By Dr Matthew Scotch

Book Chapters

Coffey JW; Pahle R; Srinivasan A; Namilae S; Scotch M, 2024, 'A Knowledge Sharing Approach to Foster Interdisciplinary Pedestrian Dynamics and Epidemiological Modeling Research and Practice', in , pp. 313 - 324, http://dx.doi.org/10.1007/978-981-97-3556-3_25

Scotch M; Brandt C; Leung S; Womack J, 2016, 'Natural Language Processing for Understanding Contraceptive Use at the VA', in Gupta A; Patel VL; Greenes RA (ed.), ADVANCES IN HEALTHCARE INFORMATICS AND ANALYTICS, SPRINGER, pp. 249 - 259, http://dx.doi.org/10.1007/978-3-319-23294-2_12

Journal articles

Faleye TOC; Skidmore P; Elyaderani A; Adhikari S; Kaiser N; Smith A; Yanez A; Perleberg T; Driver EM; Halden RU; Varsani A; Scotch M, 2024, 'Adenovirus 41 diversity in Arizona (USA) using wastewater-based epidemiology, long-range PCR, and pathogen sequencing between October 2019 and March 2020.', Epidemiol Infect, 152, pp. e142, http://dx.doi.org/10.1017/S095026882400133X

Bermudez-Rivera B; Hampton B; Wheeler C; Vargas J; Swaminathan S; Driver EM; Halden RU; Varsani A; Scotch M; Faleye TOC, 2024, 'Nine Rhizobium phage genomes recovered from wastewater in Tempe, AZ, October 2019–March 2020', Microbiology Resource Announcements, 13, http://dx.doi.org/10.1128/mra.00680-24

Wang X; Walker G; Kim KW; Stelzer-Braid S; Scotch M; Rawlinson WD, 2024, 'The resurgence of influenza A/H3N2 virus in Australia after the relaxation of COVID-19 restrictions during the 2022 season', Journal of Medical Virology, 96, http://dx.doi.org/10.1002/jmv.29922

Faleye TOC; Skidmore P; Elyaderani A; Adhikari S; Kaiser N; Smith A; Yanez A; Perleberg T; Driver EM; Halden RU; Varsani A; Scotch M, 2024, 'Exploring Canine Picornavirus Diversity in the USA Using Wastewater Surveillance: From High-Throughput Genomic Sequencing to Immuno-Informatics and Capsid Structure Modeling', Viruses, 16, http://dx.doi.org/10.3390/v16081188

Züfle A; Salim F; Anderson T; Scotch M; Xiong L; Sokol K; Xue H; Kong R; Heslop D; Paik HY; Macintyre CR, 2024, 'Leveraging Simulation Data to Understand Bias in Predictive Models of Infectious Disease Spread', ACM Transactions on Spatial Algorithms and Systems, 10, http://dx.doi.org/10.1145/3660631

Wu Y; Namilae S; Srinivasan A; Mubayi A; Scotch M, 2024, 'Parametric analysis of SARS-CoV-2 doseresponse models in transportation scenarios', PLoS ONE, 19, http://dx.doi.org/10.1371/journal.pone.0301996

Faleye TOC; Driver EM; Wright JM; Halden RU; Varsani A; Scotch M, 2024, 'Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing', Infection, Genetics and Evolution, 118, http://dx.doi.org/10.1016/j.meegid.2024.105550

Wang X; Kim KW; Walker G; Stelzer-Braid S; Scotch M; Rawlinson WD, 2024, '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 and other Respiratory Viruses, 18, http://dx.doi.org/10.1111/irv.13252

Bowes DA; Henke KB; Driver EM; Newell ME; Block I; Shaffer G; Varsani A; Scotch M; Halden RU, 2023, 'Enhanced detection of mpox virus in wastewater using a pre-amplification approach: A pilot study informing population-level monitoring of low-titer pathogens', Science of the Total Environment, 903, http://dx.doi.org/10.1016/j.scitotenv.2023.166230

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, 2023, 'Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022', mSphere, 8, http://dx.doi.org/10.1128/msphere.00232-23

Khairat S; Feldman SS; Rana A; Faysel M; Purkayastha S; Scotch M; Eldredge C, 2023, 'Foundational domains and competencies for baccalaureate health informatics education', Journal of the American Medical Informatics Association : JAMIA, 30, pp. 1599 - 1607, http://dx.doi.org/10.1093/jamia/ocad147

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, 2023, 'Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA', Science of the Total Environment, 877, http://dx.doi.org/10.1016/j.scitotenv.2023.162862

Chapman AR; Wright JM; Kaiser NA; Jones PM; Driver EM; Halden RU; Varsani A; Scotch M; Faleye TOC, 2023, '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', Microbiology Resource Announcements, 12, http://dx.doi.org/10.1128/mra.00069-23

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, 2023, 'Genomic epidemiology reveals the dominance of Hennepin County in transmission of SARS-CoV-2 in Minnesota from 2020-2022.', medRxiv, http://dx.doi.org/10.1101/2022.07.24.22277978

Faleye TOC; Driver EM; Bowes DA; Smith A; Kaiser NA; Wright JM; Chapman AR; Halden RU; Varsani A; Scotch M, 2023, '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, http://dx.doi.org/10.1155/2023/5596886

Bowes DA; Driver EM; Kraberger S; Fontenele RS; Holland LRA; 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, 2023, 'Leveraging an established neighbourhood-level, open access wastewater monitoring network to address public health priorities: a population-based study', The Lancet Microbe, 4, pp. e29 - e37, http://dx.doi.org/10.1016/S2666-5247(22)00289-0

Namilae S; Wu Y; Mubayi A; Srinivasan A; Scotch M, 2023, 'Reply to comments on “Identifying mitigation strategies for COVID-19 superspreading on flights using models that account for passenger movement”', Travel Medicine and Infectious Disease, 51, http://dx.doi.org/10.1016/j.tmaid.2022.102453

Faleye TOC; Elyaderani A; Skidmore P; Adhikari S; Smith A; Kaiser N; Sandrolini H; Finnerty S; Halden RU; Varsani A; Scotch M, 2023, 'Surveillance of rhinovirus diversity among a university community identifies multiple types from all three species including an unassigned rhinovirus A genotype', Influenza and other Respiratory Viruses, 17, http://dx.doi.org/10.1111/irv.13057

Collins CL; Faleye TOC; Kraberger S; Fontenele RS; Adams D; Adhikari S; Sandrolini H; Finnerty S; Halden RU; Scotch M; Varsani A, 2022, 'Complete Coding Sequences of Rhinovirus Types A46, A39, C56, and C48', Microbiology Resource Announcements, 11, http://dx.doi.org/10.1128/mra.00680-22

Faleye TOC; Skidmore P; Elyaderani A; Adhikari S; Kaiser N; Smith A; Yanez A; Perleberg T; Driver EM; Halden RU; Varsani A; Scotch M, 2022, 'Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology.', medRxiv, http://dx.doi.org/10.1101/2022.09.25.22280344

Smith A; Kaiser N; Yanez A; Perleberg T; Elyaderani A; Skidmore P; Adhikari S; Driver EM; Halden RU; Varsani A; Scotch M; Faleye TOC, 2022, 'Genome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding Protein', Microbiology Resource Announcements, 11, http://dx.doi.org/10.1128/mra.00337-22

Faleye TOC; Skidmore PT; Elyaderani A; Smith A; Kaiser N; Adhikari S; Yanez A; Perleberg T; Driver EM; Halden RU; Varsani A; Scotch M, 2022, 'Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021', Infection, Genetics and Evolution, 103, http://dx.doi.org/10.1016/j.meegid.2022.105315

Wang X; Stelzer-Braid S; Scotch M; Rawlinson WD, 2022, 'Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use', Reviews in Medical Virology, 32, http://dx.doi.org/10.1002/rmv.2375

Collins CL; Kraberger S; Fontenele RS; Faleye TOC; Adams D; Adhikari S; Sandrolini H; Finnerty S; Halden RU; Scotch M; Varsani A, 2022, 'Genome Sequences of Anelloviruses, Genomovirus, and Papillomavirus Isolated from Nasal Pharyngeal Swabs', Microbiology Resource Announcements, 11, http://dx.doi.org/10.1128/mra.00681-22

Namilae S; Wu Y; Mubayi A; Srinivasan A; Scotch M, 2022, 'Identifying mitigation strategies for COVID-19 superspreading on flights using models that account for passenger movement', Travel Medicine and Infectious Disease, 47, http://dx.doi.org/10.1016/j.tmaid.2022.102313

Faleye TOC; Driver EM; Bowes DA; Holm RH; Talley D; Yeager R; Bhatnagar A; Smith T; Varsani A; Halden RU; Scotch M, 2022, 'Detection of human, porcine and canine picornaviruses in municipal sewage sludge using pan-enterovirus amplicon-based long-read Illumina sequencing', Emerging Microbes and Infections, 11, pp. 1339 - 1342, http://dx.doi.org/10.1080/22221751.2022.2071173

Beard R; Wentz E; Scotch M, 2021, 'Correction to: A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks (International Journal of Health Geographics, (2018), 17, 1, (38), 10.1186/s12942-018-0157-5)', International Journal of Health Geographics, 20, http://dx.doi.org/10.1186/s12942-021-00293-x

Faleye TOC; Adams D; Adhikari S; Sandrolini H; Halden RU; Varsani A; Scotch M, 2021, '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 Infectious Diseases, 21, http://dx.doi.org/10.1186/s12879-021-06526-5

Fontenele RS; Kraberger S; Hadfield J; Driver EM; Bowes D; Holland LRA; Faleye TOC; Adhikari S; Kumar R; Inchausti R; Holmes WK; Deitrick S; Brown P; Duty D; Smith T; Bhatnagar A; Yeager RA; Holm RH; von Reitzenstein NH; Wheeler E; Dixon K; Constantine T; Wilson MA; Lim ES; Jiang X; Halden RU; Scotch M; Varsani A, 2021, 'High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants', Water Research, 205, http://dx.doi.org/10.1016/j.watres.2021.117710

Adam DC; Chen X; Scotch M; MacIntyre CR; Dwyer D; Kok J, 2021, 'The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses Among Paediatric Cases in Sydney, Australia', International Journal of Infectious Diseases, 110, pp. 69 - 74, http://dx.doi.org/10.1016/j.ijid.2021.06.046

Faleye TOC; Bowes DA; Driver EM; Adhikari S; Adams D; Varsani A; Halden RU; Scotch M, 2021, '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, 13, http://dx.doi.org/10.3390/v13091803

Islam T; Lahijani MS; Srinivasan A; Namilae S; Mubayi A; Scotch M, 2021, 'From bad to worse: Airline boarding changes in response to COVID-19', Royal Society Open Science, 8, http://dx.doi.org/10.1098/rsos.201019

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; Holm RH; von Reitzenstein NH; Wheeler E; Dixon K; Constantine T; Wilson MA; Lim ES; Jiang X; Halden RU; Scotch M; Varsani A, 2021, 'High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants.', Water Research, 205, http://dx.doi.org/10.1016/j.watres.2021.117710

Faleye TOC; Driver E; Bowes D; Adhikari S; Adams D; Varsani A; Halden RU; Scotch M, 2021, 'Pan-enterovirus amplicon-based high-throughput sequencing detects the complete capsid of a eva71 genotype c1 variant via wastewater-based epidemiology in Arizona', Viruses, 13, http://dx.doi.org/10.3390/v13010074

Vaiente MA; Scotch M, 2020, 'Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty', Infection, Genetics and Evolution, 85, http://dx.doi.org/10.1016/j.meegid.2020.104501

Magge A; Weissenbacher D; O'Connor K; Tahsin T; Gonzalez-Hernandez G; Scotch M, 2020, 'GeoBoost2: A natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography', Bioinformatics, 36, pp. 5120 - 5121, http://dx.doi.org/10.1093/bioinformatics/btaa647

Holland LRA; Kaelin EA; Maqsood R; Estifanos B; Wu LI; Varsani A; Halden RU; Hogue BG; Scotch M; Lim ES, 2020, 'An 81-nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (January to March 2020)', Journal of Virology, 94, http://dx.doi.org/10.1128/JVI.00711-20

Ngonghala CN; Iboi E; Eikenberry S; Scotch M; MacIntyre CR; Bonds MH; Gumel AB, 2020, 'Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus', Mathematical Biosciences, 325, http://dx.doi.org/10.1016/j.mbs.2020.108364

Yoo W; Koskan A; Scotch M; Pottinger H; Huh WK; Helitzer D, 2020, 'Patterns and disparities in human papillomavirus (HPV) vaccine uptake for young female adolescents among U.S. States: NIS-teen (2008–2016)', Cancer Epidemiology Biomarkers and Prevention, 29, pp. 1458 - 1467, http://dx.doi.org/10.1158/1055-9965.EPI-19-1103

Scotch M; Halden RU; Denton A; Sandrolini H; Fontenele RS; Varsanie A, 2020, 'Coding-Complete Genome Sequence of a Human Respirovirus 1 Strain from a Clinical Sample in Arizona', Microbiology Resource Announcements, 9, http://dx.doi.org/10.1128/MRA.00465-20

Chen X; Adam DC; Chughtai AA; Stelzer-Braid S; Scotch M; MacIntyre CR, 2020, 'The phylogeography of MERS-CoV in hospital outbreak-associated cases compared to sporadic cases in Saudi Arabia', Viruses, 12, http://dx.doi.org/10.3390/v12050540

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, 2020, 'Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations', Journal of Clinical Virology, 122, http://dx.doi.org/10.1016/j.jcv.2019.104216

Beard R; Scotch M, 2019, 'Identifying current and emerging resources and tools utilized for detection, prediction, and visualization of viral zoonotic disease clusters: A Delphi study', JAMIA Open, 2, pp. 306 - 311, http://dx.doi.org/10.1093/jamiaopen/ooz015

Adam DC; Scotch M; Macintyre CR, 2019, 'Phylodynamics of influenza A/H1N1pdm09 in India reveals circulation patterns and increased selection for clade 6b residues and other high mortality mutants', Viruses, 11, pp. 791, http://dx.doi.org/10.3390/v11090791

Halden R; Terlinden E; Kraberger S; Scotch M; Steele J; Varsani A, 2019, 'Tracking harmful chemicals and pathogens using the Human Health Observatory at ASU', Online Journal of Public Health Informatics, 11, http://dx.doi.org/10.5210/ojphi.v11i1.9843

Scotch M; Magge A; Valente M, 2019, 'ZooPhy: A bioinformatics pipeline for virus phylogeography and surveillance', Online Journal of Public Health Informatics, 11, http://dx.doi.org/10.5210/ojphi.v11i1.9729

Scotch M; Tahsin T; Weissenbacher D; O'Connor K; Magge A; Vaiente M; Suchard MA; Gonzalez-Hernandez G, 2019, 'Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography', Virus Evolution, 5, http://dx.doi.org/10.1093/ve/vey043

Magge A; Weissenbacher D; Sarker A; Scotch M; Gonzalez-Hernandez G, 2019, 'Bi-directional recurrent neural network models for geographic location extraction in biomedical literature', Pacific Symposium on Biocomputing, 24, pp. 100 - 111, http://dx.doi.org/10.1142/9789813279827_0010

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