Dr Matthew Scotch
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
Medicine & Health
The Kirby Institute

Matthew Scotch is Visiting Professorial Fellow at the Kirby Institute at UNSW. He is also Interim Assistant Dean of Research and Professor of Biomedical Informatics in the College of Health Solutions at Arizona State University (ASU), and Assistant Director of the Biodesign Center for Environmental Health Engineering. 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.

Please see here for a list of his publications in PubMed.

Phone
93850931
Location
Kirby Institute
  • Book Chapters | 2016
    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, edn. Annals of Information Systems, SPRINGER, pp. 249 - 259, http://dx.doi.org/10.1007/978-3-319-23294-2_12
  • Journal articles | 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, http://dx.doi.org/10.1128/mra.00681-22
    Journal articles | 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, vol. 11, pp. 1339 - 1342, http://dx.doi.org/10.1080/22221751.2022.2071173
    Journal articles | 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, vol. 103, pp. 105315, http://dx.doi.org/10.1016/j.meegid.2022.105315
    Journal articles | 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, vol. 47, http://dx.doi.org/10.1016/j.tmaid.2022.102313
    Journal articles | 2022
    Scotch M; Lauer K; Wieben ED; Cherukuri Y; Cunningham JM; Klee EW; Harrington JJ; Lau JS; McDonough SJ; Mutawe M; Oâ Horo JC; Rentmeester CE; Schlicher NR; White VT; Schneider SK; Vedell PT; Wang X; Yao JD; Pritt BS; Norgan AP, 2022, 'Genomic epidemiology and phylodynamics for county-to-county transmission of SARS-CoV-2 in Minnesota, from 19A to Omicron.', medRxiv, http://dx.doi.org/10.1101/2022.07.24.22277978
    Journal articles | 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, http://dx.doi.org/10.1128/mra.00337-22
    Journal articles | 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, http://dx.doi.org/10.1002/rmv.2375
    Journal articles | 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, vol. 110, pp. 69 - 74, http://dx.doi.org/10.1016/j.ijid.2021.06.046
    Journal articles | 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, vol. 20, http://dx.doi.org/10.1186/s12942-021-00293-x
    Journal articles | 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, vol. 21, http://dx.doi.org/10.1186/s12879-021-06526-5
    Journal articles | 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, vol. 13, pp. 1803 - 1803, http://dx.doi.org/10.3390/v13091803
    Journal articles | 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, vol. 13, pp. 74 - 74, http://dx.doi.org/10.3390/v13010074
    Journal articles | 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, vol. 205, http://dx.doi.org/10.1016/j.watres.2021.117710
    Journal articles | 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, vol. 205, pp. 117710, http://dx.doi.org/10.1016/j.watres.2021.117710
    Journal articles | 2021
    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, vol. 8, http://dx.doi.org/10.1098/rsos.201019
    Journal articles | 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, vol. 12, pp. 540 - 540, http://dx.doi.org/10.3390/v12050540
    Journal articles | 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, vol. 94, http://dx.doi.org/10.1128/JVI.00711-20
    Journal articles | 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, vol. 36, pp. 5120 - 5121, http://dx.doi.org/10.1093/bioinformatics/btaa647
    Journal articles | 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, vol. 325, pp. 108364, http://dx.doi.org/10.1016/j.mbs.2020.108364
    Journal articles | 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, vol. 9, http://dx.doi.org/10.1128/MRA.00465-20
    Journal articles | 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, vol. 122, pp. 104216 - 104216, http://dx.doi.org/10.1016/j.jcv.2019.104216
    Journal articles | 2020
    Vaiente MA; Scotch M, 2020, 'Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty', Infection, Genetics and Evolution, vol. 85, http://dx.doi.org/10.1016/j.meegid.2020.104501
    Journal articles | 2020
    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, vol. 29, pp. 1458 - 1467, http://dx.doi.org/10.1158/1055-9965.EPI-19-1103
    Journal articles | 2019
    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, vol. 11, http://dx.doi.org/10.3390/v11090791
    Journal articles | 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, vol. 2, pp. 306 - 311, http://dx.doi.org/10.1093/jamiaopen/ooz015
    Journal articles | 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, vol. 11, http://dx.doi.org/10.5210/ojphi.v11i1.9843
    Journal articles | 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, vol. 24, pp. 100 - 111, http://dx.doi.org/10.1142/9789813279827_0010
    Journal articles | 2019
    Scotch M; Magge A; Valente M, 2019, 'ZooPhy: A bioinformatics pipeline for virus phylogeography and surveillance', Online Journal of Public Health Informatics, vol. 11, http://dx.doi.org/10.5210/ojphi.v11i1.9729
    Journal articles | 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, vol. 5, http://dx.doi.org/10.1093/ve/vey043
    Journal articles | 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, vol. 35, pp. msy153 - msy153, http://dx.doi.org/10.1093/molbev/msy153
    Journal articles | 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, vol. 17, pp. 38, http://dx.doi.org/10.1186/s12942-018-0157-5
    Journal articles | 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, vol. 7, pp. 184, http://dx.doi.org/10.1038/s41426-018-0185-z
    Journal articles | 2018
    Magee D; Scotch M, 2018, 'The effects of random taxa sampling schemes in Bayesian virus phylogeography', Infection, Genetics and Evolution, vol. 64, pp. 225 - 230, http://dx.doi.org/10.1016/j.meegid.2018.07.003
    Journal articles | 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, vol. 8, http://dx.doi.org/10.1038/s41598-018-24264-8
    Journal articles | 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, vol. 643, pp. 460 - 467, http://dx.doi.org/10.1016/j.scitotenv.2018.06.206
    Journal articles | 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, vol. 119, pp. 241 - 249, http://dx.doi.org/10.1016/j.envint.2018.06.018
    Journal articles | 2018
    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, vol. 65, pp. 1339 - 1347, http://dx.doi.org/10.1111/tbed.12883
    Journal articles | 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, vol. 38, pp. 198 - 207, http://dx.doi.org/10.1007/s10669-017-9667-0
    Journal articles | 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, vol. 34, pp. 1606 - 1608, http://dx.doi.org/10.1093/bioinformatics/btx799
    Journal articles | 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, vol. 11, pp. 306 - 310, http://dx.doi.org/10.1111/irv.12458
    Journal articles | 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, vol. 13, pp. e1005389 - e1005389, http://dx.doi.org/10.1371/journal.pcbi
    Journal articles | 2017
    Namilae S; Derjany P; Mubayi A; Scotch M; Srinivasan A, 2017, 'Multiscale model for pedestrian and infection dynamics during air travel', Physical Review E, vol. 95, http://dx.doi.org/10.1103/PhysRevE.95.052320
    Journal articles | 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, vol. 465, pp. 248 - 260, http://dx.doi.org/10.1016/j.jth.2016.05.090
    Journal articles | 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, vol. 2017, http://dx.doi.org/10.1093/database/bax093
    Journal articles | 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, vol. 74, http://dx.doi.org/10.18637/jss.v074.i06
    Journal articles | 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, vol. 39, pp. 231 - 240, http://dx.doi.org/10.1007/s40264-015-0379-4
    Journal articles | 2016
    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, vol. 23, pp. 934 - 941, http://dx.doi.org/10.1093/jamia/ocv172
    Journal articles | 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, vol. 160, pp. 215 - 224, http://dx.doi.org/10.1007/s00705-014-2262-5
    Journal articles | 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, vol. 6, pp. 135 - 135, http://dx.doi.org/10.3389/fmicb.2015.00135
    Journal articles | 2015
    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, vol. 6, pp. 1456 - 1456, http://dx.doi.org/10.3389/fmicb.2015.01456
    Journal articles | 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, vol. 31, pp. i348 - i356, http://dx.doi.org/10.1093/bioinformatics/btv259
    Journal articles | 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, vol. 15, pp. 1471 - 2105, http://dx.doi.org/10.1186/15-276
    Journal articles | 2014
    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, vol. 26, pp. 185 - 193, http://dx.doi.org/10.1016/j.meegid.2014.05.029
    Journal articles | 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, vol. 13, pp. 1472 - 6947, http://dx.doi.org/10.1186/13-105
    Journal articles | 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, vol. 15, pp. e90 - e90, http://dx.doi.org/10.2196/jmir.2487
    Journal articles | 2013
    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, vol. 13, pp. 224 - 229, http://dx.doi.org/10.1016/j.meegid.2012.09.015
    Journal articles | 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, vol. 14, pp. 1471 - 2164, http://dx.doi.org/10.1186/14-871
    Journal articles | 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, vol. 10, pp. 1 - 15
    Journal articles | 2012
    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, vol. 7, pp. e43851 - e43851, http://dx.doi.org/10.1371/journal.pone.0043851
    Journal articles | 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, vol. 14, pp. e147, http://dx.doi.org/10.2196/jmir.2242
    Journal articles | 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, vol. 18, pp. 614 - 620, http://dx.doi.org/10.1136/amiajnl-2011-000093
    Journal articles | 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, vol. 8, pp. 376 - 380, http://dx.doi.org/10.1007/s10393-011-0706-x
    Journal articles | 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, vol. 58, pp. 131 - 139, http://dx.doi.org/10.1111/j.1863-2378.2009.01319.x
    Journal articles | 2011
    Scotch M; Rabinowitz P; Brandt C, 2011, 'State-level zoonotic disease surveillance in the United States', Zoonoses and Public Health, vol. 58, pp. 523 - 528, http://dx.doi.org/10.1111/j.1863-2378.2011.01401.x
    Journal articles | 2011
    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, vol. Suppl 1, pp. S44 - S47, http://dx.doi.org/10.1016/j.jbi.2011.06.005
    Journal articles | 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, vol. 12, pp. e45 - e45, http://dx.doi.org/10.2196/jmir.1538
    Journal articles | 2010
    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, vol. 48, pp. 1064 - 1070, http://dx.doi.org/10.1097/MLR.0b013e3181ef60c2
    Journal articles | 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, vol. 51, pp. 262 - 267, http://dx.doi.org/10.1093/ilar.51.3.262
    Journal articles | 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, vol. 17, pp. 3 - 5, http://dx.doi.org/10.1197/jamia.M2853
    Journal articles | 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, vol. 21, pp. 764 - 768, http://dx.doi.org/10.1097/EDE.0b013e3181f534dd
    Journal articles | 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, vol. 7, pp. 1a - 1a
    Journal articles | 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, vol. 8, pp. 67 - 67, http://dx.doi.org/10.1186/1476-072X
    Journal articles | 2009
    Rabinowitz P; Scotch M; Conti L, 2009, 'Human and animal sentinels for shared health risks', Veterinaria italiana, vol. 45, pp. 23 - 24, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000268436700003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
    Journal articles | 2009
    Scotch M; Odofin L; Rabinowitz P, 2009, 'Linkages between animal and human health sentinel data', BMC Veterinary Research, vol. 5, pp. 15 - 15, http://dx.doi.org/10.1186/5-15
    Journal articles | 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, vol. 7, pp. 38 - 38, http://dx.doi.org/10.1186/1476-072X
    Journal articles | 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, vol. 41, pp. 694 - 705, http://dx.doi.org/10.1016/j.jbi.2008.04.001
    Journal articles | 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, vol. 7, pp. 30 - 30, http://dx.doi.org/10.1186/1476-072X
    Journal articles | 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, vol. 8, pp. 22 - 22, http://dx.doi.org/10.1186/8-22
    Journal articles | 2008
    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, vol. 15, pp. 783 - 786, http://dx.doi.org/10.1197/jamia.M2731
    Journal articles | 2007
    Scotch M; Parmanto B; Monaco V, 2007, 'Usability evaluation of the Spatial OLAP Visualization and Analysis Tool (SOVAT)', Journal of Usability Studies, vol. 2, pp. 76 - 95
    Journal articles | 2006
    Scotch M; Parmanto B, 2006, 'Development of SOVAT: a numerical-spatial decision support system for community health assessment research', International Journal of Medical Informatics, vol. 75, pp. 771 - 784
    Journal articles | 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, vol. 5, pp. 39 - 39
    Journal articles | 2005
    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, vol. 2, pp. 3 - 3
  • Preprints | 2022
    Magge A; Weissenbacher D; Oâ 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
    Conference Papers | 2022
    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, IEEE, presented at 2022 IEEE Aerospace Conference (AERO), 05 March 2022 - 12 March 2022, http://dx.doi.org/10.1109/AERO53065.2022.9843497
    Preprints | 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
    Preprints | 2020
    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
    Preprints | 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
    Preprints | 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
    Preprints | 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
    Conference Papers | 2019
    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, Association for Computational Linguistics, pp. 907 - 916, presented at Proceedings of the 13th International Workshop on Semantic Evaluation, - , http://dx.doi.org/10.18653/v1/s19-2155
    Conference Papers | 2018
    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
    Conference Papers | 2017
    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
    Preprints | 2016
    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
    Conference Papers | 2016
    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
    Conference Papers | 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
    Conference Papers | 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
    Conference Papers | 2015
    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, American Medical Informatics Association Joint Summints 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
    Conference Papers | 2014
    Beard R; Magee D; Suchard MA; Lemey P; Scotch M, 2014, 'Generalized linear models for identifying predictors of the evolutionary diffusion of viruses.', in Generalized linear models for identifying predictors of the evolutionary diffusion of viruses., American Medical Informatics Association Joint Summits on Translational Science, 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/
    Conference Papers | 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
    Conference Papers | 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/
    Conference Papers | 2010
    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, Minneapolis, MN, pp. 285 - 285, presented at 33rd Annual Meeting of the Society-of-General-Internal-Medicine, Minneapolis, MN, 18 April 2010 - 01 May 2010, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000277282300181&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Papers | 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, Minneapolis, MN, pp. 386 - 387, presented at 33rd Annual Meeting of the Society-of-General-Internal-Medicine, Minneapolis, MN, 18 April 2010 - 01 May 2010, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000277282300397&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Papers | 2005
    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
    Conference Papers | 2002
    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, San Antonio, TX, pp. 1157 - 1157, presented at Annual Symposium of the American-Medical-Informatics-Association, San Antonio, TX, 09 November 2002 - 09 November 2002, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000189418100390&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Preprints |
    Adam D; Chen X; Scotch M; MacIntyre CR; Dwyer D; Kok J, The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses among Paediatric Cases in Sydney, Australia., http://dx.doi.org/10.22541/au.160614561.14239652/v1
    Preprints |
    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, 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
    Conference Papers |
    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

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)

 

  • 2018. Endeavour Fellowship. Australian Government