Matthew Ryan Dillon

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 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 (Django, Flask, 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 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

• 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