Wu Y, Namilae S, Srinivasan A, Mubayi A, Scotch M. Parametric analysis of SARS-CoV-2 dose-response models in transportation scenarios. PLoS One. 2024 Jun 12;19(6):e0301996.
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 Mar;118:105550.
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.
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 Dec 20;8(6):e0023223.
Khairat S, Feldman SS, Rana A, Faysel M, Purkayastha S, Scotch M, Eldredge C. Foundational domains and competencies for baccalaureate health informatics education. Am Med Inform Assoc. 2023 Sep 25;30(10):1599-1607.
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 Aug 11:166230.
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.
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.
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 Oct 26:e0068022.
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.
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 Aug 31:e0033722.
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.
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.
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.
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.
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.
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.
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.
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 Jun 23:S1201-9712(21)00537-3.
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.
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.
Vaiente MA*, Scotch M. Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty. Infect Genet Evol. 2020 Aug 13;85:104501.
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 Jul 19:btaa647.
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.
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.
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 May 1. pii: JVI.00711-20.
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 Apr 30:108364.
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 Apr 28. pii: cebp.1103.2019.
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.
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.
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.
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.
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.
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.
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.
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.
Magee D*, Scotch M. The effects of random taxa sampling schemes in Bayesian virus phylogeography. Infect Genet Evol. 2018 Oct;64:225-230.
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.
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.
Njoto EN, Scotch M, Bui CM, Adam DC*, Chughtai AA*, MacIntyre CR. Phylogeography of H5N1 avian influenza virus in Indonesia. Transbound Emerg Dis. 2018 Apr 24.
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.
†Joint senior authorship; order switched to facilitate counting
*Student authors