Matthew Scotch
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Phone: 480-727-2985
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Cntr for Environ. Health Engineering Biodesign Institute B240B Tempe, AZ 85287
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Mail code: 9020Campus: Dtphx
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Matthew Scotch is Associate Dean of Research and Professor of Biomedical Informatics in the College of Health Solutions. He is also Assistant Director of the Biodesign Center for Environmental Health Engineering at Arizona State University. His research focuses on genomic epidemiology and bioinformatics of RNA viruses with a particular interest in influenza A viruses. Current projects include studying approaches to advance genomic epidemiology by enrichment of virus sequence metadata (funding: NIH/NIAID R01AI164481) and analysis of viruses from wastewater using bioinformatics (funding: NSF/BIO 2412446). The latter is part of a NSF Predictive Intelligence for Pandemic Prevention (PIPP) Phase II Center.
His lab group is also interested in the molecular epidemiology of viruses including the amplification and sequencing of influenza A and B viruses for short and long-read high-throughput sequencing (HTS) and public health surveillance.
In 2024, Dr. Scotch was elected as a fellow of the American College of Medical Informatics.
- Postdoctoral Fellowship, Yale University 2006-2008
- M.P.H. Yale University 2007
- Ph.D. Biomedical Informatics, University of Pittsburgh 2006
- M.A. Biomedical Informatics, Columbia University 2002
- B. A. Health and Society, University of Rochester, NY 1998
- Genomic epidemiology of RNA viruses with a focus on influenza A (human and avian)
- Phylodynamics
- Molecular epidemiology
- Wastewater-based epidemiology
- Bioinformatics
- DNA sequence databases and metadata enrichment
- Natural Language Processing (NLP)
Related Links:
(Last 10 publications out of 109 total)
- Vargas J*, Bermudez-Rivera B*, Block I, Shaffer G, Estrada L, Dadd T, Dickerson T, Curtis C, Woods C, Driver EM, Halden RU, Varsani A, Scotch M, Faleye TOC. Canine Parvovirus and Vaccine-Origin Feline Panleukopenia Virus in Wastewater, Arizona, USA: July 2022-June 2023. Microorganisms. 2025 Sep 11;13(9):2124. doi: 10.3390/microorganisms13092124.
- Yeh KB, Bahnfleth WP, Bradforda E, Cardona C, Coleman KK, Hudson PJ, Dadonaite B, Hutchins RJ, Maresso A, MacIntyre CR, Scotch M. Three things we can do now to reduce the risk of avian influenza spillovers. Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2503565122.
- Negrete AU, Nelson S, Scotch M, Faleye TOC. Influenza B virus from respiratory samples of individuals with influenza-like illness in a university campus in Arizona USA, in February 2025. Microbiol Resour Announc. 2025 Jul 7:e0034425.
- Strike W*, Faleye TOC, Lubega B, Rockward A, Torabi S, Noble A, Banadaki MD, Keck J, Mugerwa H, Scotch M, Berry S. Implementing wastewater-based epidemiology for long-read metagenomic sequencing of antimicrobial resistance in Kampala, Uganda. Microorganisms. 2025 May 28;13(6):1240.
- Wang X*, Sevendal AT, Kamalakkannan A, Stelzer-Braid S, Kim KW, Scotch M, Walker GJ, Rawlinson WD. Influenza epidemiology and co-infections within New South Wales-based multicentre health districts between 2018 and 2023. Pathology. 2025 Apr 22:S0031-3025(25)00158-8. doi: 10.1016/j.pathol.2025.02.009.
- O'Connor K, Weissenbacher D, Elyaderani A, Lautenbach E, Scotch M, Gonzalez-Hernandez G. Patient-related metadata reported in sequencing studies of SARS-CoV-2: protocol for a scoping review and bibliometric analysis. JMIR Res Protoc. 2025 Apr 22;14:e58567.
- Chung JR, Price AM, Zimmerman RK, Moehling Geffel K, House SL, Curley T, Wernli KJ, Phillips CH, Martin ET, Vaughn IA, Murugan V, Scotch M, Saade EA, Faryar KA, Gaglani M, Ramm JD, Williams OL, Walter EB, Kirby M, Keong LM, Kondor R, Ellington SR, Flannery B; US Flu VE Network Investigators. Influenza vaccine effectiveness against medically attended outpatient illness, United States, 2023-24 season. Clin Infect Dis. 2025 Jan 6:ciae658.
- Faleye TOC, Skidmore P*, Elyaderani A*, Adhikari S, Kaiser N*, Smith A*, Yanez A, Perleberg T, Driver EM, Halden RU, Varsani A, Scotch M. Adenovirus 41 diversity in Arizona (USA) using wastewater-based epidemiology, long-range PCR, and pathogen sequencing between October 2019 and March 2020. Epidemiol Infect. 2024 Nov 18;152:e142.
- Bermudez-Rivera B*, Hampton B*, Wheeler C*, Vargas J*, Swaminathan S, Driver EM, Halden RU, Varsani A, Scotch M, Faleye TOC. Nine rhizobium phage genomes recovered from wastewater in Tempe, AZ, October 2019-March 2020. Microbiol Resour Announc. 2024 Oct 10;13(10):e0068024.
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Wang X*, Walker G, Kim KW, Stelzer-Braid S, Scotch M, Rawlinson WD. The resurgence of influenza A/H3N2 virus in Australia after the relaxation of COVID-19 restrictions during the 2022 season. J Med Virol. 2024 Sep;96(9):e29922.
*Student authors
ACTIVE GRANTS
2412446
NSF/DBI
Berry (PI) 09/01/2024-08/30/2031
PIPP Phase II: Environmental Surveillance for Assessing Pathogen Emergence (ESCAPE)
The goal of this PIPP phase II center is to develop and implement environmental surveillance systems that work for everyone, anywhere while advancing public health intelligence through communication, community-based science, and workforce development to predict and prevent infectious disease pandemics.
Role: Co-principal investigator
R21LM014467-01
NIH/NLM
Scotch, Gonzalez-Hernandez (PIs) 05/07/2024-04/30/2026
Real-time estimation of influenza vaccine effectiveness through social media mining
The goal of this project is to use natural language processing (NLP) to estimate influenza vaccine effectiveness from social media posts in order to supplement traditional studies that rely on a test-negative design.
U01IP001180
CDC
Murugan (PI) 09/30/2022-08/31/2027
Platform to Assess Influenza and COVID-19 Vaccine Effectiveness in Underserved Arizona Populations
The goal of this project is to assess seasonal influenza and SARS-CoV-2 vaccine effectiveness among diverse demographic and clinical populations in Arizona.
Role: Co-investigator
2302969
NSF/IIS
Zufle (PI) 04/01/2023-03/31/2026
Collaborative Research: NSF-CSIRO: HCC: Small: Understanding Bias in AI Models for the Prediction of Infectious Disease Spread
The goal of this study is to design, develop, and validate artificial intelligence models that consider various forms of bias in prediction of infectious disease spread.
Role: Co-principal investigator
R01AI164481
NIH/NIAID
Scotch, Gonzalez (PIs) 09/17/2021-08/30/2026
Enriching SARS-CoV-2 sequence data in public repositories with information extracted from full text articles
The goal of this project is to develop and evaluate a biomedical informatics framework for enriching SARS-CoV-2 sequence data in public repositories for studying genomic epidemiology and population health.
Courses
2026 Spring
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 614 | Curr Persp Health Informatics |
| BMI 484 | Internship |
| BMI 584 | Internship |
| BMI 590 | Reading and Conference |
| BMI 790 | Reading and Conference |
| CHS 493 | Honors Thesis |
| CHS 494 | Special Topics |
2025 Fall
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| BMI 790 | Reading and Conference |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
| BMI 484 | Internship |
| BMI 461 | Advanced Topics in BMI I |
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
| CHS 492 | Honors Directed Study |
| CHS 494 | Special Topics |
2025 Summer
| Course Number | Course Title |
|---|---|
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 484 | Internship |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 482 | Capstone I |
| BMI 483 | Capstone II |
2025 Spring
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 790 | Reading and Conference |
| BMI 484 | Internship |
| BMI 483 | Capstone II |
| BMI 584 | Internship |
| BMI 482 | Capstone I |
| BMI 590 | Reading and Conference |
| BMI 614 | Curr Persp Health Informatics |
2024 Fall
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| BMI 790 | Reading and Conference |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
| BMI 484 | Internship |
| BMI 461 | Advanced Topics in BMI I |
| BMI 482 | Capstone I |
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
| BMI 483 | Capstone II |
| BMI 792 | Research |
2024 Summer
| Course Number | Course Title |
|---|---|
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 484 | Internship |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 482 | Capstone I |
| BMI 483 | Capstone II |
2024 Spring
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BIO 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 790 | Reading and Conference |
| BMI 484 | Internship |
| BMI 483 | Capstone II |
| BMI 584 | Internship |
| BMI 482 | Capstone I |
| BMI 590 | Reading and Conference |
| BMI 614 | Curr Persp Health Informatics |
2023 Fall
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| BMI 790 | Reading and Conference |
| BIO 495 | Undergraduate Research |
| MBB 495 | Undergraduate Research |
| BMI 484 | Internship |
| BMI 461 | Advanced Topics in BMI I |
| BMI 482 | Capstone I |
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
| BMI 483 | Capstone II |
2023 Summer
| Course Number | Course Title |
|---|---|
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 484 | Internship |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 482 | Capstone I |
| BMI 483 | Capstone II |
2023 Spring
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 790 | Reading and Conference |
| BMI 484 | Internship |
| BMI 483 | Capstone II |
| BMI 584 | Internship |
| BMI 482 | Capstone I |
| BMI 590 | Reading and Conference |
| CHS 791 | Seminar |
2022 Fall
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| BMI 790 | Reading and Conference |
| MBB 495 | Undergraduate Research |
| BMI 484 | Internship |
| BMI 461 | Advanced Topics in BMI I |
| BMI 482 | Capstone I |
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
| BMI 483 | Capstone II |
2022 Summer
| Course Number | Course Title |
|---|---|
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 484 | Internship |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 482 | Capstone I |
| BMI 483 | Capstone II |
2022 Spring
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 790 | Reading and Conference |
| BMI 484 | Internship |
| BMI 483 | Capstone II |
| BMI 584 | Internship |
| BMI 482 | Capstone I |
| BMI 590 | Reading and Conference |
| CHS 791 | Seminar |
2021 Fall
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| BMI 790 | Reading and Conference |
| MBB 495 | Undergraduate Research |
| BMI 484 | Internship |
| BMI 461 | Advanced Topics in BMI I |
| BMI 482 | Capstone I |
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
| BMI 483 | Capstone II |
2021 Summer
| Course Number | Course Title |
|---|---|
| BMI 584 | Internship |
| BMI 792 | Research |
| BMI 484 | Internship |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 482 | Capstone I |
| BMI 483 | Capstone II |
2021 Spring
| Course Number | Course Title |
|---|---|
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 790 | Reading and Conference |
| BMI 484 | Internship |
| BMI 483 | Capstone II |
| BMI 584 | Internship |
| BMI 482 | Capstone I |
| BMI 590 | Reading and Conference |
| CHS 791 | Seminar |
2025, Fellow, American College of Medical Informatics
2024 Member, Advanced Leadership Initiative (ALI), Arizona State University
- Infection, Genetics, and Evolution (Elsevier)
American Medical Informatics Association (AMIA)
American Ornithological Society (AOS)
American Society for Microbiology (ASM)
International Society for Computational Biology (ISCB)
International Society for Influenza and other Respiratory Virus Diseases (ISIRV)
2023-2024: Chair (Appointed), NLM/NIH BILDS Review Committee
2021-Present: Member, Baccalaureate Educators Community, AMIA Academic Forum
2020–Present: Journal Editorial Board Member, Environment International (Elsevier)
2013–Present: Journal Editorial Board Member, Infection, Genetics and Evolution (Elsevier)