By Dr Matthew Scotch

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

Pavia MJ; Amaro IF; Xu D; Gonzalez-Hernandez G; Scotch M, An LLM enabled real-time estimation of seasonal influenza vaccine effectiveness from social media data, http://dx.doi.org/10.64898/2026.08.28.26361670

Sneddon J; Ganji M; Scotch M, Computational Approaches for Influenza Reassortment Signal Inference in Environmental and Mixed Samples: Scoping Review (Preprint), http://dx.doi.org/10.2196/preprints.110311

Klein AZ; Weissenbacher D; O'Connor K; Elyaderani A; Amaro IF; Onishi T; Golder S; Spiegel K; Scotch M; Gonzalez-Hernandez G, Detection of patient metadata in published articles for genomic epidemiology using machine learning and large language models, http://dx.doi.org/10.1101/2025.04.25.25326298

Scotch M; Lauer K; Wieben ED; Cherukuri Y; Cunningham JM; Klee EW; Harrington JJ; Lau JS; McDonough SJ; Mutawe M; O’Horo JC; Rentmeester CE; Schlicher NR; White VT; Schneider SK; Vedell PT; Wang X; Yao JD; Pritt BS; Norgan AP, Genomic epidemiology reveals the dominance of Hennepin County in transmission of SARS-CoV-2 in Minnesota from 2020-2022, http://dx.doi.org/10.1101/2022.07.24.22277978

Fontenele RS; Kraberger S; Hadfield J; Driver EM; Bowes D; Holland LA; Faleye TOC; Adhikari S; Kumar R; Inchausti R; Holmes WK; Deitrick S; Brown P; Duty D; Smith T; Bhatnagar A; Yeager RA; Holm RH; von Reitzenstein NH; Wheeler E; Dixon K; Constantine T; Wilson MA; Lim ES; Jiang X; Halden RU; Scotch M; Varsani A, High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants, http://dx.doi.org/10.1101/2021.01.22.21250320

Faleye TOC; Skidmore P; Elyaderani A; Adhikari S; Kaiser N; Smith A; Yanez A; Perleberg T; Driver EM; Halden RU; Varsani A; Scotch M, Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology, http://dx.doi.org/10.1101/2022.09.25.22280344

Chung JR; Price AM; Zimmerman RK; Geffel KM; House SL; Curley T; Wernli KJ; Phillips CH; Martin ET; Vaughn IA; Murugan V; Scotch M; Saade EA; Faryar KA; Gaglani M; Ramm JD; Williams OL; Walter EB; Kirby M; Keong LM; Kondor R; Ellington SR; Flannery B; Investigators FVN, Influenza vaccine effectiveness against medically attended outpatient illness, United States, 2023–24 season, http://dx.doi.org/10.1101/2024.10.29.24316377

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, http://dx.doi.org/10.1101/2020.04.15.20066480

Xu D; García GL; O’Connor K; Holston H; Klein AZ; Amaro IF; Scotch M; Gonzalez-Hernandez G, Mining Social Media Data for Influenza Vaccine Effectiveness Using a Large Language Model and Chain-of-Thought Prompting, http://dx.doi.org/10.1101/2025.03.26.25324701

O’Connor K; Weissenbacher D; Elyaderani A; Lautenbach E; Scotch M; Gonzalez-Hernandez G, Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis, http://dx.doi.org/10.1101/2023.07.14.23292681

O'Connor K; Weissenbacher D; Elyaderani A; Lautenbach E; Scotch M; Gonzalez-Hernandez G, Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis (Preprint), http://dx.doi.org/10.2196/preprints.58567

Stone H; Jindal M; Lim S; Dawson R; Quigley A; Scotch M; MacIntyre CR, Potential Pathways of Spread of Highly Pathogenic Avian Influenza A/H5N1 Clade 2.3.4.4b Across Dairy Farms in the United States, http://dx.doi.org/10.1101/2024.05.02.24306785

Magge A; Weissenbacher D; O’Connor K; Scotch M; Gonzalez-Hernandez G, SEED: Symptom Extraction from English Social Media Posts using Deep Learning and Transfer Learning, http://dx.doi.org/10.1101/2021.02.09.21251454

Weissenbacher D; O’Connor K; Klein A; Golder S; Flores I; Elyaderani A; Scotch M; Gonzalez-Hernandez G, 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, http://dx.doi.org/10.1101/2023.07.29.23293370

Adam D; Chen X; Scotch M; MacIntyre CR; Dwyer D; Kok J, The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses among Paediatric Cases in Sydney, Australia., http://dx.doi.org/10.22541/au.160614561.14239652/v1

Bowes DA; Driver EM; Kraberger S; Fontenele RS; Holland LA; Wright J; Johnston B; Savic S; Newell ME; Adhikari S; Kumar R; Goetz H; Binsfeld A; Nessi K; Watkins P; Mahant A; Zevitz J; Deitrick S; Brown P; Dalton R; Garcia C; Inchausti R; Holmes W; Tian X-J; Varsani A; Lim ES; Scotch M; Halden RU, Unrestricted Online Sharing of High-frequency, High-resolution Data on SARS-CoV-2 in Wastewater to Inform the COVID-19 Public Health Response in Greater Tempe, Arizona, http://dx.doi.org/10.1101/2021.07.29.21261338

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