Matthew Scotch

Cntr for Environ. Health Engineering
Biodesign Institute
B240B
Tempe
Faculty Member
Faculty
SCOTTSDALE Campus
Mailcode
9020
Assoc Professor
Faculty
SCOTTSDALE Campus
Mailcode
9020

Biography

Matthew Scotch is an associate professor of biomedical informatics in the College of Health Solutions and assistant director of the Biodesign Center for Environmental Health Engineering at Arizona State University. His research focuses on the theory and application of phylogeography to study the migration of zoonotic RNA viruses with a particular interest in influenza A viruses. Work in his lab includes the integration, analysis, and presentation of viral genetics for public health/animal health surveillance.

Current projects include studying approaches to advance phylogeography models and geospatial metadata in virus sequence databases for virus surveillance (funding: NIH/NIAID R01AI117011) and analysis of viruses from wastewater using bioinformatics (funding: NIH/NLM 1R01LM013129).

His lab group is also interested in the molecular epidemiology of zoonotic viruses including the amplification and sequencing of influenza A genes for studying spread among avian and human hosts.

Education

  • Postdoctoral Fellowship, Yale University 2006-2008
  • M.P.H. Yale University 2007
  • Ph.D. Biomedical Informatics, University of Pittsburgh 2006
  • M.A. Biomedical Informatics, Columbia University 2002
  • B. A. Health and Society, University of Rochester, NY 1998

Google Scholar

Research Interests

  • Genomic epidemiology of RNA viruses but mostly influenza
  • Phylodynamics
  • Molecular epidemiology
  • Bioinformatics
  • DNA sequence databases and metadata enrichment
  • Natural Language Processing (NLP)

Related Links:

Publications

Articles indexed in PubMed.

1.     Magge A, Weissenbacher D, O'Connor K, Tahsin T, Gonzalez-Hernandez G, Scotch M. GeoBoost2: A natural language processing pipeline for GenBank metadata enrichment for virus phylogeography. Bioinformatics. 2020 Jul 19:btaa647.

2.     Scotch M, Halden RU, Denton A, Sandrolini H, Fontenele RS, Varsani A. Coding-complete genome sequence of a human respirovirus 1 strain from a clinical sample in Arizona. Microbiol Resour Announc. 2020 Jun 11;9(24):e00465-20.

3.     Chen X, Adam DC, Chughtai AA, Stelzer-Braid S, Scotch M, MacIntyre CR. The phylogeography of MERS-CoV in hospital outbreak-associated cases compared to sporadic cases in Saudi Arabia. Viruses. 2020 May 14;12(5):E540.

4.     Holland LA, Kaelin EA, Maqsood R, Estifanos B, Wu LI, Varsani A, Halden RU, Hogue BG, Scotch M, Lim ES. An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020). J Virol. 2020 May 1. pii: JVI.00711-20.

5.     Ngonghala CN, Iboi E, Eikenberry S, Scotch M, MacIntyre CR, Bonds MH, Gumel AB. Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus. Math Biosci. 2020 Apr 30:108364.

6.     Yoo W, Koskan A, Scotch M, Pottinger H, Huh WK, Helitzer D. Patterns and disparities in human papillomavirus (HPV) vaccine uptake for young female adolescents among us states: NIS-Teen (2008-2016). Cancer Epidemiol Biomarkers Prev. 2020 Apr 28. pii: cebp.1103.2019.

7.     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. Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations. J Clin Virol. 2020 Jan;122:104216.

8.     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. 2019 Oct; 2(3): 306–311.

9.     Adam DC*, MacIntyre CR†, Scotch M†. Phylodynamics of influenza A/H1N1pdm09 in India reveals circulation patterns and increased selection for clade 6b residues and other high mortality mutants. Viruses. 2019 Aug 27;11(9). pii: E791.

10.  Scotch M, Tahsin T*, Weissenbacher D, O'Connor K, Magge A*, Vaiente M*, Suchard MA, Gonzalez-Hernandez G. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol. 2019 Feb 28;5(1):vey043.

11.  Magee HY, Maurer MM, Cobos A, Pycke BFG, Venkatesan AK, Magee D, Scotch M, Halden RU. U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids. Sci Total Environ. 2018 Dec 1;643:460-467.

12.  Bui CM*, Adam DC*, Njoto E*, Scotch M, MacIntyre CR. Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis. Emerg Microbes Infect. 2018 Nov 21;7(1):184.

13.  Adam DC*, MacIntyre CR†, Scotch M†. Bayesian phylogeography and pathogenic characterisation of smallpox based on HA, ATI and CrmB genes. Mol Biol Evol. 2018 Nov 1;35(11):2607-2617.

14.  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. 2018 Oct 30;17(1):38.

15.  Magee D*, Scotch M. The effects of random taxa sampling schemes in Bayesian virus phylogeography. Infect Genet Evol. 2018 Oct;64:225-230.

16.  Magge A*, Weissenbacher D, Sarker A, Scotch M, Gonzalez-Hernandez G. Deep neural networks and distant supervision for geographic location mention extraction. Bioinformatics. 2018 Jul 1;34(13):i565-i573.

17.  Tahsin T*, Weissenbacher D, O'Connor K, Magge A, Scotch M, Gonzalez-Hernandez G. GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. Bioinformatics. 2018 May 1;34(9):1606-1608.

18.  Njoto EN*, Scotch M, Bui CM*, Adam DC*, Chughtai AA*, MacIntyre CR. Phylogeography of H5N1 avian influenza virus in Indonesia. Transbound Emerg Dis. 2018 Apr 24.

19.  Magee D*, Taylor JE, Scotch M. The effects of sampling location and predictor point estimate certainty on posterior support in Bayesian phylogeographic generalized linear models. Sci Rep. 2018 Apr 12;8(1):5905.

20.  Tahsin T*, Weissenbacher D, Jones-Shargani D*, Magee D*, Vaiente M*, Gonzalez G, Scotch M. Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. Database. 2017 Dec 28; bax093.

21.  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;95(5-1):052320.

22.  Magee D*, Suchard MA, Scotch M. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction. PLoS Comput Biol. 2017 Feb 7;13(2):e1005389.

23.  Namilae S, Srinivasan A, Mubayi A, Scotch M, Pahle R. Self-propelled pedestrian dynamics model: Application to passenger movement and infection propagation in airplanes. Physica A. 2017 Jan 1; 465(1):248-260.

24.  Jirjies S*, Wallstrom G, Halden RU, Scotch M. pyJacqQ: python implementation of Jacquez's Q-statistics for space-time clustering of disease exposure in case-control studies. J Stat Softw. 2016 Oct;74(6).

25.  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 Sep;23(5):934-41.

26.  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.

27.  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.

28.  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.

29.  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 Feb 19;6:135.

30.  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 Jan;160(1):215-24.

31.  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 Aug 13;15(1):276.

32.  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. Infect Genet Evol. 2014 Aug;26:185-193.

33.  Scotch M, Mei C, Makonnen YJ, Pinto J, Ali A, Vegso S, Kane M, Sarkar IN, Rabinowitz P. Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt. BMC genomics. 2013 Dec 10;14(1):871.

34.  Womack JA, Scotch M, Leung S, Brandt CA. Use of structured and unstructured data to identify contraceptive use in women veterans. Perspect Health Inf Manag. 2013. Summer: 1-15.

35.  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;15(4):e90.

36.  Scotch M, Mei C. Phylogeography of swine influenza H3N2 in the United States: translational public health for zoonotic disease surveillance. Infect Genet Evol. 2013 Jan;13:224-9.

37.  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 2006-2001. PLoS One. 2012;7(9):e43851. Epub 2012 Sep 27.

38.  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 Sep;8(3):376-80.

39.  Scotch M, Sarkar IN, Mei C, Leaman R, Cheung KH, Ortiz P*, Singraur A*, Gonzalez G. Enhancing phylogeography by improving geographical information from GenBank. J Biomed Inform. 2011;44(S1):S44-47.

40.  Garla V, Re VL 3rd, Dorey-Stein Z, Kidwai F, Scotch M, Womack J, Justice A, Brandt C. The Yale cTAKES extensions for document classification: architecture and application. J Am Med Inform Assoc. 2011. 18(5):614-20.

41.  Scotch M, Rabinowitz P, Brandt C. State-level zoonotic disease surveillance in the United States. Zoonoses and Public Health. 2011;58(8):523-8.

42.  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;58(2):131-139.

43.  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. Perspect Health Inf Manag. 2010; Oct 1;7:1a.

44.  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; 21(6):764-8.

45.  Konovalov S, Scotch M, Post L, Brandt C. Biomedical informatics techniques for processing and analyzing web blogs of military service members. J Med Internet Res. 2010; 12(4):e45.

46.  Rabinowitz PR, Scotch M, Conti LA. Animals as sentinels: using comparative medicine to move beyond the laboratory. Institute for Laboratory Animal Research Journal. 2010; 51(3):262-267.

47.  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 (HIV) infection. Medical Care. 2010 Dec;48(12):1064-1070.

48.  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; 17(1):3-5.

49.  Liu A, Lee V, Galusha D, Slade MD, Diuk-Wasser M, Andreadis T, Scotch M, Rabinowitz P.  Risk factors for human infection with West Nile virus in Connecticut: a multi-year analysis.  International Journal of Health Geographics. 2009, 8:67.

50.  Scotch M, Odofin L, Rabinowitz P. Linkages between animal and human health sentinel data. BMC Veterinary Research. 2009, 5:15.

51.  Rabinowitz, P, Scotch M, Conti L. Human and animal sentinels for shared health risks. Veterinaria Italiana. 2009; 45(1):23-34.

52.  Boulos MNK, Scotch M, Cheung K, Burden D. Web GIS in practice VI: a demo "playlist" of geo-mashups for public health neogeographers. International Journal of Health Geographics. 2008, 7:38.

53.  Scotch M, Yip K, Cheung K. Development of grid-like applications for public health using Web 2.0 mashup techniques. Journal of the American Medical Informatics Association. 2008;15(6):783-786.

54.  Cheung K, Yip K, Townsend JP, Scotch M. HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. Journal of Biomedical Informatics. 2008;41(5):694-705.

55.  Scotch M, Parmanto B, Monaco V. Evaluation of SOVAT: an OLAP-GIS decision support system for community health assessment data analysis. BMC Medical Informatics and Decision Making. 2008; 8(1):22.

56.  Parmanto B, Paramita M, Sugiantara W, Pramana G, Scotch M, Burke DS. Spatial and multidimensional visualization of Indonesia's village health statistics. International Journal of Health Geographics.  2008; 7:30.

57.  Scotch M, Parmanto B, Monaco V. Usability evaluation of the Spatial OLAP Visualization and Analysis Tool (SOVAT).  Journal of Usability Studies. 2007;2(2):76-95.

58.  Scotch M, Parmanto B, Gadd CS, Sharma RK. Exploring the role of GIS during community health assessment problem solving: experiences of public health professionals.  International Journal of Health Geographics. 2006;5;39.

59.  Scotch M, Parmanto B. Development of SOVAT: A numerical-spatial decision support system for community health assessment research. International Journal of Medical Informatics. 2006;75(10-11):771-84.

60.  Parmanto B, Scotch M, Ahmad S. A framework for designing a healthcare outcome data warehouse. Perspectives in Health Information Management. 2005; 2:3.

61.  Morin CW, Stoner-Duncan B, Winker K, Scotch M, Hess JJ, Meschke JS, Ebi KL, Rabinowitz PM. Avian influenza virus ecology and evolution through a climatic lens. Environ Int. 2018 Jul 3;119:241-249.

62.  MacIntyre RC, Engells TE, Scotch M, Heslop DJ, Gumel AB, Poste G, Chen X, Herche W, Steinhöfel K, Lim S, Broom A. Converging and emerging threats to health security. Environ Syst Decis. 2018 Jun; 38(2):198–207.

63.  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.

64.  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 Sep 11;13(1):105.

65.  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. 2019;24:100-111.

66.  Magge A*, Scotch M, Gonzalez-Hernandez G. Clinical NER and Relation Extraction using Bi-Char-LSTMs and Random Forest Classifiers. Proceedings of Machine Learning Research 90:25–30, 2018 Medication and Adverse Drug Event Detection Workshop.

67.  Weissenbacher D, Sarker A, Tahsin T*, Scotch M, Gonzalez G. Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:114-122.

68.  Magge A*, Scotch M, Gonzalez G. CSaRUS-CNN at AMIA-2017 tasks 1, 2: under sampled CNN for text classification. In: Proceedings of the Second Workshop on Social Media Mining for Health Research and Applications Workshop Co-located AMIA 2017; 2017: 76–78.

69.  Paul MJ, Sarker A, Brownstein JS, Nikfarjam A*, Scotch M, Smith KL, Gonzalez G. Social media mining for public health monitoring and surveillance. Pac Symp Biocomput. 2016;21:468-79. (Review)

70.  Magee D*, Beard R*, Scotch M. Analyses of Merging Clinical and Viral Genetic Data for Influenza Surveillance. AMIA Annu Symp Proc. 2015 Nov 5;2015:1995-2004.

71.  Scotch M, Suchard MA, Rabinowitz P. Analysis of viral genetics for estimating diffusion of influenza A H6N1. AMIA 2015 Joint Summits on Translational Science; 2015:36-40.

72.  Magee D*, Scotch M. Conceptualizing a Novel Quasi-Continuous Bayesian Phylogeographic Framework for Spatiotemporal Hypothesis Testing. AMIA 2015 Joint Summits on Translational Science; 2015:212-216.

73.  Tahsin T*, Rivera R*, Beard R*, Lauder R*, Weissenbacher D, Scotch M, Wallstrom G, Gonzalez G. Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses. AMIA 2014 Joint Summits on Translational Science; 2014:102-111.

74.  Beard R*, Magee D*, Suchard MA, Lemey P, Scotch M. Generalized Linear Models for Identifying Predictors of the Evolutionary Diffusion of Viruses. AMIA 2014 Joint Summits on Translational Science; 2014:23-28.

75.  Tahsin T*, Rivera R*, Beard R*, Lauder R*, Weissenbacher D, Scotch M, Wallstrom G, Gonzalez G. Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses. Proceedings of the 2014 Workshop on Biomedical Natural Language Processing (BioNLP 2014); 2014:1-9.

76.  Rabinowitz P, Vegso S, Chudnov, Odofin L, Scotch M, Wilcox M. The 'Canary Database': Assembling Evidence for One Health Linkages between Human, Animal, and Environmental Health. 2013 Annual Meeting and Exhibition of the Medical Library Association (MLA ’13).

77.  Scotch M, Parmanto B. SOVAT: Spatial OLAP Visualization and Analysis Tool in Proceedings of HICSS-38; 2005;142.2.

78.  Parmanto B, Scotch M. Mining Information from Mountains of Electronic Health Record: Unique Challenges and Solutions in Proceedings of AHIMA National Convention. 2003.

79.  Stetson, PD, Johnson SB, Scotch M, Hripcsak, G. The Sublanguage of Cross Coverage in Proceedings of AMIA Fall Symposium. 2002;742-746.

Research Activity

ACTIVE RESEARCH SUPPORT

COVID-19 Seed Grant    Scotch (PI)    06/01/2020-05/31/2021
ASU/CHS
Next-generation sequencing and genomic epidemiology of SARS-CoV-2 patients in Arizona

The goal of this seed grant is to use next-generation sequencing on processed clinical specimens of COVID-19 positive patients in Arizona seen at a Abrazo Health Network hospital and to link subsequent genetic sequence analysis to clinical phenotypes including disease severity.

CNS 2027529    Scotch (PI)    05/15/2020-04/30/2021
NSF    
Collaborative:RAPID: Leveraging new data sources to analyze the risk of COVID-19 in crowded locations

The goal of this RAPID project is to utilize new data sources such as location-based services data and videos of pedestrian movement to develop local and global models of COVID-19 risk.
Role: Co-PI

CBET 2028564    Halden    05/01/2020-04/30/2021
NSF    
Collaborative:RAPID: COVID-19’s impact on the urban environment, behavior, and wellbeing

The goal of this RAPID project is to leverage novel data sources from community wastewater including the concentrations of 130+ wastewater-borne biomarkers of environmental stress and human wellbeing and report the resultant data to city stakeholders via an online dashboard for public health decision-making during COVID-19.
Role: Co-PI

OAC 1931560    Scotch (PI)    11/01/2019–10/31/2022
NSF    
Collaborative:Elements:Cyberinfrastructure for pedestrian dynamics-based analysis of infection propagation through air travel

The goal of this project is to develop a novel software to simulate the movement of people in order to understand how movement patterns influence transmission of infection at local as well as global scales.

1R01LM013129-01    Scotch, Halden, Varsani (PIs)    06/03/2019-05/31/2023
NIH/NLM    
Bioinformatics framework for wastewater-based surveillance of infectious diseases
The goal of this project is to develop and evaluate a bioinformatics framework that uses metagenomic data generated from sampling of wastewater to monitor local epidemics and outbreaks of infectious diseases.

5R01AI117011-04    Scotch, Gonzalez-Hernandez (PIs)    04/01/2016–03/31/2021
NIH/NIAID    
Tracking evolution and spread of viral genomes by geospatial observation error
The goal of this project is to enhance the geospatial data used for the phylogeography of zoonotic viruses by applying natural language processing techniques to biomedical text and statistical phylogeography to viral genetic data.

Courses

Fall 2020
Course Number Course Title
BMI 461 Advanced Topics in BMI I
BMI 482 Capstone I
BMI 484 Internship
MBB 495 Undergraduate Research
BMI 560 Teachng Biomedical Informatics
BMI 584 Internship
BMI 590 Reading and Conference
BMI 593 Applied Project
BMI 790 Reading and Conference
BMI 792 Research
BMI 799 Dissertation
Summer 2020
Course Number Course Title
BMI 482 Capstone I
BMI 483 Capstone II
BMI 484 Internship
BMI 560 Teachng Biomedical Informatics
BMI 584 Internship
BMI 792 Research
BMI 799 Dissertation
Spring 2020
Course Number Course Title
BMI 482 Capstone I
BMI 483 Capstone II
BMI 484 Internship
CHS 493 Honors Thesis
MBB 495 Undergraduate Research
BMI 560 Teachng Biomedical Informatics
BMI 584 Internship
BMI 593 Applied Project
BMI 595 Continuing Registration
BMI 790 Reading and Conference
CHS 791 Seminar
BMI 792 Research
BMI 799 Dissertation
Fall 2019
Course Number Course Title
BMI 461 Advanced Topics in BMI I
BMI 484 Internship
CHS 492 Honors Directed Study
MBB 495 Undergraduate Research
BMI 560 Teachng Biomedical Informatics
BMI 584 Internship
BMI 590 Reading and Conference
BMI 593 Applied Project
BMI 790 Reading and Conference
BMI 792 Research
BMI 799 Dissertation
Summer 2019
Course Number Course Title
BMI 584 Internship
BMI 792 Research
Spring 2019
Course Number Course Title
BMI 482 Capstone I
BMI 483 Capstone II
BMI 484 Internship
BMI 493 Honors Thesis
MBB 495 Undergraduate Research
BMI 560 Teachng Biomedical Informatics
BMI 593 Applied Project
BMI 790 Reading and Conference
BMI 792 Research
BMI 799 Dissertation
Fall 2018
Course Number Course Title
BMI 484 Internship
BMI 492 Honors Directed Study
MBB 495 Undergraduate Research
BMI 560 Teachng Biomedical Informatics
BMI 584 Internship
BMI 590 Reading and Conference
BMI 593 Applied Project
BMI 790 Reading and Conference
BMI 792 Research
BMI 799 Dissertation
Summer 2018
Course Number Course Title
BMI 484 Internship
BMI 584 Internship
BMI 792 Research
Spring 2018
Course Number Course Title
BMI 484 Internship
BMI 493 Honors Thesis
MBB 495 Undergraduate Research
BMI 499 Individualized Instruction
BMD 502 Foundations BMI Methods I
BMI 560 Teachng Biomedical Informatics
BMI 593 Applied Project
BMI 601 Health Informatics
BMI 790 Reading and Conference
BMI 792 Research
BMI 799 Dissertation
Summer 2017
Course Number Course Title
BMI 484 Internship
BMI 584 Internship
BMI 593 Applied Project
BMI 792 Research
BMI 799 Dissertation
Spring 2017
Course Number Course Title
BMI 493 Honors Thesis
BMD 502 Foundations BMI Methods I
BMI 560 Teachng Biomedical Informatics
BMI 570 BMI Symposium
BMI 590 Reading and Conference
BMI 593 Applied Project
BMI 790 Reading and Conference
BMI 792 Research
BMI 799 Dissertation
Fall 2016
Course Number Course Title
BMI 102 Intro Public Hlth/Imagng Infor
BMI 492 Honors Directed Study
MBB 495 Undergraduate Research
BMI 560 Teachng Biomedical Informatics
BMI 593 Applied Project
BMI 792 Research
BMI 799 Dissertation
Summer 2016
Course Number Course Title
BMI 792 Research
BMI 799 Dissertation
Spring 2016
Course Number Course Title
BMD 502 Foundations BMI Methods I
BMI 560 Teachng Biomedical Informatics
BMI 592 Research
BMI 593 Applied Project
BMI 790 Reading and Conference
BMI 792 Research

Presentations

  • Matthew Scotch. A pipeline for virus phylogeography that accounts for geospatial observation error. 12th Annual Rocky Mountain Bioinformatics Conference (Dec 2014).
  • Matthew Scotch and Graciela Gonzalez. Text processing and geospatial uncertainty for phylogeography of zoonotic viruses. Webinar on NIH-funded projects on spatial uncertainty, surveillance research program (Oct 2014).
  • Matthew Scotch. Challenges and promises of bioinformatics for translational applications. Lecture to first-year medical students at UA-COM (Sep 2014).
  • Matthew Scotch. Tracking the spread of viruses. Spirit of the senses salon (Sep 2014).
  • Matthew Scotch and Daniel Magee. Phylogeographic generalized linear model for identifying predictors driving H5N1 diffusion within Egypt. Intelligent Systems for Molecular Biology (ISMB) (Jul 2014).
  • Matthew Scotch. Translational public health: using viral sequence data for zoonotic disease surveillance. Epi Presents! series (Apr 2014).
  • Matthew Scotch. Phylogeography of avian and human influenza in the Southwest United States. Influenza2013: One Influenza, One World, One Health, Oxford, United Kingdom (Sep 2013).
  • Matthew Scotch. Phylogeography of avian and human influenza in the southwest United States. 10th Annual Rocky Bioinformatics Conference (Dec 2012).
  • Matthew Scotch. Phylogeography of influenza A in human and avian species in the southwest United States. Molecular Epidemiology and Evolutionary Genetics of Infectious Disease (MEEGID)11 (Nov 2012).
  • Matthew Scotch. Public health informatics to support public health decision making. Society for Medical Decision Making Annual Meeting (Oct 2012).
  • Scotch M. Integrated Human-Animal Surveillance Systems for Emerging Threats to Health. Electronic Medical Records: How They Can Improve Animal Health conference (Nov 2010).

Service

  • Infection Genetics Evolution, Editorial Board (2014 - Present)
  • Influenza Research Database and Virus Pathogen Resource, Member, User Advisory Group (2014 - Present)
  • Infection, Genetics, and Evolution, Editorial Board (2013 - Present)
  • Influenza Research Database and Virus Pathogen Resource, Member, User Advisory Group (2013 - Present)
  • Biomedical Informatics Academic Program Committee, Member (2014 - 2014)
  • NIH/NLM Information Resource Grants to Reduce Health Disparities (G08), ZLM1 ZH-G 01, Reviewer (2014 - 2014)
  • Biomedical Informatics Admissions Committee, Chair (2014 - 2014)
  • NIH/NLM Special Emphasis Panel, ZLM1 ZH-C 01, Reviewer (2014 - 2014)
  • Biomedical Informatics Academic Program Committee, Member (2013 - 2013)
  • Biomedical Informatics Admissions Committee, Chair (2013 - 2013)
  • Biomedical Informatics Academic Program Committee, Member (2012 - 2012)
  • Biomedical Informatics Admissions Committee, Chair (2012 - 2012)
  • Biomedical Informatics Media Team, Member (2012 - 2012)
  • NIH/NLM Information Resource Grants to Reduce Health Disparities (G08), ZLM1 ZH-G 01, Reviewer (2012 - 2012)
  • NIH/NIAID, Bioinformatics Integration Support Contract (BISC), ZAI1-QV-I (C1), Reviewer (2012 - 2012)
  • Biomedical Informatics Admissions Committee, Chair (2011 - 2011)
  • American Medical Informatics Association, Public Health Informatics Working Group, Past Chair (2011 - 2011)
  • American Medical Informatics Association, Public Health Informatics Working Group, Chair (2009 - 2010)
  • American Medical Informatics Association, Student Working Group, Executive Committee, Member-at-Large (2008 - 2010)