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  1. Stelzer-Braid, S. et al. Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations. J Clin Virol 122, 104216, doi:10.1016/j.jcv.2019.104216 (2020).


  1. Scotch, M. et al. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol 5, vey043, doi:10.1093/ve/vey043 (2019).

  2. Magge, A., Weissenbacher, D., Sarker, A., Scotch, M. & Gonzalez-Hernandez, G. Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature. Pac Symp Biocomput 24, 100-111 (2019).

  3. Beard, R. & Scotch, M. Identifying current and emerging resources and tools utilized for detection, prediction, and visualization of viral zoonotic disease clusters: a Delphi study. JAMIA Open 2, 306-311, doi:10.1093/jamiaopen/ooz015 (2019).

  4. Adam, D. C., Scotch, M. & MacIntyre, C. R. Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants. Viruses 11, doi:10.3390/v11090791 (2019).​


  1. Adam, D. C., Scotch, M. & MacIntyre, C. R. Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes. Mol Biol Evol 35, 2607-2617, doi:10.1093/molbev/msy153 (2018).

  2. Tahsin, T. et al. GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. Bioinformatics 34, 1606-1608, doi:10.1093/bioinformatics/btx799 (2018).

  3. Njoto, E. N. et al. Phylogeography of H5N1 avian influenza virus in Indonesia. Transbound Emerg Dis 65, 1339-1347, doi:10.1111/tbed.12883 (2018).

  4. Morin, C. W. et al. Avian influenza virus ecology and evolution through a climatic lens. Environ Int 119, 241-249, doi:10.1016/j.envint.2018.06.018 (2018).

  5. Magge, A., Weissenbacher, D., Sarker, A., Scotch, M. & Gonzalez-Hernandez, G. Deep neural networks and distant supervision for geographic location mention extraction. Bioinformatics 34, i565-i573, doi:10.1093/bioinformatics/bty273 (2018).

  6. Magee, H. Y. et al. U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids. Sci Total Environ 643, 460-467, doi:10.1016/j.scitotenv.2018.06.206 (2018).

  7. Magee, D., Taylor, J. E. & Scotch, M. The Effects of Sampling Location and Predictor Point Estimate Certainty on Posterior Support in Bayesian Phylogeographic Generalized Linear Models. Sci Rep 8, 5905, doi:10.1038/s41598-018-24264-8 (2018).

  8. Magee, D. & Scotch, M. The effects of random taxa sampling schemes in Bayesian virus phylogeography. Infect Genet Evol 64, 225-230, doi:10.1016/j.meegid.2018.07.003 (2018).

  9. Bui, C. M., Adam, D. C., Njoto, E., Scotch, M. & MacIntyre, C. R. Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis. Emerg Microbes Infect 7, 184, doi:10.1038/s41426-018-0185-z (2018).

  10. Beard, R., Wentz, E. & Scotch, M. A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks. Int J Health Geogr 17, 38, doi:10.1186/s12942-018-0157-5 (2018).


  1. Namilae S, Derjany P, Mubayi A, Scotch M, Srinivasan A. Multiscale model for pedestrian and infection dynamics during air travel. Phys. Rev. E. 2017 May 31; 95(5): 052320.

  2. Adam DC, Magee DJ, Bui CM, Scotch M, MacIntyre CR. Does influenza pandemic preparedness and mitigation require gain-of-function research?. Influenza Other Respir Viruses. 2017 May 14.

  3. Magee, D., Suchard, M. A., 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. 2017 February 7. PMID: 28170397. [In Press]


  1. Jirjies, S., G. Wallstrom, R. U. Halden and M. Scotch. 2016. pyJacqQ: Python Implementation of Jacquez’s Q-Statistics for Space-Time Clustering of Disease Exposure in Case-Control Studies. J. Stat Software 2016 (74) doi: 10.18637/jss.v074.i06 

  2. Tahsin T, Weissenbacher D, Rivera R, Beard R, Firago M, Wallstrom G, Scotch M, Gonzalez G. A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. J Am Med Inform Assoc. 2016 Jan 17. [Ahead of Print]

  3. Sarker A, O'Connor K, Ginn R, Scotch M, Smith K, Malone D, Gonzalez G. Social media mining for toxicovigilance: automatic monitoring of prescription medication abuse from Twitter. Drug Saf. 2016 Mar;39(3):231-40.


  1. Veljkovic V, Paessler S, Glisic S, Prljic J, Perovic VR, Veljkovic N, Scotch M. Evolution of 2014/15 H3N2 influenza viruses circulating in US: consequences for vaccine effectiveness and possible new pandemic. Front Microbiol. 2015 Dec 22;6:1456.

  2. Veljkovic V, Glisic S, Muller CP, Scotch M, Branch DR, Perovic VR, Sencanski M, Veljkovic N, Colombatti A. In silico analysis suggests interaction between Ebola virus and the extracellular matrix. Front Microbiol (2015) Refereed Articles.

  3. Weissenbacher D, Tahsin T, Beard R, Figaro M, Rivera R, Scotch M, Gonzalez G. Knowledge-driven geospatial location resolution for phylogeographic models of virus migration. Bioinformatics. 2015 Jun 15;31(12):i348-i356. ISMB/ECCB 2015 Proceedings.

  4. Magee D, Beard R, Suchard MA, Lemey P, Scotch M. Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion. Arch Virol (2015) Refereed Articles.


  1. Kane MJ, Price N, Scotch M, Rabinowitz P. Comparison of ARIMA and random forest time series models for prediction of avian influenza H5N1 outbreaks. BMC Bioinformatics (2014) Refereed Articles.

  2. Magee D, Beard R, Suchard MA, Lemey P, Scotch M. Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion. Archives of Virology (2014) Refereed Articles.

  3. Scotch M, Lam TT, Pabilonia KL, Anderson T, Baroch J, Kohler D, DeLiberto TJ. Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States. Infection Genetics Evolution (2014) Refereed Articles.


  1. Braithwaite RS, Scotch M.. Using value of information to guide evaluation of decision supports for differential diagnosis: is it time for a new look?. BMC Med Inform Decis Mak (2013) Refereed Articles.

  2. Matthew Scotch, Cynthia Brandt, Sylvia Leung, Julie Womack. Natural Language Processing for Understanding Contraceptive Use at the VA. Annals of Information Science (2013) Refereed Articles.

  3. Scotch M, Baarson B, Beard R, Lauder R, Varman A, Halden RU.. Examining the differences in format and characteristics of zoonotic virus surveillance data on state agency websites.. J Med Internet Res. (2013) Refereed Articles.

  4. Scotch M, Mei C, Makonnen YJ, Pinto J, Ali A, Vegso S, Kane M, Sarkar IN, Rabinowitz P.. Phylogeography of influenza A H5N1 clade in Egypt.. BMC Genomics (2013) Refereed Articles.

  5. Scotch M, Mei C.. Phylogeography of swine influenza H3N2 in the United States: Translational public health for zoonotic disease surveillance.. Infect Genet Evol (2013) Refereed Articles.

  6. Womack JA, Scotch M, Leung SN, Skanderson M, Bathulapalli H, Haskell SG, Brandt CA.. Use of structured and unstructured data to identify contraceptive use in women veterans.. Perspect Health Inf Manag. (2013) Refereed Articles.


  1. Rabinowitz PM, Galusha D, Vegso S, Michalove J, Rinne S, Scotch M, Kane M.. Comparison of human and animal surveillance data for H5N1 influenza A in Egypt 2006-2011. PLoS One (2012) Refereed Articles.


  1. Garla V, Lo Re V 3rd, Dorey-Stein Z, Kidwai F, Scotch M, Womack J, Justice A, Brandt C. The Yale cTAKES extensions for document classification: architecture and application. Journal of the American Medical Informatics Association (2011) Refereed Articles.

  2. Scotch M, Brownstein JS, Vegso S, Galusha D, Rabinowitz P. Human vs. Animal Outbreaks of the 2009 Swine-Origin H1N1 Influenza A epidemic. Ecohealth (2011) Refereed Articles.

  3. Scotch M, Mattocks K, Rabinowitz P, Brandt C. A Qualitative Study of State-Level Zoonotic Disease Surveillance in New England. Zoonoses and Public Health (2011) Refereed Articles.

  4. Scotch M, Rabinowitz P, Brandt C. State-level zoonotic disease surveillance in the United States. Zoonoses and Public Health (2011) Refereed Articles.

  5. Scotch M, Sarkar IN, Mei C, Leaman R, Cheung KH, Ortiz P, Singraur A, Gonzalez G. Enhancing phylogeography by improving geographical information from GenBank. Journal of Biomedical Informatics (2011) Refereed Articles.


  1. Konovalov S, Scotch M, Post L, Brandt C. Biomedical informatics techniques for processing and analyzing web blogs of military service members. Journal of Medical Internet Research (2010) Refereed Articles.

  2. Ohl M, Tate J, Duggal M, Skanderson M, Scotch M, Kaboli P, Vaughan-Sarrazin M, Justice A. Rural residence is associated with delayed care entry and increased mortality among veterans with human immunodeficiency virus infection. Medical Care (2010) Refereed Articles.

  3. Rabinowitz PR, Scotch M, Conti LA. Animals as Sentinels: Using Comparative Medicine to Move Beyond the Laboratory. Institute for Laboratory Animal Research Journal (2010) Refereed Articles.

  4. Scotch M, Duggal M, Brandt C, Lin Z, Shiffman R. Use of Statistical Analysis in the Biomedical Informatics Literature. Journal of the American Medical Informatics Association (2010) Refereed Articles.

  5. Scotch M, Mei C, Brandt C, Sarkar IN, Cheung K. At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography. Epidemiology (2010) Refereed Articles.

  6. Womack JA, Scotch M, Gibert C, Chapman W, Yin M, Justice AC, Brandt C. A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records. Perspectives in Health Information Management (2010) Refereed Articles.


  1. Liu A, Lee V, Galusha D, Slade MD, Diuk-Wasser M, Andreadis T, Scotch M, Rabinowitz PM. Risk factors for human infection with West Nile Virus in Connecticut: a multi-year analysis. Int J Health Geogr (2009) Refereed Articles.

  2. Rabinowitz P, Scotch M, Conti L. Human and animal sentinels for shared health risks. Vet Ital (2009) Refereed Articles.

  3. Scotch M, Odofin L, Rabinowitz P. Linkages between animal and human health sentinel data. BMC Vet Res (2009) Refereed Articles.


  1. Boulos MN, Scotch M, Cheung KH, Burden D. Web GIS in practice VI: a demo playlist of geo-mashups for public health neogeographers. Int J Health Geogr (2008) Refereed Articles.

  2. Cheung KH, Yip KY, Townsend JP, Scotch M. HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0. J Biomed Inform (2008) Refereed Articles.

  3. Parmanto B, Paramita MV, Sugiantara W, Pramana G, Scotch M, Burke DS. Spatial and multidimensional visualization of Indonesia's village health statistics. Int J Health Geogr (2008) Refereed Articles.

  4. Scotch M, Parmanto B, Monaco V. Evaluation of SOVAT: an OLAP-GIS decision support system for community health assessment data analysis. BMC Med Inform Decis Mak (2008) Refereed Articles.

  5. Scotch M, Yip KY, Cheung KH. Development of grid-like applications for public health using Web 2.0 mashup techniques. Journal of the American Medical Informatics Association (2008) Refereed Articles.


  1. Scotch M, Parmanto B, Monaco V. Usability Evaluation of the Spatial OLAP Visualization and Analysis Tool (SOVAT). Journal of Usability Studies (2007) Refereed Articles.


  1. Scotch M, Parmanto B, Gadd CS, Sharma RK. Exploring the role of GIS during community health assessment problem solving: experiences of public health professionals. Int J Health Geogr (2006) Refereed Articles.


  1. Parmanto B, Scotch M, Ahmad S. A framework for designing a healthcare outcome data warehouse. Perspect Health Inf Manag (2005) Refereed Articles.