Matthew Scotch

Matthew Scotch

Assistant Dean & Professor, College of Health Solutions
Assistant Center Director & Professor, Biodesign Center for Environmental Health Engineering
Senior Global Futures Scientist, Global Futures Scientists and Scholars
  • matthew.scotch@asu.edu
  • 480-727-2985
  • ‌
  • Cntr for Environ. Health Engineering Biodesign Institute B240B Tempe, AZ 85287
  • Mail code: 9020
    Campus: Dtphx
  • ‌
Biography Research Teaching Public Work
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Long Bio

Matthew Scotch is Assistant 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 1R01AI164481-01A1) and analysis of viruses from wastewater using bioinformatics (funding: NIH/NLM U01LM013129). The latter is partially funded by the NIH RADx-rad initiative.

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.

Education
  • 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
CV
Curriculum Vitae (341 KB)
Google Scholar URL
https://scholar.google.com/citations?user=ZpZiJYIAAAAJ&hl=en
Experts.asu.edu URL
https://asu.pure.elsevier.com/en/persons/matthew-scotch
ORCID Profile ID
https://orcid.org/0000-0001-5100-9724
Research Interests
  • 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:

  • Biodesign Center for Environmental Health Engineering
Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Faleye TOC, Driver EM, Bowes DA, Holm RH, Talley D, Yeager R, Bhatnagar A, Smith T, Varsani A, Halden  RU, Scotch M. Detection of human, porcine and canine picornaviruses in municipal sewage sludge using pan-enterovirus amplicon-based long-read Illumina sequencing. Emerg Microbes Infect. 2022 Dec;11(1):1339-1342.
  6. Collins CL, Faleye TOC, Kraberger S, Fontenele RS, Adams D, Adhikari S, Sandrolini H, Finnerty S, Halden RU, Scotch M, Varsani A. Complete Coding Sequences of Rhinovirus Types A46, A39, C56, and C48. Microbiol Resour Announc. 2022 Nov 17;11(11):e0068022.
  7. Smith A*, Kaiser N*, Yanez A, Perleberg T, Elyaderani A*, Skidmore P*, Adhikari S, Driver EM, Halden RU, Varsani A, Scotch M, Faleye TOC. Genome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding Protein. Microbiol Resour Announc. 2022 Oct 20;11(10):e0033722. 
  8. Collins CL, Kraberger S, Fontenele RS, Faleye TOC, Adams D, Adhikari S, Sandrolini H, Finnerty S, Halden RU, Scotch M, Varsani A. Genome Sequences of Anelloviruses, Genomovirus, and Papillomavirus Isolated from Nasal Pharyngeal Swabs.  Microbiol Resour Announc. 2022 Sep 15;11(9):e0068122.
  9. Faleye TOC, Skidmore PT*, Elyaderani A*, Smith A*, Kaiser N*, Adhikari S, Yanez A, Perleberg T, Driver EM, Halden RU, Varsani A, Scotch M. Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021. Infect Genet Evol. 2022 Sep;103:105315.
  10. Namilae S, Wu Y, Mubayi A, Srinivasan A, Scotch M. Identifying mitigation strategies for COVID-19 superspreading on flights using models that account for passenger movement. Travel Med Infect Dis. 2022 May-Jun;47:102313.
  11. Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA 2nd, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. Water Res. 2021 Oct 15;205:117710.
  12. Faleye TOC, Bowes DA, Driver EM, Adhikari S, Adams D, Varsani A, Halden RU, Scotch M. Wastewater-based epidemiology and long-read sequencing to identify enterovirus circulation in three municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020. Viruses. 2021 Sep 10;13(9):1803. doi: 10.3390/v13091803.
  13. Adam DC, Chen X, Scotch M, MacIntyre CR, Dwyer D, Kok J. The molecular epidemiology and clinical phylogenetics of rhinoviruses among paediatric cases in Sydney, Australia. Int J Infect Dis. 2021 Sep;110:69-74.
  14. Faleye TOC, Adams D, Adhikari S, Sandrolini H, Halden RU, Varsani A, Scotch M. Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting. BMC Infect Dis. 2021 Aug 13;21(1):810.
  15. Islam T, Lahijani MS, Srinivasan A, Namilae S, Mubayi A, Scotch M. From bad to worse: airline boarding changes in response to COVID-19. R Soc Open Sci. 2021 Apr 28;8(4):201019.
  16. Faleye TOC, Driver E, Bowes D, Adhikari S, Adams D, Varsani A, Halden RU, Scotch M. Pan-Enterovirus Amplicon-Based High-Throughput Sequencing Detects the Complete Capsid of a EVA71 Genotype C1 Variant via Wastewater-Based Epidemiology in Arizona. Viruses. 2021 Jan 7;13(1):E74. doi: 10.3390/v13010074.
  17. Magge A, Weissenbacher D, O'Connor K, Tahsin T, Gonzalez-Hernandez G, Scotch M. GeoBoost2: A natural language processing pipeline for GenBank metadata enrichment for virus phylogeography. Bioinformatics. 2020 Dec 22;36(20):5120-5121.
  18. Vaiente MA*, Scotch M. Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty. Infect Genet Evol. 2020 Nov;85:104501.
  19. Ngonghala CN, Iboi E, Eikenberry S, Scotch M, MacIntyre CR, Bonds MH, Gumel AB. Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus. Math Biosci. 2020 Jul;325:108364.
  20. Holland LA, Kaelin EA, Maqsood R, Estifanos B, Wu LI, Varsani A, Halden RU, Hogue BG, Scotch M, Lim ES. An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020). J Virol. 2020 Jul 1;94(14):e00711-20.
  21. Yoo W, Koskan A, Scotch M, Pottinger H, Huh WK, Helitzer D. Patterns and disparities in human papillomavirus (HPV) vaccine uptake for young female adolescents among us states: NIS-Teen (2008-2016). Cancer Epidemiol Biomarkers Prev. 2020 Jul;29(7):1458-1467.
  22. Scotch M, Halden RU, Denton A, Sandrolini H, Fontenele RS, Varsani A. Coding-complete genome sequence of a human respirovirus 1 strain from a clinical sample in Arizona. Microbiol Resour Announc. 2020 Jun 11;9(24):e00465-20.
  23. Chen X, Adam DC*, Chughtai AA, Stelzer-Braid S, Scotch M, MacIntyre CR. The phylogeography of MERS-CoV in hospital outbreak-associated cases compared to sporadic cases in Saudi Arabia. Viruses. 2020 May 14;12(5):E540.
  24. Stelzer-Braid S, Wynn M, Chatoor R, Scotch M, Ramachandran V, Teoh HL, Farrar MA, Sampaio H, Andrews PI, Craig ME, MacIntyre CR, Varadhan H, Kesson A, Britton PN, Newcombe J, Rawlinson WD. Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations. J Clin Virol. 2020 Jan;122:104216.
  25. Beard R*, Scotch M. Identifying current and emerging resources and tools utilized for detection, prediction, and visualization of viral zoonotic disease clusters: a Delphi study. JAMIA Open. 2019 Oct; 2(3): 306–311.
  26. Adam DC*, MacIntyre CR†, Scotch M†. Phylodynamics of influenza A/H1N1pdm09 in India reveals circulation patterns and increased selection for clade 6b residues and other high mortality mutants. Viruses. 2019 Aug 27;11(9). pii: E791.
  27. Scotch M, Tahsin T*, Weissenbacher D, O'Connor K, Magge A*, Vaiente M*, Suchard MA, Gonzalez-Hernandez G. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol. 2019 Feb 28;5(1):vey043.
  28. Magee HY, Maurer MM, Cobos A, Pycke BFG, Venkatesan AK, Magee D, Scotch M, Halden RU. U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids. Sci Total Environ. 2018 Dec 1;643:460-467.
  29. Bui CM, Adam DC*, Njoto E, Scotch M, MacIntyre CR. Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis. Emerg Microbes Infect. 2018 Nov 21;7(1):184.
  30. Adam DC*, MacIntyre CR†, Scotch M†. Bayesian phylogeography and pathogenic characterisation of smallpox based on HA, ATI and CrmB genes. Mol Biol Evol. 2018 Nov 1;35(11):2607-2617.
  31. Beard R*, Wentz E, Scotch M. A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks. Int J Health Geogr. 2018 Oct 30;17(1):38.
  32. Magee D*, Scotch M. The effects of random taxa sampling schemes in Bayesian virus phylogeography. Infect Genet Evol. 2018 Oct;64:225-230.
  33. Njoto EN, Scotch M, Bui CM, Adam DC*, Chughtai AA*, MacIntyre CR. Phylogeography of H5N1 avian influenza virus in Indonesia. Transbound Emerg Dis. 2018 Oct;65(5):1339-1347.
  34. Magge A*, Weissenbacher D, Sarker A, Scotch M, Gonzalez-Hernandez G. Deep neural networks and distant supervision for geographic location mention extraction. Bioinformatics. 2018 Jul 1;34(13):i565-i573.
  35. Tahsin T*, Weissenbacher D, O'Connor K, Magge A, Scotch M, Gonzalez-Hernandez G. GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. Bioinformatics. 2018 May 1;34(9):1606-1608.
  36. Magee D*, Taylor JE, Scotch M. The effects of sampling location and predictor point estimate certainty on posterior support in Bayesian phylogeographic generalized linear models. Sci Rep. 2018 Apr 12;8(1):5905.
  37. Namilae S, Derjany P, Mubayi A, Scotch M, Srinivasan A. Multiscale model for pedestrian and infection dynamics during air travel. Phys Rev E. 2017 May;95(5-1):052320.
  38. Magee D*, Suchard MA, Scotch M. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction. PLoS Comput Biol. 2017 Feb 7;13(2):e1005389.
  39. Tahsin T*, Weissenbacher D, Jones-Shargani D*, Magee D*, Vaiente M*, Gonzalez G, Scotch M. Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. Database (Oxford). 2017 Jan 1;2017:bax093.
  40. Namilae S, Srinivasan A, Mubayi A, Scotch M, Pahle R. Self-propelled pedestrian dynamics model: Application to passenger movement and infection propagation in airplanes. Physica A. 2017 Jan 1; 465(1):248-260.
  41. Tahsin T*, Weissenbacher D, Rivera R*, Beard R*, Firago M*, Wallstrom G, Scotch M, Gonzalez G. A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. J Am Med Inform Assoc. 2016 Sep;23(5):934-41.
  42. Jirjies S*, Wallstrom G, Halden RU, Scotch M. pyJacqQ: python implementation of Jacquez's Q-statistics for space-time clustering of disease exposure in case-control studies. J Stat Softw. 2016 Oct;74(6). 
  43. Sarker A, O'Connor K*, Ginn R, Scotch M, Smith K, Malone D, Gonzalez G. Social media mining for toxicovigilance: automatic monitoring of prescription medication abuse from Twitter. Drug Saf. 2016 Mar;39(3):231-40.
  44. Veljkovic V, Paessler S, Glisic S, Prljic J, Perovic VR, Veljkovic N, Scotch M. Evolution of 2014/15 H3N2 influenza viruses circulating in US: consequences for vaccine effectiveness and possible new pandemic. Front Microbiol. 2015 Dec 22;6:1456.
  45. Weissenbacher D, Tahsin T*, Beard R*, Figaro M*, Rivera R*, Scotch M, Gonzalez G. Knowledge-driven geospatial location resolution for phylogeographic models of virus migration. Bioinformatics. 2015 Jun 15;31(12):i348-i356. ISMB/ECCB 2015 Proceedings.
  46. Veljkovic V, Glisic S, Muller CP, Scotch M, Branch DR, Perovic VR, Sencanski M, Veljkovic N, Colombatti A. In silico analysis suggests interaction between Ebola virus and the extracellular matrix. Front Microbiol. 2015 Feb 19;6:135.
  47. Magee D*, Beard R*, Suchard MA, Lemey P, Scotch M. Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion. Arch Virol. 2015 Jan;160(1):215-24.
  48. Kane MJ, Price N, Scotch M, Rabinowitz P. Comparison of ARIMA and random forest time series models for prediction of avian influenza H5N1 outbreaks. BMC Bioinformatics. 2014 Aug 13;15(1):276.
  49. Scotch M, Lam TT, Pabilonia KL, Anderson T, Baroch J, Kohler D, DeLiberto TJ. Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States. Infect Genet Evol. 2014 Aug;26:185-193.
  50. Scotch M, Mei C, Makonnen YJ, Pinto J, Ali A, Vegso S, Kane M, Sarkar IN, Rabinowitz P. Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt. BMC genomics. 2013 Dec 10;14(1):871.
  51. Womack JA, Scotch M, Leung S, Brandt CA. Use of structured and unstructured data to identify contraceptive use in women veterans. Perspect Health Inf Manag. 2013. Summer: 1-15.
  52. Scotch M, Baarson B*, Beard R*, Lauder R*, Varman A*, Halden RU. Examining the differences in format and characteristics of zoonotic virus surveillance data on state agency websites. J Med Internet Res. 2013;15(4):e90.
  53. Scotch M, Mei C. Phylogeography of swine influenza H3N2 in the United States: translational public health for zoonotic disease surveillance. Infect Genet Evol. 2013 Jan;13:224-9.
  54. Rabinowitz PM, Galusha D, Vegso S, Michalove J*, Rinne S, Scotch M, Kane M. Comparison of human and animal surveillance data for H5N1 influenza A in Egypt 2006-2011. PLoS One. 2012;7(9):e43851. Epub 2012 Sep 27.
  55. Scotch M, Rabinowitz P, Brandt C. State-level zoonotic disease surveillance in the United States. Zoonoses Public Health. 2011 Dec;58(8):523-8.
  56. Scotch M, Sarkar IN, Mei C, Leaman R, Cheung KH, Ortiz P*, Singraur A*, Gonzalez G. Enhancing phylogeography by improving geographical information from GenBank. J Biomed Inform. 2011 Dec;44 Suppl 1:S44-S47.
  57. Scotch M, Brownstein JS, Vegso S, Galusha D, Rabinowitz P. Human vs. animal outbreaks of the 2009 swine-origin H1N1 influenza A epidemic. Ecohealth. 2011 Sep;8(3):376-80.
  58. Garla V, Re VL 3rd, Dorey-Stein Z, Kidwai F, Scotch M, Womack J, Justice A, Brandt C. The Yale cTAKES extensions for document classification: architecture and application. J Am Med Inform Assoc. 2011 Sep-Oct;18(5):614-20.
  59. Scotch M, Mattocks K, Rabinowitz P, Brandt C. A qualitative study of state-level zoonotic disease surveillance in New England. Zoonoses Public Health. 2011 Mar;58(2):131-9.
  60. Ohl M, Tate J, Duggal M, Skanderson M, Scotch M, Kaboli P, Vaughan-Sarrazin M, Justice A. Rural residence is associated with delayed care entry and increased mortality among veterans with Human Immunodeficiency Virus (HIV) infection. Med Care. 2010 Dec;48(12):1064-70.
  61. Scotch M, Mei C, Brandt C, Sarkar IN, Cheung K. At the intersection of public-health informatics and bioinformatics: Using advanced Web technologies for phylogeography. Epidemiology. 2010 Nov;21(6):764-8.
  62. Konovalov S, Scotch M, Post L, Brandt C. Biomedical informatics techniques for processing and analyzing web blogs of military service members. J Med Internet Res. 2010 Oct 5;12(4):e45.
  63. Womack JA, Scotch M, Gibert C, Chapman W, Yin M, Justice AC, Brandt C. A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records. Perspect Health Inf Manag. 2010; Oct 1;7:1a.
  64. Rabinowitz PR, Scotch M, Conti LA. Animals as sentinels: using comparative medicine to move beyond the laboratory. Institute for Laboratory Animal Research Journal. 2010; 51(3):262-267.
  65. Scotch M, Duggal M, Brandt C, Lin Z, Shiffman R. Use of statistical analysis in the biomedical informatics literature. J Am Med Inform Assoc. 2010 Jan-Feb;17(1):3-5.
  66. Liu A, Lee V, Galusha D, Slade MD, Diuk-Wasser M, Andreadis T, Scotch M, Rabinowitz P.  Risk factors for human infection with West Nile virus in Connecticut: a multi-year analysis. Int J Health Geogr. 2009 Nov 27;8:67.
  67. Scotch M, Odofin L, Rabinowitz P. Linkages between animal and human health sentinel data. BMC Vet Res. 2009 Apr 23;5:15.
  68. Rabinowitz, P, Scotch M, Conti L. Human and animal sentinels for shared health risks. Vet Ital. 2009 Jan-Mar;45(1):23-4.
  69. Scotch M, Yip K, Cheung K. Development of grid-like applications for public health using Web 2.0 mashup techniques. J Am Med Inform Assoc. 2008 Nov-Dec;15(6):783-6.
  70. Cheung K, Yip K, Townsend JP, Scotch M. HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. J Biomed Inform. 2008 Oct;41(5):694-705.
  71. Boulos MNK, Scotch M, Cheung K, Burden D. Web GIS in practice VI: a demo "playlist" of geo-mashups for public health neogeographers. Int J Health Geogr. 2008 Jul 18;7:38.
  72. Parmanto B, Paramita M, Sugiantara W, Pramana G, Scotch M, Burke DS. Spatial and multidimensional visualization of Indonesia's village health statistics. Int J Health Geogr. 2008 Jun 11;7:30.
  73. Scotch M, Parmanto B, Monaco V. Evaluation of SOVAT: an OLAP-GIS decision support system for community health assessment data analysis. BMC Med Inform Decis Mak. 2008 Jun 9;8:22.
  74. Scotch M, Parmanto B, Monaco V. Usability evaluation of the Spatial OLAP Visualization and Analysis Tool (SOVAT). J Usability Stud. 2007 Feb;2(2):76-95.
  75. Scotch M, Parmanto B. Development of SOVAT: A numerical-spatial decision support system for community health assessment research. Int J Med Inform. 2006 Oct-Nov;75(10-11):771-84.
  76. Scotch M, Parmanto B, Gadd CS, Sharma RK. Exploring the role of GIS during community health assessment problem solving: experiences of public health professionals. Int J Health Geogr. 2006 Sep 18;5:39.
  77. Parmanto B, Scotch M, Ahmad S. A framework for designing a healthcare outcome data warehouse. Perspect Health Inf Manag. 2005 Sep 6;2:3.

†Joint senior authorship; order switched to facilitate counting *Student authors

Research Activity

ACTIVE RESEARCH SUPPORT

AEGIS    Scotch (PI)    06/01/2023-05/31/2024 University of ArizonaGenomic epidemiology of avian influenza viruses in the Southwest US The goal of this study is to sequence avian influenza viruses from multiple species and the environment to study the evolution and spread of the viruses in Arizona.

IIS 2302969    Zufle (PI)    04/01/2023-03/31/2026 NSF        Collaborative Research: NSF-CSIRO: HCC: Small: Understanding Bias in AI Models for the Prediction of Infectious Disease Spread The goal of this proposal is to design, develop, and validate artificial intelligence models that consider various forms of bias in prediction of infectious disease spread. Role: Co-PI

CCF 2154934 Berry S (PI) 08/01/2022-01/31/2024 NSFPIPP 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

1R01AI164481-01A1 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.

1R15LM013382-01A1 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

OAC 2027529 Scotch (PI) 05/15/2020-12/31/2022 NSFCollaborative:RAPID: Leveraging new data sources to analyze the risk of COVID-19 in crowded locations The goal of this RAPID project is to utilize new data sources such as location-based services data and videos of pedestrian movement to develop local and global models of COVID-19 risk.

OAC 1931560 Scotch (PI) 11/01/2019–10/31/2023 NSFCollaborative:Elements:Cyberinfrastructure for pedestrian dynamics-based analysis of infection propagation through air travel The goal of this project is to develop a novel software to simulate the movement of people in order to understand how movement patterns influence transmission of infection at local as well as global scales.

U01LM013129 Scotch, Halden, Varsani (PIs) 06/03/2019-05/31/2023 NIH/NLMBioinformatics framework for wastewater-based surveillance of infectious diseases 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.

3U01LM013129-04S1 Scotch, Halden, Varsani (PIs) 06/03/2022-11/30/2022 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.

Courses
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
2019 Summer
Course Number Course Title
BMI 584 Internship
BMI 792 Research
2019 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 593 Applied Project
BMI 493 Honors Thesis
BMI 484 Internship
BMI 593 Applied Project
BMI 483 Capstone II
BMI 482 Capstone I
2018 Fall
Course Number Course Title
BMI 799 Dissertation
BMI 790 Reading and Conference
MBB 495 Undergraduate Research
BMI 484 Internship
BMI 492 Honors Directed Study
BMI 584 Internship
BMI 792 Research
BMI 593 Applied Project
BMI 560 Teachng Biomedical Informatics
BMI 590 Reading and Conference
BMI 792 Research
Presentations

2022    Genomic epidemiology and bioinformatics for RNA virus surveillance, Honors College Symposium. Embry-Riddle Aeronautical University, Daytona Beach, Florida 2022    Wastewater-based epidemiology (WBE) and bioinformatics for surveillance of SARS-CoV-2 across US cities, Biological Design Seminar Series, Arizona State University, Tempe, Arizona. 2021    Genomic epidemiology of the SARS-CoV-2 Delta variant in Arizona USA. Rocky Mountain Bioinformatics Conference. Aspen, Colorado. 2021    High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. CIVV-olics Seminar Series. Biodesign Institute. Arizona State University. Tempe, Arizona. 2021    High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. American Medical Informatics Association (AMIA) Annual Conference. San Diego, California. 2021    Panelist, COVID-19 Variants: What Should You Know? College of Health Solutions Health Talk, ASU. 2020    Data-Driven Computing-Intensive Modeling. Webinar on Battling Emerging & Re-emerging Epidemics & Designing Mitigating Strategies - COVID-19. 2020    Bioinformatics framework for wastewater-based surveillance of infectious diseases. Webinar on Spirit of the Senses.  2020    How will polar ice melt impact the migration of infectious disease? Sip of Science Lecture Series hosted by the Biodesign Institute. The Henry Restaurant. Phoenix, Arizona. 2019    Bioinformatics framework for wastewater-based surveillance of infectious diseases. The National Academies of Sciences, Engineering, and Medicine. Board on Life Sciences Fall Meeting. Tempe, Arizona. 2019    An online end-to-end pipeline for virus phylogeography that leverages natural language processing for finding host locations. Rocky Mountain Bioinformatics Conference. Aspen, Colorado. 2019    Informatics for genomics-informed surveillance of RNA viruses, NLM Informatics and Data Science Lecture Series, National Library of Medicine, National Institutes of Health, Bethesda, Maryland. 2019    Virus phylogeography for public health surveillance, Computer Science Colloquium, University of West Florida, Pensacola, Florida. 2019    Use of Sampling Uncertainty in Virus Phylogeography. Yale Center for Biomedical Data Science Seminar Series. Yale University School of Medicine. New Haven, Connecticut. 2019    ZooPhy: A bioinformatics pipeline for virus phylogeography and surveillance. International Society for Disease Surveillance Annual Conference. San Diego, California. 2018    (Keynote) Avian influenza virus ecology and evolution. Egyptian Society of Virology. 7th International Conference on Emerging and Re-Emerging Viral Diseases. Hurghada, Red Sea Governorate, Egypt. 2018    ZooPhy and ZoDo: Bringing virus phylogeography to the public health epidemiologist. MEEGID-14. Sitges, Spain. 2018    Use of genetic data in the grey zone & global security PLuS, Public Health Laboratory Network meeting. Australian Department of Health. Canberra, Australian Capital Territory. 2018    NLP and phylogeography: studying the evolution and spread of viruses by finding locations of the infected host. Seminar Series. School of Civil and Environmental Engineering, UNSW. Sydney, NSW, Australia. 2018    Use of genetic data in the grey zone. Seminar Series. Kirby Institute, UNSW. Sydney, NSW, Australia. 2018    NLP and phylogeography: studying the evolution and spread of viruses by finding locations of the infected host. University of Pennsylvania Health Language Processing Forum. Philadelphia, Pennsylvania. 2018    Incorporating observation error in the geospatial assignment of taxa for virus phylogeography. AMIA 2018 Informatics Summit. San Francisco, California. 2017    Demystifying the genetic evolution of pathogens. Arizona Biosecurity Workshop. Arizona State University. Tempe, Arizona 2017    Influenza phylogeography for public health surveillance. INFORMS Annual Conference. Houston, TX 2017    Linking geospatial mentions in journal articles to GenBank records for virus phylogeography. Great Lakes Bioinformatics Conference. Chicago, Illinois 2017    Merging viral genetics with climate and population data for zoonotic surveillance. NIH/NLM Board of Regents (Council). Bethesda, Maryland 2017    Surveillance of RNA viruses using discrete Bayesian phylogeography. Fusion 2017: ASU Biodesign Institute Scientific Retreat. Carefree, Arizona 2016    Population health surveillance of RNA viruses through phylogeography. The Kirby Institute, UNSW. Sydney, Australia 2016    Incorporating geospatial observation error in discrete Bayesian virus phylogeography. MEEGID-13. Antwerp, Belgium 2015    Analysis of viral genetics for estimating diffusion of influenza A H6N1. AMIA 2015 Joint Summits on Translational Science. San Francisco, California 2014    A pipeline for virus phylogeography that accounts for geospatial observation error. Rocky Mountain Bioinformatics Conference. Aspen, Colorado 2014    Text processing and geospatial uncertainty for phylogeography of zoonotic viruses. Webinar on NIH-funded projects on spatial uncertainty, surveillance research program of the National Cancer Institute (NCI) Division of Cancer Control and Population Sciences 2014    Challenges and promises of bioinformatics for translational applications. Lecture to first-year medical students. University of Arizona College of Medicine-Phoenix, Arizona 2014    Tracking the spread of viruses. Spirit of the senses salon. Tempe, Arizona 2014    Phylogeographic generalized linear model for identifying predictors driving H5N1 diffusion within Egypt. Intelligent Systems for Molecular Biology (ISMB). Boston, Massachusetts 2014    Translational public health: using viral sequence data for zoonotic disease surveillance. Epi Presents! Series. Maricopa County Department of Public Health. Phoenix, Arizona 2013    Phylogeography of avian and human influenza in the Southwest United States. Influenza2013: one influenza, one world, one health. Oxford, United Kingdom 2012    Phylogeography of avian and human influenza in the southwest United States. Rocky Mountain Bioinformatics Conference. Aspen, Colorado 2012    Phylogeography of influenza A in human and avian species in the southwest United States. MEEGID-11. New Orleans, Louisiana 2012    Public health informatics to support public health decision making. Society for Medical Decision Making (SMDM). Phoenix, Arizona 2011    ZooPhy: an informatics system for phylozoonoses. Translational Genomics Research Institute (TGen) weekly bioinformatics seminar. Phoenix, Arizona 2010    Integrated human-animal surveillance systems for emerging threats to health. Cummings School of Veterinary Medicine Symposium on The Electronic Medical Records. Grafton, Massachusetts 2010    Using advanced web technologies to combine disparate data for public health research. Society for Epidemiologic Research (SER). Seattle, Washington 2009    Advanced web technologies for translational informatics across different biomedical domains. AMIA Joint Summits on Translational Science. San Francisco, California 2009    A mashup to help public health professionals. NIH/NLM Board of Regents (Council). Bethesda, Maryland 2008    Informatics for zoonotic disease surveillance: combining animal and human data. NLM Training conference. Bethesda, Maryland 2007    Informatics for zoonotic disease surveillance: combining animal and human data. University of Pittsburgh Department of Biomedical Informatics lecture series. Pittsburgh, Pennsylvania 2005    Usability assessment of the Spatial OLAP Visualization and Analysis Tool (SOVAT). NIH/NLM training conference. Bethesda, Maryland 2004    A GIS tool for community health assessments. Pennsylvania Rural Health Association. State College, Pennsylvania 2003    Constructing a community health database: an early demonstration. Pennsylvania Public Health Association. Harrisburg, Pennsylvania

Honors / Awards

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, Enhancing phylogeography by improving geographical information from GenBank, American Medical Informatics Association (AMIA) Joint Summits 2007    Awardee, Tuition and Travel, Cold Spring Harbor Laboratory Workshop on Infectious Disease Ontology, Supported by the Burroughs Wellcome Fund 2002    Winner, Best Paper, Sublanguage of cross coverage, AMIA Fall Symposium 2002    Nominee, Homer R. Warner Award, Sublanguage of cross coverage, AMIA Fall Symposium

Editorships
  • Infection, Genetics, and Evolution (Elsevier)
  • Viruses (MDPI)
Professional Associations

American Medical Informatics Association (AMIA) American Society for Microbiology (ASM) International Society for Computational Biology (ISCB) International Society for Influenza and other Respiratory Virus Diseases (ISIRV)

Service
  • Infection Genetics Evolution, Editorial Board (2014 - Present)
  • Influenza Research Database and Virus Pathogen Resource, Member, User Advisory Group (2014 - Present)
  • Infection, Genetics, and Evolution, Editorial Board (2013 - Present)
  • Influenza Research Database and Virus Pathogen Resource, Member, User Advisory Group (2013 - Present)
  • Biomedical Informatics Academic Program Committee, Member (2014 - 2014)
  • NIH/NLM Information Resource Grants to Reduce Health Disparities (G08), ZLM1 ZH-G 01, Reviewer (2014 - 2014)
  • Biomedical Informatics Admissions Committee, Chair (2014 - 2014)
  • NIH/NLM Special Emphasis Panel, ZLM1 ZH-C 01, Reviewer (2014 - 2014)
  • Biomedical Informatics Academic Program Committee, Member (2013 - 2013)
  • Biomedical Informatics Admissions Committee, Chair (2013 - 2013)
  • Biomedical Informatics Academic Program Committee, Member (2012 - 2012)
  • Biomedical Informatics Admissions Committee, Chair (2012 - 2012)
  • Biomedical Informatics Media Team, Member (2012 - 2012)
  • NIH/NLM Information Resource Grants to Reduce Health Disparities (G08), ZLM1 ZH-G 01, Reviewer (2012 - 2012)
  • NIH/NIAID, Bioinformatics Integration Support Contract (BISC), ZAI1-QV-I (C1), Reviewer (2012 - 2012)
  • Biomedical Informatics Admissions Committee, Chair (2011 - 2011)
  • American Medical Informatics Association, Public Health Informatics Working Group, Past Chair (2011 - 2011)
  • American Medical Informatics Association, Public Health Informatics Working Group, Chair (2009 - 2010)
  • American Medical Informatics Association, Student Working Group, Executive Committee, Member-at-Large (2008 - 2010)
Expertise Areas
Bioinformatics
Public Health
Viruses
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