Matthew Scotch

Publications

• Use of structured and unstructured data to identify contraceptive use in women veterans.
• Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States
• Evolution of 2014/15 H3N2 influenza viruses circulating in US: Consequences for vaccine effectiveness and possible new pandemic
• Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter
• Phylogeography of swine influenza H3N2 in the United States: Translational public health for zoonotic disease surveillance
• Examining the differences in format and characteristics of zoonotic virus surveillance data on state agency websites
• Using value of information to guide evaluation of decision supports for differential diagnosis: Is it time for a new look?
• Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020
• The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
• Pan-Enterovirus Amplicon-Based High-Throughput Sequencing Detects the Complete Capsid of a EVA71 Genotype C1 Variant via Wastewater-Based Epidemiology in Arizona
• High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants.
• Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography.
• Coding-Complete Genome Sequence of a Human Respirovirus 1 Strain from a Clinical Sample in Arizona.
• Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes.
• A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks.
• Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research.
• Patterns and Disparities in Human Papillomavirus (HPV) Vaccine Uptake for Young Female Adolescents among U.S. States: NIS-Teen (2008-2016).
• An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020).
• Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus.
• Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting.
• The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses Among Paediatric Cases in Sydney, Australia.
• From bad to worse: airline boarding changes in response to COVID-19.
• GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography.
• Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty.
• Identifying current and emerging resources and tools utilized for detection, prediction, and visualization of viral zoonotic disease clusters: a Delphi study.
• Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants.
• Avian influenza virus ecology and evolution through a climatic lens.
• Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature.
• U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids.
• Phylogeography of H5N1 avian influenza virus in Indonesia.
• Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis.
• The effects of random taxa sampling schemes in Bayesian virus phylogeography.
• Deep neural networks and distant supervision for geographic location mention extraction.
• The Effects of Sampling Location and Predictor Point Estimate Certainty on Posterior Support in Bayesian Phylogeographic Generalized Linear Models.
• Converging and emerging threats to health security.
• Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods.
• Does influenza pandemic preparedness and mitigation require gain-of-function research?
• Multiscale model for pedestrian and infection dynamics during air travel.
• Conceptualizing a Novel Quasi-Continuous Bayesian Phylogeographic Framework for Spatiotemporal Hypothesis Testing.
• Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
• A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.
• Analyses of Merging Clinical and Viral Genetic Data for Influenza Surveillance.
• Analysis of Viral Genetics for Estimating Diffusion of Influenza A H6N1.
• Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses.
• Generalized linear models for identifying predictors of the evolutionary diffusion of viruses.
• Comparison of ARIMA and Random Forest time series models for prediction of avian influenza H5N1 outbreaks
• Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt
• Knowledge-driven geospatial location resolution for phylogeographic models of virus migration
• In silico analysis suggests interaction between Ebola virus and the extracellular matrix
• Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion
• SOVAT: Spatial OLAP visualization and analysis tool
• The sublanguage of cross-coverage.
• Rural residence is associated with delayed care entry and increased mortality among veterans with human immunodeficiency virus infection
• Comparison of Human and Animal Surveillance Data for H5N1 Influenza A in Egypt 2006-2011
• A Qualitative Study of State-Level Zoonotic Disease Surveillance in New England
• HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0
• Web GIS in practice VI: A demo playlist of geo-mashups for public health neogeographers
• Linkages between animal and human health sentinel data
• The Yale cTAKES extensions for document classification: Architecture and application
• Evaluation of SOVAT: An OLAP-GIS decision support system for community health assessment data analysis
• Development of SOVAT: A numerical-spatial decision support system for community health assessment research
• Development of grid-like applications for public health using Web 2.0 mashup techniques.
• Human and animal sentinels for shared health risks.
• Usability Evaluation of the Spatial OLAP Visualization and Analysis Tool (SOVAT).
• Risk factors for human infection with West Nile Virus in Connecticut: A multi-year analysis
• Animals as sentinels: Using comparative medicine to move beyond the laboratory
• A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records.
• Enhancing phylogeography by improving geographical information from GenBank
• Biomedical informatics techniques for processing and analyzing Web blogs of military service members
• Human vs. animal outbreaks of the 2009 swine-origin H1N1 influenza A epidemic
• Use of statistical analysis in the biomedical informatics literature
• At the intersection of public-health informatics and bioinformatics: Using advanced Web technologies for phylogeography
• Spatial and multidimensional visualization of Indonesia's village health statistics
• State-level zoonotic disease surveillance in the United States
• Exploring the role of GIS during community health assessment problem solving: Experiences of public health professionals
• Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations
• Correction to: A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks
• Genomic epidemiology reveals the dominance of Hennepin County in transmission of SARS-CoV-2 in Minnesota from 2020-2022
• GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records
• SEED: Symptom Extraction from English Social Media Posts using Deep Learning and Transfer Learning
• Identifying mitigation strategies for COVID-19 superspreading on flights using models that account for passenger movement
• Genome Sequences of Anelloviruses, Genomovirus, and Papillomavirus Isolated from Nasal Pharyngeal Swabs
• Complete Coding Sequences of Rhinovirus Types A46, A39, C56, and C48
• Rhizobium Phage-Like Microvirus Genome Sequence Identified in Wastewater in Arizona, USA, in November 2020 Encodes an Endolysin and a Putative Multiheme Cytochrome c -like Protein
• Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis
• Foundational Domains and Competencies for Baccalaureate Health Informatics Education
• Text mining biomedical literature to identify extremely unbalanced data for digital epidemiology and systematic reviews: dataset and methods for a SARS-CoV-2 genomic epidemiology study
• Foundational domains and competencies for baccalaureate health informatics education
• Canine Parvovirus 2C Identified in Dog Feces from Poop Bags Collected from Outdoor Waste Bins in Arizona USA, June 2022
• Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022
• Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high‐throughput whole genome sequencing