By Dr Matthew Scotch

Journal articles

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

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, pp. 1 - 8, http://dx.doi.org/10.1038/s41426-018-0185-z

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

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

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

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

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

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

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, 35, pp. msy153 - msy153, http://dx.doi.org/10.1093/molbev/msy153

Raina MacIntyre C; Engells TE; Scotch M; Heslop DJ; Gumel AB; Poste G; Chen X; Herche W; Steinhöfel K; Lim S; Broom A; MacIntyre R, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Scotch M; Rabinowitz P; Brandt C, 2011, 'State-level zoonotic disease surveillance in the United States', Zoonoses and Public Health, 58, pp. 523 - 528

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

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

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

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

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

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

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

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

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

Rabinowitz P; Scotch M; Conti L, 2009, 'Human and animal sentinels for shared health risks', Veterinaria italiana, 45, pp. 23 - 24

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

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