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Visiting Professorial Fellow

Dr Matthew Scotch

  • PhD. 2006. Biomedical Informatics. University of Pittsburgh, Pittsburgh, PA USA
  • MPH. 2007. Public Health. Yale University, New Haven, CT, USA
  • Postdoctoral fellowship. 2008. Biomedical Informatics. Yale University, New Haven, CT, USA
Phone
93850931
E-mail
m.scotch@unsw.edu.au
Location
Kirby Institute
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
2024
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
2024
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
2023
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
2023
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
2023
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
2023
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
2023
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
2023
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
2023
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
2023
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
2023
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
2023
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
2022
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
2022
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
2022
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
2022
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
2022
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
2022
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
2022
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
2022
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
2021
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
2021
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
2021
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
2021
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
2021
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
2021
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
2021
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
2021
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
2020
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
2020
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
2020
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
2020
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
2020
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
2020
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
2020
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
2020
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, http://dx.doi.org/10.3390/v11090791
2019
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
2019
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
2019
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
2019
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
2019
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
2019
Njoto EN; Scotch M; Bui CM; Adam DC; Chughtai AA; MacIntyre CR, 2018, 'Phylogeography of H5N1 avian influenza virus in Indonesia', Transboundary and Emerging Diseases, 65, pp. 1339 - 1347, http://dx.doi.org/10.1111/tbed.12883
2018
Bui CM; Adam DC; Njoto E; Scotch M; MacIntyre CR, 2018, 'Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis', Emerging Microbes and Infections, 7, http://dx.doi.org/10.1038/s41426-018-0185-z
2018
Morin CW; Stoner-Duncan B; Winker K; Scotch M; Hess JJ; Meschke JS; Ebi KL; Rabinowitz PM, 2018, 'Avian influenza virus ecology and evolution through a climatic lens', Environment International, 119, pp. 241 - 249, http://dx.doi.org/10.1016/j.envint.2018.06.018
2018
Beard R; Wentz E; Scotch M, 2018, '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, 17, http://dx.doi.org/10.1186/s12942-018-0157-5
2018
Magee D; Scotch M, 2018, 'The effects of random taxa sampling schemes in Bayesian virus phylogeography', Infection, Genetics and Evolution, 64, pp. 225 - 230, http://dx.doi.org/10.1016/j.meegid.2018.07.003
2018
Magee HY; Maurer MM; Cobos A; Pycke BFG; Venkatesan AK; Magee D; Scotch M; Halden RU, 2018, 'U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids', Science of the Total Environment, 643, pp. 460 - 467, http://dx.doi.org/10.1016/j.scitotenv.2018.06.206
2018
Adam DC; Scotch M; MacIntyre CR, 2018, 'Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes', Molecular Biology and Evolution, pp. msy153 - msy153, http://dx.doi.org/10.1093/molbev/msy153
2018
Tahsin T; Weissenbacher D; O'Connor K; Magge A; Scotch M; Gonzalez-Hernandez G, 2018, 'GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records', Bioinformatics, 34, pp. 1606 - 1608, http://dx.doi.org/10.1093/bioinformatics/btx799
2018
Magee D; Taylor JE; Scotch M, 2018, 'The Effects of Sampling Location and Predictor Point Estimate Certainty on Posterior Support in Bayesian Phylogeographic Generalized Linear Models', Scientific Reports, 8, http://dx.doi.org/10.1038/s41598-018-24264-8
2018
Raina MacIntyre C; Engells TE; Scotch M; Heslop DJ; Gumel AB; Poste G; Chen X; Herche W; Steinhöfel K; Lim S; Broom A, 2018, 'Converging and emerging threats to health security', Environment Systems and Decisions, 38, pp. 198 - 207, http://dx.doi.org/10.1007/s10669-017-9667-0
2018
Namilae S; Derjany P; Mubayi A; Scotch M; Srinivasan A, 2017, 'Multiscale model for pedestrian and infection dynamics during air travel', Physical Review E, 95, http://dx.doi.org/10.1103/PhysRevE.95.052320
2017
Tahsin T; Weissenbacher D; Jones-Shargani D; Magee D; Vaiente M; Gonzalez G; Scotch M, 2017, 'Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research', Database, 2017, http://dx.doi.org/10.1093/database/bax093
2017
Adam DC; Magee D; Bui CM; Scotch M; MacIntyre CR, 2017, 'Does influenza pandemic preparedness and mitigation require gain-of-function research?', Influenza and other Respiratory Viruses, 11, pp. 306 - 310, http://dx.doi.org/10.1111/irv.12458
2017
Namilae S; Srinivasan A; Mubayi A; Scotch M; Pahle R, 2017, 'Self-propelled pedestrian dynamics model: Application to passenger movement and infection propagation in airplanes', Physica A: Statistical Mechanics and its Applications, 465, pp. 248 - 260, http://dx.doi.org/10.1016/j.jth.2016.05.090
2017
Magee D; Suchard MA; Scotch M, 2017, 'Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.', PLoS Computational Biology, 13, pp. e1005389 - e1005389, http://dx.doi.org/10.1371/journal.pcbi
2017
Tahsin T; Weissenbacher D; Rivera R; Beard R; Firago M; Wallstrom G; Scotch M; Gonzalez G, 2016, 'A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records', Journal of the American Medical Informatics Association, 23, pp. 934 - 941, http://dx.doi.org/10.1093/jamia/ocv172
2016
Jirjies S; Wallstrom G; Halden RU; Scotch M, 2016, 'pyJacqQ: Python Implementation of Jacquez's Q-Statistics for Space-Time Clustering of Disease Exposure in Case-Control Studies', Journal of Statistical Software, 74, http://dx.doi.org/10.18637/jss.v074.i06
2016
Sarker A; O'Connor K; Ginn R; Scotch M; Smith K; Malone D; Gonzalez G, 2016, 'Social media mining for toxicovigilance: automatic monitoring of prescription medication abuse from Twitter.', Drug Safety, 39, pp. 231 - 240, http://dx.doi.org/10.1007/s40264-015-0379-4
2016
Veljkovic V; Paessler S; Glisic S; Prljic J; Perovic VR; Veljkovic N; Scotch M, 2015, 'Evolution of 2014/15 H3N2 influenza viruses circulating in US: consequences for vaccine effectiveness and possible new pandemic', Front Microbiol, 6, pp. 1456 - 1456, http://dx.doi.org/10.3389/fmicb.2015.01456
2015
Veljkovic V; Glisic S; Muller CP; Scotch M; Branch DR; Perovic VR; Sencanski M; Veljkovic N; Colombatti A, 2015, 'In silico analysis suggests interaction between Ebola virus and the extracellular matrix', Frontiers in Microbiology, 6, pp. 135 - 135, http://dx.doi.org/10.3389/fmicb.2015.00135
2015
Magee D; Beard R; Suchard MA; Lemey P; Scotch M, 2015, 'Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion', Archives of Virology, 160, pp. 215 - 224, http://dx.doi.org/10.1007/s00705-014-2262-5
2015
Weissenbacher D; Tahsin T; Beard R; Firago M; Rivera R; Scotch M; Gonzalez G, 2015, 'Knowledge-driven geospatial location resolution for phylogeographic models of virus migration', Bioinformatics, 31, pp. i348 - i356, http://dx.doi.org/10.1093/bioinformatics/btv259
2015
Scotch M; Lam TT; Pabilonia KL; Anderson T; Baroch J; Koehler D; DeLiberto TJ, 2014, 'Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States', Infection, Genetics and Evolution, 26, pp. 185 - 193, http://dx.doi.org/10.1016/j.meegid.2014.05.029
2014
Kane MJ; Price N; Scotch M; Rabinowitz P, 2014, 'Comparison of ARIMA and random forest time series models for prediction of avian influenza H5N1 outbreaks', BMC Bioinformatics, 15, pp. 1471 - 2105, http://dx.doi.org/10.1186/15-276
2014
Scotch M; Mei C, 2013, 'Phylogeography of swine influenza H3N2 in the United States: translational public health for zoonotic disease surveillance', Infection, Genetics and Evolution, 13, pp. 224 - 229, http://dx.doi.org/10.1016/j.meegid.2012.09.015
2013
Scotch M; Baarson B; Beard R; Lauder R; Varman A; Halden RU, 2013, 'Examining the differences in format and characteristics of zoonotic virus surveillance data on state agency websites', Journal of Medical Internet Research, 15, pp. e90 - e90, http://dx.doi.org/10.2196/jmir.2487
2013
Womack JA; Scotch M; Leung SN; Brandt CA, 2013, 'Use of structured and unstructured data to identify contraceptive use in women veterans', Perspectives in health information management / AHIMA, American Health Information Management Association, pp. 1 - 15
2013
Braithwaite RS; Scotch M, 2013, 'Using value of information to guide evaluation of decision supports for differential diagnosis: is it time for a new look?', BMC Medical Informatics and Decision Making, 13, pp. 1472 - 6947, http://dx.doi.org/10.1186/13-105
2013
Scotch M; Mei C; Makonnen YJ; Pinto J; Ali A; Vegso S; Kane M; Sarkar IN; Rabinowitz P, 2013, 'Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt', BMC Genomics, 14, pp. 1471 - 2164, http://dx.doi.org/10.1186/14-871
2013
Rabinowirz PM; Galusha D; Vegso S; Michalove J; Rinne S; Scotch M; Kane M, 2012, 'Comparison of human and animal surveillance data for H5N1 influenza A in Egypt 2006-2001', PLoS One, 7, pp. e43851 - e43851, http://dx.doi.org/10.1371/journal.pone.0043851
2012
Wu SJ; Raghupathi W, 2012, 'A panel analysis of the strategic association between information and communication technology and public health delivery.', J Med Internet Res, 14, pp. e147, http://dx.doi.org/10.2196/jmir.2242
2012
Scotch M; Sarkar IN; Mei C; Leaman R; Cheung KH; Ortiz P; Singraur A; Gonzalez G, 2011, 'Enhancing phylogeography by improving geographical information from GenBank', Journal of Biomedical Informatics, Suppl 1, pp. S44 - S47, http://dx.doi.org/10.1016/j.jbi.2011.06.005
2011
Garla V; Lo Re V; Dorey-Stein Z; Kidwai F; Scotch M; Womack J; Justice A; Brandt C, 2011, 'The Yale cTAKES extensions for document classification: architecture and application', Journal of the American Medical Informatics Association, 18, pp. 614 - 620
2011
Scotch M; Mattocks K; Rabinowitz P; Brandt C, 2011, 'A qualitative study of state-level zoonotic disease surveillance in New England', Zoonoses and Public Health, 58, pp. 131 - 139
2011
Scotch M; Brownstein JS; Vegso S; Galusha D; Rabinowitz P, 2011, 'Human vs. animal outbreaks of the 2009 swine-origin H1N1 influenza A epidemic', Ecohealth, 8, pp. 376 - 380, http://dx.doi.org/10.1007/s10393-011-0706-x
2011
Scotch M; Rabinowitz P; Brandt C, 2011, 'State-level zoonotic disease surveillance in the United States', Zoonoses and Public Health, 58, pp. 523 - 528
2011
Ohl M; Tate J; Duggal M; Skanderson M; Scotch M; Kaboli P; Vaughan-Sarrazin M; Justice A, 2010, 'Rural residence is associated with delayed care entry and increased mortality among veterans with human immunodeficiency virus infection', Medical Care, 48, pp. 1064 - 1070, http://dx.doi.org/10.1097/MLR.0b013e3181ef60c2
2010
Scotch M; Duggal M; Brandt C; Lin Z; Shiffman R, 2010, 'Use of statistical analysis in the biomedical informatics literature', Journal of the American Medical Informatics Association, 17, pp. 3 - 5, http://dx.doi.org/10.1197/jamia.M2853
2010
Rabinowitz PR; Scotch M; Conti LA, 2010, 'Animals as sentinels: using comparative medicine to move beyond the laboratory', Institute for Laboratory Animal Research (ILAR) Journal, 51, pp. 262 - 267
2010
Konovalov S; Scotch M; Post L; Brandt C, 2010, 'Biomedical informatics techniques for processing and analyzing web blogs of military service members', Journal of Medical Internet Research, 12, pp. e45 - e45, http://dx.doi.org/10.2196/jmir.1538
2010
Scotch M; Mei C; Brandt C; Sarkar IN; Cheung K, 2010, 'At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography', Epidemiology, 21, pp. 764 - 768, http://dx.doi.org/10.1097/EDE.0b013e3181f534dd
2010
Womack JA; Scotch M; Gilbert C; Chapman W; Yin M; Justice AC; Brandt C, 2010, 'A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records', Perspectives in health information management / AHIMA, American Health Information Management Association, 7, pp. 1a - 1a
2010
Rabinowitz P; Scotch M; Conti L, 2009, 'Human and animal sentinels for shared health risks', Veterinaria italiana, 45, pp. 23 - 24
2009
Scotch M; Odofin L; Rabinowitz P, 2009, 'Linkages between animal and human health sentinel data', BMC Veterinary Research, 5, pp. 15 - 15, http://dx.doi.org/10.1186/5-15
2009
Liu A; Lee V; Galusha D; Slade MD; Diuk-Wasser M; Andreadis T; Scotch M; Rabinowitz PM, 2009, 'Risk factors for human infection with West Nile Virus in Connecticut: a multi-year analysis', International Journal of Health Geographics, 8, pp. 67 - 67, http://dx.doi.org/10.1186/1476-072X
2009
Scotch M; Yip KY; Cheung KH, 2008, 'Development of grid-like applications for public health using Web 2.0 mashup techniques', Journal of the American Medical Informatics Association, 15, pp. 783 - 786, http://dx.doi.org/10.1197/jamia.M2731
2008
Cheung KH; Yip KY; Townsend JP; Scotch M, 2008, 'HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0', Journal of Biomedical Informatics, 41, pp. 694 - 705, http://dx.doi.org/10.1016/j.jbi.2008.04.001
2008
Scotch M; Parmanto B; Monaco V, 2008, 'Evaluation of SOVAT: an OLAP-GIS decision support system for community health assessment data analysis', BMC Medical Informatics and Decision Making, 8, pp. 22 - 22, http://dx.doi.org/10.1186/8-22
2008
Parmanto B; Paramita MV; Sugiantara W; Pramana G; Scotch M; Burke DS, 2008, 'Spatial and multidimensional visualization of Indonesia's village health statistics', International Journal of Health Geographics, 7, pp. 30 - 30, http://dx.doi.org/10.1186/1476-072X
2008
Boulos MN; Scotch M; Cheung KH; Burden D, 2008, 'Web GIS in practice VI: a demo playlist of geo-mashups for public health neogeographers', International Journal of Health Geographics, 7, pp. 38 - 38, http://dx.doi.org/10.1186/1476-072X
2008
Scotch M; Parmanto B; Monaco V, 2007, 'Usability evaluation of the Spatial OLAP Visualization and Analysis Tool (SOVAT)', Journal of Usability Studies, 2, pp. 76 - 95
2007
Scotch M; Parmanto B, 2006, 'Development of SOVAT: a numerical-spatial decision support system for community health assessment research', International Journal of Medical Informatics, 75, pp. 771 - 784
2006
Scotch M; Parmanto B; Gadd CS; Sharma RK, 2006, 'Exploring the role of GIS during community health assessment problem solving: experiences of public health professionals', International Journal of Health Geographics, 5, pp. 39 - 39
2006
Parmanto B; Scotch M; Ahmad S, 2005, 'A framework for designing a healthcare outcome data warehouse', Perspectives in health information management / AHIMA, American Health Information Management Association, 2, pp. 3 - 3
2005
O'Connor K; Weissenbacher D; Elyaderani A; Scotch M; Gonzalez-Hernandez G, 2023, Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis., , http://dx.doi.org/10.1101/2023.07.14.23292681
2023
Weissenbacher D; O'Connor K; Klein A; Golder S; Flores I; Elyaderani A; Scotch M; Gonzalez-Hernandez G, 2023, Text mining biomedical literature to identify extremely unbalanced data for digital epidemiology and systematic reviews: dataset and methods for a SARS-CoV-2 genomic epidemiology study., , http://dx.doi.org/10.1101/2023.07.29.23293370
2023
Magge A; Weissenbacher D; O'Connor K; Scotch M; Gonzalez-Hernandez G, 2022, SEED: Symptom Extraction from English Social Media Posts using Deep Learning and Transfer Learning., , http://dx.doi.org/10.1101/2021.02.09.21251454
2022
Bowes DA; Driver EM; Kraberger S; Fontenele RS; Holland LA; Wright J; Johnston B; Savic S; Newell ME; 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 X-J; Varsani A; Lim ES; Scotch M; Halden RU, 2021, Unrestricted Online Sharing of High-frequency, High-resolution Data on SARS-CoV-2 in Wastewater to Inform the COVID-19 Public Health Response in Greater Tempe, Arizona, , http://dx.doi.org/10.1101/2021.07.29.21261338
2021
Namilae S; Wu Y; Mubayi A; Srinivasan A; Scotch M, 2021, Identifying Mitigation Strategies for COVID-19 Superspreading on Flights using Models that Account for Passenger Movement, , http://dx.doi.org/10.48550/arxiv.2106.10313
2021
Holland LA; Kaelin EA; Maqsood R; Estifanos B; Wu LI; Varsani A; Halden RU; Hogue BG; Scotch M; Lim ES, 2020, An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)., , http://dx.doi.org/10.1101/2020.04.17.20069641
2020
Ngonghala C; Iboi E; Eikenberry S; Scotch M; MacIntyre CR; Bonds M; Gumel A, 2020, Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus, , http://dx.doi.org/10.1101/2020.04.15.20066480
2020
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, , http://dx.doi.org/10.48550/arxiv.2004.07391
2020
Adam D; Chen X; Scotch M; MacIntyre CR; Dwyer D; Kok J, 2020, The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses among Paediatric Cases in Sydney, Australia., , http://dx.doi.org/10.22541/au.160614561.14239652/v1
2020
Islam T; Lahijani MS; Srinivasan A; Namilae S; Mubayi A; Scotch M, 2020, From Bad to Worse: Airline Boarding Changes in Response to COVID-19, , http://dx.doi.org/10.48550/arxiv.2006.06403
2020
Namilae S; Srinivasan A; Mubayi A; Scotch M; Pahle R, 2016, Self-Propelled Pedestrian Dynamics Model: Application to Passenger Movement and Infection Propagation in Airplanes, , http://dx.doi.org/10.48550/arxiv.1603.08380
2016
Wu Y; Namilae S; Mubayi A; Scotch M; Srinivasan A, 2022, 'Incorporating Pedestrian Movement in Computational Models of COVID-19 Spread during Air-travel', in IEEE Aerospace Conference Proceedings, http://dx.doi.org/10.1109/AERO53065.2022.9843497
2022
Weissenbacher D; Magge A; O'Connor K; Scotch M; Gonzalez-Hernandez G, 2019, 'SemEval-2019 task 12: Toponym resolution in scientific papers', in NAACL HLT 2019 - International Workshop on Semantic Evaluation, SemEval 2019, Proceedings of the 13th Workshop, pp. 907 - 916
2019
Magge A; Weissenbacher D; Sarker A; Scotch M; Gonzalez-Hernandez G, 2018, 'Deep neural networks and distant supervision for geographic location mention extraction', in Bioinformatics, pp. i565 - i573, http://dx.doi.org/10.1093/bioinformatics/bty273
2018
Magge A; Scotch M; Gonzalez-Hernandez G, 2018, 'Clinical NER and Relation Extraction using Bi-Char-LSTMs and Random Forest Classifiers', in Proceedings of Machine Learning Research, pp. 25 - 30
2018
Magge A; Scotch M; Gonzalez G, 2017, 'CSaRUS-CNN at AMIA-2017 Tasks 1, 2: Under sampled CNN for text classification', in CEUR Workshop Proceedings, pp. 76 - 78
2017
Paul MJ; Sarker A; Brownstein JS; Nikfarjam A; Scotch M; Smith KL; Gonzalez G, 2016, 'Social media mining for public health monitoring and surveillance', in Pacific Symposium on Biocomputing 2016, PSB 2016, Kohala Coast, Hawaii, USA, pp. 468 - 479, presented at Pacific Symposium on Biocomputing (PSB) 2016, Kohala Coast, Hawaii, USA, 04 January 2016 - 08 January 2016, https://psb.stanford.edu/psb-online/proceedings/psb16/intro-smm.pdf
2016
Scotch M; Suchard MA; Rabinowitz PM, 2015, 'Analysis of Viral Genetics for Estimating Diffusion of Influenza A H6N1', in American Medical Informatics Association Joint Summits on Translational Science, San Francisco, CA, pp. 36 - 40, presented at American Medical Informatics Association Joint Summints on Translational Science, San Francisco, CA, 23 March 2015 - 27 March 2015
2015
Magee D; Scotch M, 2015, 'Conceptualizing a Novel Quasi-Continuous Bayesian Phylogeographic Framework for Spatiotemporal Hypothesis Testing.', in Conceptualizing a Novel Quasi-Continuous Bayesian Phylogeographic Framework for Spatiotemporal Hypothesis Testing., AMIA Jt Summits Transl Sci Proc, San Francisco, CA, presented at AMIA Jt Summits Transl Sci Proc, San Francisco, CA, 23 March 2015 - 27 March 2015, https://www.ncbi.nlm.nih.gov/pubmed/26306274
2015
Magee D; Beard R; Scotch M, 2015, 'Analyses of Merging Clinical and Viral Genetic Data for Influenza Surveillance', in Proceedings - a conference of the American Medical Informatics Association / . AMIA Annual Fall Symposium. AMIA Fall Symposium, San Francisco, CA, pp. 1995 - 2004, presented at American Medical Informatics Association Annual Conference, San Francisco, CA, 14 November 2015 - 18 November 2015
2015
Beard R; Magee D; Suchard MA; Lemey P; Scotch M, 2014, 'Generalized linear models for identifying predictors of the evolutionary diffusion of viruses.', San Francisco, CA, pp. 23 - 28, presented at American Medical Informatics Association Joint Summits on Translational Science, San Francisco, CA, 07 April 2014 - 11 April 2014, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333690/
2014
Tahsin T; Lauder R; Beard R; Weissenbacher D; Rivera R; Wallstrom G; Scotch M; Gonzalez G, 2014, 'Natural Language Processing Methods for Enhancing Geographic Metadata for Phylogeography of Zoonotic Viruses', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 1 - 9
2014
Tahsin T; Beard R; Rivera R; Lauder R; Wallstrom G; Scotch M; Gonzalez G, 2014, 'Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses.', in AMIA Jt Summits Transl Sci Proc, United States, pp. 102 - 111, United States, https://www.ncbi.nlm.nih.gov/pubmed/25717409
2014
Tahsin T; Beard R; Rivera R; Lauder R; Wallstrom G; Scotch M; Gonzalez G, 2014, 'Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses.', in Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses., American Medical Informatics Association Joint Summints on Translational Science, San Francisco, CA, pp. 102 - 111, presented at American Medical Informatics Association Joint Summints on Translational Science, San Francisco, CA, 07 April 2014 - 11 April 2014, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333696/
2014
Duggal M; Ebisu K; Scotch M; Anderson D; Brandt CA; Justice AC, 2010, 'GEOGRAPHIC VARIATION OF MISSED VISITS AMONG HIV INFECTED VETERANS', in JOURNAL OF GENERAL INTERNAL MEDICINE, SPRINGER, MN, Minneapolis, pp. 285 - 285, presented at 33rd Annual Meeting of the Society-of-General-Internal-Medicine, MN, Minneapolis, 18 April 2010 - 01 May 2010, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000277282300181&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2010
Ohl M; Vaughan-Sarrazin M; Kaboli P; Scotch M; Skanderson M; Tate J; Duggal M; Justice A, 2010, 'RURAL RESIDENCE IS ASSOCIATED WITH INCREASED MORTALITY AMONG VETERANS INITIATING HIGHLY ACTIVE ANTIRETROVIRAL THERAPY FOR HIV INFECTION', in JOURNAL OF GENERAL INTERNAL MEDICINE, SPRINGER, MN, Minneapolis, pp. 386 - 387, presented at 33rd Annual Meeting of the Society-of-General-Internal-Medicine, MN, Minneapolis, 18 April 2010 - 01 May 2010, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000277282300397&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2010
Scotch M; Parmanto B, 2005, 'SOVAT: Spatial OLAP visualization and analysis tool', in Proceedings of the Annual Hawaii International Conference on System Sciences, pp. 142
2005
Scotch M; Hripcsak G, 2002, 'The companion project - A wearable computing device for the patient for reducing medical errors and improving patient care', in Kohane IS (ed.), AMIA 2002 SYMPOSIUM, PROCEEDINGS, HANLEY & BELFUS INC MED PUBLISHERS, TX, San Antonio, pp. 1157 - 1157, presented at Annual Symposium of the American-Medical-Informatics-Association, TX, San Antonio, 09 November 2002 - 09 November 2002, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000189418100390&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2002
Scotch M; Parmanto B, 'SOVAT: Spatial OLAP Visualization and Analysis Tool', in Proceedings of the 38th Annual Hawaii International Conference on System Sciences, IEEE, presented at 38th Annual Hawaii International Conference on System Sciences, http://dx.doi.org/10.1109/hicss.2005.550
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
2016
  • 2018. Endeavour Fellowship. Australian Government

Current NIH grants as PI:

  • Bioinformatics Framework for Wastewater-based Surveillance of Infectious Diseases (U01LM013129)
  • Enriching SARS-CoV-2 sequence data in public repositories with information extracted from full text articles (R01AI164481)

Current NSF grants as PI:

  • Collaborative:RAPID: Leveraging New Data Sources to Analyze the Risk of COVID-19 in Crowded Locations (2027529)
  • Collaborative:Elements:Cyberinfrastructure for Pedestrian Dynamics-Based Analysis of Infection Propagation Through Air Travel (1931560)