare, M. Huang, A. Nalla, G. Pepper, A. Reinhardt, H. Xie, L. Shrestha, T. N. Nguyen, A. Adler, E. Brandstetter, S. Cho, D. Giroux, P. D. Han, K. Fay, C. D. Frazar, M. Ilcisin, K. Lacombe, J. Lee, A. Kiavand, M. Richardson, T. R. Sibley, M. Truong, C. R. Wolf, D. A. Nickerson, M. J. Rieder, J. A. Englund, the Seattle Flu Study Investigators, J. Hadfield, E. B. Hodcroft, J. Huddleston, L. H. Moncla, N. F. Mu ̈ller, R. A. Neher, X. Deng, W. Gu, S. Federman, C. Chiu, J. Duchin, R. Gautom, G. Melly, B. Hiatt, P. Dykema, S. Lindquist, K. Queen, Y. Tao, A. Uehara, S. Tong, D. MacCannell, G. L. Armstrong, G. S. Baird, H. Y. Chu, J. Shendure, and K. R. Jerome. Cryptic transmission of SARS-CoV-2 in Washington State. Science, Sep 2020.

• T. Bedford, J. Huddleston, et al. Seasonal influenza circulation patterns and projections for September 2019 to September 2020. bioRxiv, 2019.

• B. I. Potter, R. Kondor, J. Hadfield, J. Huddleston, J. Barnes, T. Rowe, L. Guo, X. Xu, R. A. Neher, T. Bedford, and D. E. Wentworth. Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season. Virus Evolution, 5(2), 12 2019. vez046.

• J. Hadfield, C. Megill, S. M. Bell, J. Huddleston, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, page bty407, May 2018.

Talks

• “Patterns of seasonal influenza circulation in 2022”. Centers of Excellence for Influenza Research and Response (CEIRR) Network Lecture Series. June 2022.
• “Visualization of seasonal influenza antigenic evolution”. Invited speaker at Visualizing Biological Data (VIZBI). Online. March 2022.
• “Nextstrain’s tools for the genomic epidemiology of SARS-CoV-2”, Models of Infectious Disease Agent Study (MIDAS) Network Meeting. Online. May 2021.
• “Integrative forecasting of seasonal influenza A/H3N2 evolution by genotype and phenotype”, Epidemics: 7th International Conference on Infectious Disease Dynamics, Charleston, SC. December 2019.
• “Integrative forecasting of seasonal influenza A/H3N2 evolution by genotype and phenotype”, Models of Infectious Disease Agent Study (MIDAS) Network Meeting, Bethesda, MD. May 2019.
• “Structural variation detection and genotyping in human genomes”, Pacific Biosciences User Group Meeting (West Coast), Palo Alto, CA. 2015.
• “Reconstructing complex regions of genomes using long-read sequencing technology”, Pacific Biosciences User Group Meeting (West Coast), Menlo Park, CA. 2013.
• “Programming LEGO robots in Linux”, Linuxfest Northwest, Bellingham, WA. 2008.

Posters

• “Integrated forecasts of seasonal influenza A/H3N2 evolution”, From Molecular Basis to Predictability and Control of Evolution, NORDITA Institute, Stockholm, Sweden. July 2019.
• “Single molecule sequencing of a human genome reveals novel structural variation that is highly variable in human populations”, American Genetics Association (AGA), Seattle, WA. 2014.
• “Evolutionary relationships of cytochrome P450s implicated in apple maggot host specificity”, EVO-WIBO, Port Townsend, WA. 2012.
• “Effects of musically meaningful operators in evolutionary composition.”, International Computer Music Conference (ICMC), Copenhagen, Denmark. 2007.

Awards and funding

• R01 to improve long-term influenza forecasting (6R01AI165821-02)
• Dr. Paul Neiman Outstanding Graduate Student Award. 2019.
• Ruth L. Kirschstein National Research Service Award (NRSA) F31. 2019.
• Finalist for National Defense Science and Engineering Graduate Fellowship (top 200 of 3,600 applicants). 2018.
• Enhancement of Graduate Research Award, $1000, awarded Spring 2012
• Hodgson Family Endowment for agricultural research, $2000, awarded Winter 2011
• Graduate Tuition Fee Waiver Scholarship: Spring 2006 - Spring 2007
• First Prize in Computer Science Department Robot Competition: Spring 2006
• Western Washington University President’s List: Fall 2003, Fall 2005

Mentorship

• 2022 (July–August): Allison Li, “Adaptive evolution of norovirus”, Fred Hutch Summer Undergraduate Research Program (SURP).
• 2021 (July–August): Eslam Abousamra, “Estimating effects of vaccination on lineage-specific effective reproduction numbers of SARS-CoV-2”, Fred Hutch Summer Undergraduate Research Program (SURP).
• 2019–present: Sravani Nanduri, “Genetic cartography reveals ancestral relationships of human pathogenic viruses”, Fred Hutch Summer High School Internship (SHIP) Program and independent continuing mentorship.
• 2019 (July–August): Dorien Simon, “Calculating expected number of transitions between geographic states in a phylogeny in a given amount of time”, Fred Hutch Summer High School Intership (SHIP) Program.
• 2018 (April–July): Ashley Anderson, MiT, “Developing a curriculum about the genomic epidemiology of Ebola virus for high school students”, Fred Hutch Science Education Partnership (SEP).

Scientific outreach and teaching experience

• Certified Carpentry Instructor (Sep 2019 - present)
• MCB Student Area Director for Computational Biology (Sep 2018 - present)
• Teaching assistant for MCB 517A “Tools for Computational Biology” (Sep - Oct 2018)
• Mentor a local high school biology teacher as part of the Science Education Partnership at FHCRC (Jul 2018)
• Teaching assistant and guest lecturer for BIOL 419/519 “Data Science for Biologists” (Jan - Mar 2018)
• Designer and facilitator for 3-hour bioinformatics workshop at Western Washington University’s Fraser Symposium (Apr 2016)
• 2-hour introduction to programming workshop for Central Washington University Psychology Club students (Jan 2016)
• 4-day bioinformatics workshop for Italian Agricultural Research Council (Oct 2014)
• Teaching assistant for organismal biology lab (Sep 2010 - Jun 2011)
• Member of Bellingham Artificial Intelligence and Robotics Society (BAIRS) (2006 - 2008)

Volunteer history

Biology Department Graduate Committee Elected January 2011 - June 2011

• Attended bi-weekly meetings to discuss issues affecting biology faculty, staff, and graduate students
• Represented biology graduate students during decisions about the graduate program
• Recommended improvements to the program and provided feedback about the state of the program

Sardis Raptor Center August 2009 - June 2011

• Prepared and distributed food for over forty raptors
• Cleaned raptor enclosures
• Moved glove-trained birds of prey
• Assisted in construction of new raptor enclosures

Pacific Northwest Moths Website November 2008 - December 2009, September 2010 - February 2012

• Maintained existing website and content infrastructure as needed
• Developed and maintained dynamic map system for moth factsheets