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.
- 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)
- Zufle A, Salim F, Anderson T, Scotch M, Xiong L, Sokol K, Xue H, Kong R, Heslop D, Paik H-Y, MacIntyre CR. Leveraging Simulation Data to Understand Bias in Predictive Models of Infectious Disease Spread. ACM Trans Spatial Algorithms Syst. 2024. doi: 10.1145/3660631.
- Wang X, Kim KW, Walker G, Stelzer-Braid S, Scotch M, Rawlinson WD. Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high-throughput whole genome sequencing. Influenza Other Respir Viruses. 2024 Jan;18(1):e13252.
- Faleye TOC, Driver EM, Wright JM, Halden RU, Varsani A, Scotch M. Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing. Infect Genet Evol. 2024 Jan 8;118:105550.
- Scotch M, Lauer K, Wieben ED, Cherukuri Y, Cunningham JM, Klee EW, Harrington JJ, Lau JS, McDonough SJ, Mutawe M, O'Horo JC, Rentmeester CE, Schlicher NR, White VT, Schneider SK, Vedell PT, Wang X, Yao JD, Pritt BS, Norgan AP. Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022. mSphere. 2023 Oct 26:e0023223. doi: 10.1128/msphere.00232-23.
- Faleye TOC, Driver EM, Bowes DA, Smith A, Kaiser NA, Wright JM, Chapman AR, Halden RU, Varsani A, Scotch M. Canine parvovirus 2C identified in dog feces from poop bags collected from outdoor waste bins in Arizona USA, June 2022. Transboundary and Emerging Diseases. 2023;2023:5596886. doi: 10.1155/2023/5596886.
- Bowes DA, Henke KB, Driver EM, Newell ME, Block I, Shaffer G, Varsani A, Scotch M, Halden RU. Enhanced detection of mpox virus in wastewater using a pre-amplification approach: A pilot study informing population-level monitoring of low-titer pathogens. Sci Total Environ. 2023 Dec 10;903:166230.
- Fontenele RS, Yang Y, Driver EM, Magge A, Kraberger S, Custer JM, Dufault-Thompson K, Cox E, Newell ME, Varsani A, Halden RU, Scotch M, Jiang X. Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA. Sci Total Environ. 2023 Jun 15;877:162862.
- Chapman AR, Wright JM, Kaiser NA, Jones PM, Driver EM, Halden RU, Varsani A, Scotch M, Faleye TOC. Rhizobium Phage-Like Microvirus Genome Sequence Identified in Wastewater in Arizona, USA, in November 2020 Encodes an Endolysin and a Putative Multiheme Cytochrome c-like Protein. Microbiol Resour Announc. 2023 May 17;12(5):e0006923.
- Faleye TOC, Elyaderani A, Skidmore P, Adhikari S, Smith A, Kaiser N, Sandrolini H, Finnerty S, Halden RU, Varsani A, Scotch M. Surveillance of rhinovirus diversity among a university community identifies multiple types from all three species including an unassigned rhinovirus A genotype. Influenza Other Respir Viruses. 2023 Jan;17(1):e13057.
- Bowes DA, Driver EM, Kraberger S, Fontenele RS, Holland LA, Wright J, Johnston B, Savic S, Engstrom Newell M, Adhikari S, Kumar R, Goetz H, Binsfeld A, Nessi K, Watkins P, Mahant A, Zevitz J, Deitrick S, Brown P, Dalton R, Garcia C, Inchausti R, Holmes W, Tian XJ, Varsani A, Lim ES, Scotch M, Halden RU. Leveraging an established neighbourhood-level, open access wastewater monitoring network to address public health priorities: a population-based study. Lancet Microbe. 2023 Jan;4(1):e29-e37.
ACTIVE GRANTS
R21LM014467-01 Scotch, Gonzalez-Hernandez (PIs) 05/07/2024-04/30/2026 NIH/NLMReal-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) 09/30/2022-08/31/2027Platform 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) 04/01/2023-03/31/2026Collaborative 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-PI
R01AI164481 Scotch, Gonzalez (PIs) 09/17/2021-08/30/2024 NIH/NIAIDEnriching 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.
R15LM013382 Namilae, Srinivasan (PIs) 08/05/2021–07/31/2024 NIH/NLMA data analytics framework for the application of pedestrian dynamics to public health The goal of this project is to develop and evaluate an agnostic data analytics framework for the application of pedestrian dynamics to address a wide range of public health applications. Role: Co-investigator
U01LM013129 Scotch, Halden, Varsani (PIs) 06/03/2019-05/31/2024 NIH/NLMBioinformatics framework for wastewater-based surveillance of infectious disease The goal of this project is to develop and evaluate a bioinformatics framework that uses metagenomic data generated from sampling of wastewater to monitor local epidemics and outbreaks of infectious diseases.
U01LM013129-04S1 Scotch, Halden, Varsani (PIs) 06/03/2022-05/31/2024 NIH/NLMCOVID-19 RADx-rad Administrative supplement to the parent award The goal of this RADx-rad administrative supplement is to implement and evaluate a bioinformatics framework for wastewater-based epidemiology of SARS-CoV-2 across multiple cities in the United States of America.
2154934 Berry S (PI) 08/01/2022-01/31/2025 NSF/CCFPIPP Phase I: Advancing Environmental Surveillance for Pandemic Prediction in Remote and Resource Poor Settings The goal of this planning grant is the founding of the Center for the Discovery of Emerging Environmental Pathogens (C-DEEP). The vision of C-DEEP is to advance the science of environmental surveillance and metagenomics, specifically in regions where pandemics are likely to emerge and where current disease surveillance processes are inadequate. Role: Co-investigator
Courses
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 |
2020 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 593 | Applied Project |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
2020 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 |
| BMI 799 | Dissertation |
2020 Spring
| Course Number | Course Title |
|---|---|
| BMI 595 | Continuing Registration |
| BMI 799 | Dissertation |
| MBB 495 | Undergraduate Research |
| BMI 792 | Research |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 790 | Reading and Conference |
| BMI 593 | Applied Project |
| BMI 484 | Internship |
| BMI 483 | Capstone II |
| BMI 584 | Internship |
| BMI 595 | Continuing Registration |
| BMI 482 | Capstone I |
| CHS 493 | Honors Thesis |
| CHS 791 | Seminar |
2019 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 584 | Internship |
| BMI 792 | Research |
| BMI 593 | Applied Project |
| BMI 560 | Teachng Biomedical Informatics |
| BMI 590 | Reading and Conference |
| CHS 492 | Honors Directed Study |
2024 Member, Advanced Leadership Initiative (ALI), Arizona State University 2018 Awardee, Endeavour Research Fellowship (Australian Government) 2014 Nominee, New York Academy of Sciences Blavatnik Award for Young Scientists 2013 Nominee, Pew Biomedical Scholars Program (Limited Submission) 2011 Finalist, Best Paper, American Medical Informatics Association (AMIA) Joint Summits
- 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-Present: 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)