Matthew Ryan Dillon
Senior Research Software Engineer
Address: 1350 S. Knoles Drive, Building 56, Room 224, Flagstaff, AZ 86011
Phone: (907) 750-0414
Email: matthewrdillon@gmail.com
GitHub: https://github.com/thermokarst
Stack Overflow: https://stackoverflow.com/users/313548
References Available Upon Request
Education
M.S. in Civil Engineering
University of Alaska Fairbanks
2012
Thesis: The impact of a fluctuating freezing front on ice formation in freezing soil
Advisor: Yuri Shur, Ph.D, Sc.D
B.S. in Civil Engineering, cum laude
University of Alaska Fairbanks
2007
Positions Held
Senior Research Software Engineer
Caporaso Lab, Pathogen and Microbiome Institute, Northern Arizona University
Flagstaff, Arizona
January 2019 - Present
Designed and developed the open source software suite QIIME 2 as part of a diverse, worldwide team. Lead and co-taught QIIME 2 instructional workshops, designed user-documentation, and provided interactive support for end-users of QIIME 2. Supervised engineering staff and undergraduate student interns working in the Caporaso Lab. Managed and supported global QIIME 2 Workshop efforts.
Research Software Engineer
Caporaso Lab, Pathogen and Microbiome Institute, Northern Arizona University
Flagstaff, Arizona
July 2016 - December 2018
Designed and developed the open source software suite QIIME 2 as part of a diverse, worldwide team. Co-taught QIIME 2 instructional workshops, designed user-documentation, and provided interactive support for end-users of QIIME 2. Mentored undergraduate student interns working in the Caporaso Lab.
Software Engineer/Owner
MD Solutions
Flagstaff, Arizona & Anchorage, Alaska
October 2013 - Present
Developed custom web applications for management of scientific data on multi-disciplinary teams. Deployed multiple high performance compute-clusters, bare-metal and cloud-based. Designed data management schemes for long-term data integrity.
Web Application Developer
GeoNorth, LLC
Anchorage, Alaska
June 2013 - August 2014
Determined and fulfilled client needs through the maintenance, design, and development of custom web applications for private organizations and government entities throughout the United States.
Staff Engineer
Golder Associates Inc.
Anchorage, Alaska
September 2010 - August 2013
Directed, organized, and supported geotechnical engineering projects, including field explorations, lab work, and computer-based engineering simulations and analysis. Lead small to medium-sized teams in related field efforts. Interfaced with clients to determine requirements. Tracked and handled project budget and client invoicing.
EPSCoR Research Fellow
Alaska Experimental Program to Stimulate Cooperative Research, University of Alaska Fairbanks
Fairbanks, Alaska
September 2008 - August 2010
Researched frost heave mechanics, frozen soil properties and behavior. Developed software to automate and interpret live testing equipment and results.
Graduate Research Intern
Institute of Northern Engineering, University of Alaska Fairbanks
Fairbanks, Alaska
September 2007 - August 2009
Directed and planned fieldwork involving permafrost sampling, including core drilling, exposure description, field testing.
Teaching Assistant, Fluid Dynamics Laboratory
College of Engineering and Mines, University of Alaska Fairbanks
Fairbanks, Alaska
September 2007 - May 2008
Prepared, instructed, and graded student labs. Redesigned lab procedures in conjunction with faculty guidance.
Undergraduate Research Assistant
Institute of Northern Engineering, University of Alaska Fairbanks
Fairbanks, Alaska
September 2006 - May 2007
Performed ASTM soil tests. Synthesized data and prepared reports.
Grants and Awards
- 2015, INBRE Bioinformatics Award, Clostridium Database: Initial Data Population & Creation of Public Site
- 2015, INBRE Bioinformatics Award, Upgrades to the Existing Arctic Hibernators Database to Ensure Current and Future Functionality
- 2008, Alaska EPSCoR Research Fellowship, Graduate research support, 2 years full stipend
- 2008, UAF Graduate School Travel Grant, American Geophysical Union Annual Meeting, San Francisco
- 2007, Flint Hills Undergraduate Research Symposium Award, 3rd place student presenter
- 2007, Alaska EPSCoR International Travel Award, Skyscan user conference, Belgium
- 2006, Flint Hills Undergraduate Research Award, CT scanning of frozen soil
- 2005, Flint Hills Undergraduate Research Award, Hydraulic conductivity studies
Technical Skills
Python (QIIME 2, Django, Celery, Scipy, Numpy, Pandas), Javascript (Vue, Ember.js), Go, Docker, Git, Ansible, Vagrant, Latex, HTML, Postgresql (w/ PostGIS), Linux/Unix system administration, CI/CD.
Teaching
- Microbiome Bioinformatics with QIIME 2
January 2021 (5 days)
Lead Organizer, Host/MC, and Instructor
Foundation for Advanced Education in the Sciences - National Institutes of Health, Online - Microbiome Bioinformatics with QIIME 2
October 2020 (5 days)
Lead Organizer, Host/MC, and Instructor
Chan-Zuckerberg Initiative-CABANA, Online - Microbiome Bioinformatics with QIIME 2
January 2020 (3 days)
Lead Organizer and Instructor
Foundation for Advanced Education in the Sciences - National Institutes of Health, Bethesda, Maryland - Microbiome Bioinformatics with QIIME 2
June 2019 (3 days)
Lead Organizer and Instructor
Staten Serum Institut
Copenhagen, Denmark - QIIME 2 Guest Lecture, Microbial ecology
NAU BIO 471/578, Dr. Bridget Barker
March 2019
Guest lecture
Northern Arizona University - Flagstaff, Arizona - QIIME 2 Workshop
December 2018 (2 days)
Instructor
Universidad de Costa Rica - San José, Costa Rica - Microbiome Bioinformatics with QIIME 2
December 2018 (3 days)
Instructor
Foundation for Advanced Education in the Sciences - National Institutes of Health, Bethesda, Maryland - Microbial Communities Profiling via QIIME 2
October 2018 (3 days)
Instructor
Istituto Zooprofilattico Sperimentale delle Venezie - Padova, Italy - Teaching and Developing QIIME 2
May 2018 (3 days)
Instructor
University of California San Diego - San Diego, California - Microbiome Bioinformatics with QIIME 2
March 2018 (2 days)
Instructor
Oulon Yliopisto - Oulu, Finland - QIIME 2 Guest Lecture, Ecology of the Human microbiome
NAU BIO 499/599, Dr. Emily Cope
April 2018
Guest lecture
Northern Arizona University - Flagstaff, Arizona - Microbiome Bioinformatics with QIIME 2
February 2018 (2 days)
Instructor
Foundation for Advanced Education in the Sciences - National Institutes of Health, Bethesda, Maryland - Microbiome Bioinformatics with QIIME 2
June 2017 (3 days)
Instructor
Las Vegas, Nevada - Guest Lecture, Microbiome Bioinformatics with QIIME 2
NAU BIO 698, Dr. Greg Caporaso
April 2017; May 2017
Guest lectures
Northern Arizona University - Flagstaff, Arizona - QIIME 2 Workshop
February 2017 (2 days)
Instructor
University of New Hampshire - Durham, New Hampshire - QIIME 2 Workshop
November 2016 (2 days)
Instructor
Phoenix, Arizona - Guest Lecture, Honors Seminar: Enduring Books, Field Notes From a Catastrophe: Climate Change
UAA HNRS A192, Dr. Paula Williams
April 2012
Guest lecture
University of Alaska Anchorage - Anchorage, Alaska - Fluid Dynamics
UAF ES F341
September 2007 - May 2008
Laboratory Instructor
University of Alaska Fairbanks - Fairbanks, Alaska - Introduction to Engineering
June 2007 - July 2007
Course Designer and Instructor
Upward Bound High School Summer Program - Fairbanks, Alaska
Publications
- Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. Matthew R Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R Keefe, Jamie T Morton, Renato RM Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vázquez-Baeza, Michal Ziemski, Hazuki E Miwa, Terry A Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D Kaehler, Emily K Cope, Jessica L Metcalf, Michael S Robeson Ii, Nicholas A Bokulich, J Gregory Caporaso. PLoS Computational Biology (2021).
- QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. Mehrbod Estaki, Lingjing Jiang, Nicholas A Bokulich, Daniel McDonald, Antonio González, Tomasz Kosciolek, Cameron Martino, Qiyun Zhu, Amanda Birmingham, Yoshiki Vázquez‐Baeza, Matthew R Dillon, Evan Bolyen, J Gregory Caporaso, Rob Knight. Current Protocols in Bioinformatics (2020).
- Microbiotyping the Sinonasal Microbiome. D Scott Merrell, Fabio S Lima, Julio Villena, Alkis J Psaltis, Christos Georgalas, A Bassiouni, S Paramasivan, A Shiffer, MR Dillon, EK Cope, C Cooksley, M Ramezanpour, S Moraitis, MJ Ali, BS Bleier, C Callejas, ME Cornet, RG Douglas, D Dutra, C Georgalas, RJ Harvey, PH Hwang, AU Luong, RJ Schlosser, P Tantilipikorn, MA Tewfik, S Vreugde, PJ Wormald, JG Caporaso, AJ Psaltis. Frontiers in Cellular and Infection Microbiology (2020).
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Bolyen E, Rideout JR, Dillon M, Bokulich NA, [and 105 others]. Nature Biotechnology (2019).
- q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data. Bokulich NA, Dillon M, Zhang Y, Rideout JR, Bolyen E, Li H, Albert PS, Caporaso JG. mSystems (2018).
- QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science (PREPRINT). Bolyen E, Rideout JR, Dillon M, Bokulich NA, [and 105 others]. PeerJ Preprints (2018).
- q2-sample-classifier: machine-learning tools for microbiome classification and regression. Bokulich N, Dillon M, Bolyen E, Kaehler BD, Huttley GA, Caporaso JG. Journal of Open Source Software (2018).
- An Introduction to Applied Bioinformatics: a free, open, and interactive text. Boylen, E, Rideout, JR, Chase, J, Pitman, TA, Shiffer, A, Mercurio, W, Dillon, MR, Caporaso JG. Journal of Open Source Education (2018).
- Qiita’s web-enabled platform accelerates microbiome meta-analyses from months to minutes. Gonzalez, A, Navas-Molina, JA, Kosciolek, T, McDonald, D, Vázquez-Baeza, Y, Swafford, AD, Orchanian, SB, Sanders, JG, Shorenstein, J, Brislawn, CJ, Holste, H, Robbins-Pianka, A, Wang, M, Rideout, JR, Bolyen, E, Dillon, M, Caporaso, JG, Dorrestein, PC and Knight, R. Nature Methods (2018).
- Optimizing taxonomic classification of marker gene sequences with QIIME 2’s q2-feature-classifier plugin. Bokulich, NA, Kaehler, BD, Rideout, JR, Dillon, M, Bolyen, E, Knight, R, Huttley, GA, Caporaso, JG. Microbiome (2018).
- The impact of a fluctuating freezing front on ice formation in freezing soil. Dillon MR. University of Alaska Fairbanks (2012).
- Ground ice in the upper permafrost of the Beaufort Sea coast of Alaska. Kanevskiy M, Shur Y, Jorgenson MT, Ping CL, Michaelson GJ, Fortier D, Stephani E, Dillon M, Tumskoy V. Cold Regions Science and Technology (2012).Cryostructures of Basal Glacier Ice as an object of Permafrost Study: Observations from the Matanuska Glacier, Alaska. Fortier D, Kanevskiy M, Shur Y, Stephani E, Dillon M, Jorgenson MT. Proceedings of the Tenth International Conference on Permafrost (2012).
- Study of Ice-Rich Syngenetic Permafrost for Road Design (Interior Alaska). Kanevskiy M, Shur Y, Connor B, Dillon M, Stephani E, O'Donnell J. Proceedings of the Tenth International Conference on Permafrost (2012).
- Permafrost Degradation and thaw settlement under Lakes in Yedoma Environment. Shur Y, Kanevskiy M, Jorgenson T, Dillon M, Stephani E, Bray M, Fortier D. Proceedings of the Tenth International Conference on Permafrost (2012).
- Permafrost of Northern Alaska. Kanevskiy, M.Z., Shur, Y., Jorgenson, M.T., Ping, C.L., Fortier, D., Stephani, E., Dillon, M. Proceedings of the International Offshore and Polar Engineering Conference (2011).
- Geotechnical investigations for the Dalton Highway Innovation Project as a case study of the ice-rich syngenetic permafrost. Shur Y, Kanevskiy M, Dillon M, Stephani E, O'Donnell J. Prepared for Alaska University Transportation Center Project #207122 (2010).
- Buried glacial basal ice along the Beaufort Sea Coast, Northern Alaska. Kanevskiy M, Jorgenson T, Shur Y, Dillon M. Fall Meeting Supplementary Abstracts, American Geophysical Union (2008).
- Quantifying Ice Formation in Coarse Grain Soils using Tomodensitometry. Dillon M, Fortier D, Shur Y. Abstracts of Arctic Science Conference (2008).
- Tomodensitometric analysis of basal ice. Dillon M, Fortier D, Kanevskiy M, Shur Y. Proceedings of the Ninth International Conference on Permafrost (2007).
- Tomodensitometric analysis of basal ice. Dillon M, Fortier D, Kanevskiy M, Shur Y. Abstracts of Arctic Science Conference (2007).
Presentations
- Open Microbiome Science With QIIME 2
Co-presented with Greg Caporaso
April 2019
Association for Computing Machinery, Northern Arizona University Chapter - (Invited) Contextualizing Biological Data For Computers
December 2018
Investigación en Microbiomas y Bioinformática - Universidad de Costa Rica - QIIME 2 2018 Status Update
May 2018
PMI Microbiome Center Seminar - Flagstaff, Arizona - Decentralized, Extensible, and Reproducible Microbiome Analysis
Co-presented with Evan Bolyen
January 2018
PMI Informatics Seminar - Flagstaff, Arizona - (Invited) Interactive web-based visualization for microbiome science
May 2017
PLOTCON 2017 - Oakland, California - QIIME 2: Decentralized, Extensible, and Reproducible Microbiome Analysis
Co-presented with Evan Bolyen
February 2017
Statistical and Algorithmic Challenges in Microbiome Data Analysis (Broad) - Cambridge, Massachusetts - QIIME 2 2016 Status Update
Co-presented with Greg Caporaso, Jai Ram Rideout, and Evan Bolyen
September 2016
MGGEN Seminar - Flagstaff, Arizona - Tomodensitometric analysis of basal ice (Poster)
July 2008
Ninth International Conference on Permafrost - Fairbanks, Alaska - Quantifying Ice Formation in Coarse Grain Soils using Tomodensitometry
September 2008
Arctic Science Conference - Fairbanks, Alaska - Tomodensitometric Analysis of Basal Ice
April 2007
SKYCAN User Meeting - Brugges, Belgium - Tomodensitometric Analysis of Basal Ice
September 2007
Arctic Science Conference - Anchorage, Alaska
Involvement
- 2016; Developer Evangelist, Code For Anchorage --- a social hacking brigade under the Code For America umbrella.
- 2011-2013; Member, Future Leaders of Golder professional development group for junior staff at Golder Associates Inc.
- 2009-2010; Organizer, AK EPSCoR Graduate Student Dessert Discussions seminar series
- 2005-2007; Member, Chi Epsilon civil engineering honor society, UAF chapter