Publications

1. Meyer AG and Santillana M. (2026) In Review

   Interpretable sequence-based machine learning consolidates candidate Influenza H3N2 hemagglutinin antigenic sites. PNAS (submitted). Preprint at bioRxiv, 2026.

2. Meyer AG, Dewey G, Blasick S, Hovland C, and Santillana M. (2026) In Press

   Quantifying the protection gap: RSV activity outside the recommended RSV prophylaxis administration window. J Pediatric Infect Dis Soc (in press).

3. Meyer AG. (2026) In Press

   Explainable machine learning reveals evolutionary signals in Influenza hemagglutinin. J R Soc Interface (in press). Preprint at bioRxiv, 2026.

4. Garrido Garcia R, Clemente L, Meyer AG, Dewey G, Yang S, and Santillana M. (2026) In Press

   A prospective real-time early warning system to anticipate onsets and peaks of respiratory disease outbreaks at the state level in the US: a transfer learning approach leveraging digital traces. Nat Commun (in press).

5. Meyer AG, Blasick S, Yang S, and Santillana M. (2026) Published

   An introduction to machine learning for the pediatric hospitalist. Hosp Pediatr. 16:e2025008939.

6. Dewey G, Meyer AG, Garrido Garcia R, and Santillana M. (2026) Published

   Uncovering the post-pandemic timing of Influenza, RSV, and COVID-19 driving seasonal Influenza-like illness in the United States. Lancet Reg Health Am. 55:101359.

7. Wu S*, Meyer AG*, Clemente L, et al. (2025) Published

   Ensemble approaches for short-term Dengue fever forecasts: A global evaluation study. Proc Natl Acad Sci USA. 122:e2422335122.

   *equal contribution

8. Meyer AG, Lu F, Clemente L, and Santillana M. (2025) Published

   A prospective real-time transfer learning approach to estimate Influenza hospitalizations with limited data. Epidemics. 50:100816.

9. Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Bedford AJ, Hu J, Rosenfeld R, et al. (CDC FluSight Team) (2024) Published

   Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target: laboratory-confirmed influenza hospitalizations. Nat Commun. 15:6289.

10. Iyengar P, Meyer AG, Steadman E, Casale S, Kalsi AJ, Hale AJ, and Freed A. (2024) Published

    A predictive algorithm for discriminating myeloid malignancies and leukemoid reactions. Am J Med. 137:658–665.

11. Rajmohan RC, Anderson DO, Fang A, Meyer AG, Laengvejkal P, Julayanont P, Hannabas G, Linton J, Culberson J, Khan HMR, DeToledo P, Reddy H, and O'Boyle M. (2017) Published

    White matter deterioration may foreshadow impairment of emotional valence determination in early-stage dementia of the Alzheimer type. Front Aging Neurosci. 9:37.

12. Rajmohan RC, Anderson DO, Fang A, Meyer AG, Laengvejkal P, Julayanont P, Hannabas G, Linton J, Culberson J, Khan HMR, DeToledo P, Reddy H, and O'Boyle M. (2017) Published

    Lower activation in frontal cortex and posterior cingulate cortex observed during sex determination test in early-stage dementia of the Alzheimer type. Front Aging Neurosci. 9:156.

13. McWhite CD, Meyer AG, and Wilke CO. (2016) Published

    Serial passaging causes extensive positive selection in seasonal influenza A hemagglutinin. Virus Evol. 2:vew006.

14. Jack BR, Meyer AG, Echave J, and Wilke CO. (2016) Published

    Functional sites induce long-range evolutionary constraints in enzymes. PLOS Biol. 14:e1002452.

15. Meyer AG and Wilke CO. (2015) Published

    The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins. J R Soc Interface. 12:20150579.

16. Meyer AG and Wilke CO. (2015) Published

    Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin. PLOS Pathog. 11:e1004940.

17. Meyer AG, Spielman SJ, Bedford T, and Wilke CO. (2015) Published

    Time dependence of evolutionary metrics during the 2009 pandemic Influenzavirus outbreak. Virus Evol. 1:vev006.

18. Kerr SA, Jackson EL, Lungu OI, Meyer AG, Demogines A, Ellington A, Georgiou C, Wilke CO, and Sawyer SL. (2015) Published

    Computational and functional analysis of the GP1-TfR1 interface reveals host range trade-offs in New-World arenaviruses. J Virol. 89:11643–11653.

19. Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, and Marcotte EM. (2015) Published

    Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science. 348:921–925.

20. Meyer AG, Sawyer SL, Ellington AD, and Wilke CO. (2014) Published

    Analyzing Machupo virus-receptor binding by molecular dynamics simulations. PeerJ. 2:e266.

21. Sridhara V, Meyer AG, Ravikumar P, Barrick JE, Segre D, and Wilke CO. (2014) Published

    Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. PLOS ONE. 9:e114608.

22. Shahmoradi A, Sydykova DK, Spielman SJ, Jackson EL, Dawson ET, Meyer AG, and Wilke CO. (2014) Published

    Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. J Mol Evol. 79:130–142.

23. Fuson KL, Rice A, Mahling R, Snow A, Nayak PK, Meyer AG, Cooper ST, and Sutton RB. (2014) Published

    Alternate splicing of dysferlin C2A confers Ca²⁺-dependent and Ca²⁺-independent binding for membrane repair. Structure. 22:104–115.

24. Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, and Meyer AG. (2014) Published

    Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics. 15:1039.

25. Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, and Wilke CO. (2013) Published

    Maximum allowed solvent accessibilities of residues in proteins. PLOS ONE. 8:e80635.

26. Tien M, Sydykova DK, Meyer AG, and Wilke CO. (2013) Published

    A simple Python library to generate model peptides. PeerJ. 1:e80.

27. Meyer AG and Wilke CO. (2013) Published

    Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol. 30:36–44. Fast Tracked.

28. Meyer AG, Dawson ET, and Wilke CO. (2013) Published

    Cross-species comparison of site-specific evolutionary-rate variation in Influenza hemagglutinin. Phil Trans R Soc B. 368:20120334.

29. Scherrer MP, Meyer AG, and Wilke CO. (2012) Published

    Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol Biol. 12:179.

30. Reba A, Meyer AG, and Barrick J. (2012) Published

    Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. Artif Life. 13:473–480. Awarded Best Synthetic Biology Paper.

31. Celebi YG, Lichti RL, Bani-Salameh HN, Meyer AG, Carroll B, Vernon PJ, King PJ, and Cox SF. (2009) Published

    Muonium transitions in 4H silicon carbide. Physica B. 404:845–848.

32. Bani-Salameh HN, Meyer AG, Carroll RL, Lichti RL, Chow KH, Vernon PJ, King PJ, and Cox SF. (2007) Published

    Charge-state transitions of muonium in 6H silicon carbide. Physica B. 401–402:631–634.

Presentations & Lectures

Web Apps & Code Examples

Live App

Leukemoid.com

Web app for calculating risk of myeloid malignancy vs. leukemoid reaction.

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GitHub

Turtle Chat

AWS-based chatbot for analyzing PHI documents.

View Repository

GitHub

Ohio COVID-19 Dashboard

R Shiny app visualizing Ohio Department of Health data.

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GitHub

COVID-19 US State Tracker

R Shiny app visualizing COVID Tracking Project data.

View Repository

GitHub

Protein Evolution Toolbox

Python, C++, R tools for protein structure/sequence analysis.

View Repository

Live App

Compartmental Disease Models

R Shiny app demonstrating compartmental models (SIR, SEIR) for infectious disease outbreaks.

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Live App

Clinical Statistics Demo

R Shiny app demonstrating predictive values and other clinical statistics.

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Live App

PE Probability Calculator (Morning Report)

R Shiny app from a morning report, including calculators for PE probability (Wells', D-dimer, CT Angio).

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