Dr Matthew Scotch

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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/

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/

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

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

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

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