By Dr Matthew Scotch

Journal articles

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

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

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

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

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

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

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

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

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

Conference Papers

Khaokaew Y; Kong R; Züfle A; Xue H; Anderson T; Macintyre CR; Scotch M; Salim FD; Heslop DJ, 2026, 'An Infectious Disease Spread Simulation Based on Large Language Model Decision Making', in Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 11248 - 11259, http://dx.doi.org/10.1145/3770855.3818983

Stone H; Du J; Xue H; Scotch M; Heslop D; Zufle A; Macintyre CR; Salim F, 2025, 'A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models', in 33rd ACM Sigspatial International Conference on Advances in Geographic Information Systems ACM Sigspatial 2025, pp. 646 - 655, http://dx.doi.org/10.1145/3748636.3762779

Kong R; Anderson T; Heslop DJ; Scotch M; Salim FD; Macintyre CR; Zufle A, 2025, 'EpiScale: Large-Scale Simulation of Infectious Disease Based on Human Mobility', in 33rd ACM Sigspatial International Conference on Advances in Geographic Information Systems ACM Sigspatial 2025, pp. 828 - 831, http://dx.doi.org/10.1145/3748636.3762791

Kong R; Anderson T; Scotch M; Heslop DJ; Khaokaew Y; Xue H; Xiong L; Macintyre CR; Salim FD; Züfle A, 2025, 'Simulated Infectious Diseases Datasets with Controlled Data Bias', in Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 5551 - 5559, http://dx.doi.org/10.1145/3711896.3737401

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

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, http://dx.doi.org/10.18653/v1/s19-2155

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

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

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

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

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

Magee D; Scotch M, 2015, 'Conceptualizing a Novel Quasi-Continuous Bayesian Phylogeographic Framework for Spatiotemporal Hypothesis Testing.', 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

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

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/

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.', 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/

Tahsin T; Rivera R; Beard R; Lauder R; Weissenbacher D; Scotch M; Wallstrom G; Gonzalez G, 2014, 'Natural Language Processing Methods for Enhancing Geographic Metadata for Phylogeography of Zoonotic Viruses', in AMIA Joint Summits on Translational Science Proceedings, Association for Computational Linguistics (ACL), pp. 1 - 9, presented at Proceedings of BioNLP 2014, http://dx.doi.org/10.3115/v1/w14-3401

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

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

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

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; Parmanto B, 2005, 'SOVAT: Spatial OLAP Visualization and Analysis Tool', Institute of Electrical and Electronics Engineers (IEEE), pp. 1 - 7, presented at Proceedings of the 38th Annual Hawaii International Conference on System Sciences, http://dx.doi.org/10.1109/hicss.2005.550

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

Preprints

Khaokaew Y; Kong R; Zufle A; Xue H; Anderson T; MacIntyre CR; Scotch M; Salim FD; Heslop DJ, 2026, An Infectious Disease Spread Simulation Based on Large Language Model Decision Making, http://dx.doi.org/10.48550/arxiv.2606.06360

Pavia M; O'Connor K; Gonzalez-Hernandez G; Scotch M, 2026, A Metadata-Driven Framework for Strengthening Pathogen Genomics: Lessons from SARS-CoV-2 (Preprint), http://dx.doi.org/10.2196/preprints.92529

Stone H; Du J; Yang Y; Desai A; Dawson R; Xue H; Heslop D; Scotch M; Züfle A; MacIntyre CR; Salim F, 2026, From Ecological Connectivity to Outbreak Risk: A Heterogeneous Graph Network for Epidemiological Reasoning under Sparse Spatiotemporal Data, http://dx.doi.org/10.48550/arxiv.2601.09738

Stone H; Du J; Xue H; Scotch M; Heslop D; Züfle A; MacIntyre CR; Salim F, 2025, A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models, http://dx.doi.org/10.48550/arxiv.2506.09076

Scotch M; Faleye TOC; Wright JM; Finnerty S; Halden RU; Varsani A, 2025, Campus-based genomic surveillance uncovers early emergence of a future dominant A(H3N2) influenza clade., http://dx.doi.org/10.1101/2025.06.13.25329559

Khaokaew Y; Salim FD; Züfle A; Xue H; Anderson T; MacIntyre CR; Scotch M; Heslop DJ, 2025, Evaluating the Bias in LLMs for Surveying Opinion and Decision Making in Healthcare, http://dx.doi.org/10.48550/arxiv.2504.08260

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

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

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

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

Pavia MJ; O’Connor K; Gonzalez-Hernandez G; Scotch M, A Metadata-Driven Framework for Strengthening Pathogen Genomics Lessons from SARS-CoV-2, http://dx.doi.org/10.1101/2025.11.04.25339514

Holland LA; Kaelin EA; Maqsood R; Estifanos B; Wu LI; Varsani A; Halden RU; Hogue BG; Scotch M; Lim ES, 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

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