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• Analysis for Li et. al., 2023: Li, Y, Arcos, S, Sabsay, K.R., te Velthuis, A.J.W., Lauring, A.S. Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein. https://doi.org/10.1101/2023.08.27.554986.

• Analysis for Arcos et. al., 2023: Arcos, S, Han, A.X., te Velthuis, A.J.W., Russell, C.A., Lauring, A.S. Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase. https://doi.org/10.1093/ve/vead037.

• Analysis for Bendall et. al., 2022: Bendall, E.E., Callear, A.P., Getz, A. et al. Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants. Nat Commun 14, 272 (2023). https://doi.org/10.1038/s41467-023-36001-5.

• Analysis for Bendall et. al., 2022: Bendall, E., Paz-Bailey, G., Santiago, G. A., Porucznik, C. A., Stanford, J. B., Stockwell, M. S., Duque, J., Jeddy, A., Veguilla, V., Major, C>, Rivera-Amill, V., Rolfes, M. A., Dawood, F. S., Lauring, A. S. (2022). SARS-CoV-2 genomic diversity in households highlights the challenges of sequence-based transmission inference. American Society for Microbiology - mSphere; doi: https://doi.org/10.1128/msphere.00400-22.

• Analysis for Valesano et. al., 2021: Valesano, A. L., Fitzsimmons, W. J., Blair, C. N., Woods, R. J., Gilbert, J., Rudnik, D., Mortenson, L., Friedrich, T. C., O'Connor, D. H., MacCannell, D. R., Petrie, J. G., Martin, E. T., & Lauring, A. S. (2021). SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community. Open forum infectious diseases, 8(11), ofab518. https://doi.org/10.1093/ofid/ofab518

• Analysis for Valesano et. al., 2021: Valesano, A. L., Rumfelt, K. E., Dimcheff, D. E., Blair, C. N., Fitzsimmons, W. J., Petrie, J. G., Martin, E. T., & Lauring, A. S. (2021). Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. PLoS pathogens, 17(4), e1009499. https://doi.org/10.1371/journal.ppat.1009499

• Analysis for Kaul et. al., 2021: Kaul, D. R., Valesano, A. L., Petrie, J. G., Sagana, R., Lyu, D., Lin, J., Stoneman, E., Smith, L. M., Lephart, P., & Lauring, A. S. (2021). Donor to recipient transmission of SARS-CoV-2 by lung transplantation despite negative donor upper respiratory tract testing. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 21(8), 2885–2889. https://doi.org/10.1111/ajt.16532

• Analysis for Baang et. al., 2021: Baang, J. H., Smith, C., Mirabelli, C., Valesano, A. L., Manthei, D. M., Bachman, M. A., Wobus, C. E., Adams, M., Washer, L., Martin, E. T., & Lauring, A. S. (2021). Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Replication in an Immunocompromised Patient. The Journal of infectious diseases, 223(1), 23–27. https://doi.org/10.1093/infdis/jiaa666

• Analysis for Valesano et. al., 2021: Valesano, A. L., Taniuchi, M., Fitzsimmons, W. J., Islam, M. O., Ahmed, T., Zaman, K., Haque, R., Wong, W., Famulare, M., & Lauring, A. S. (2021). The Early Evolution of Oral Poliovirus Vaccine Is Shaped by Strong Positive Selection and Tight Transmission Bottlenecks. Cell host & microbe, 29(1), 32–43.e4. https://doi.org/10.1016/j.chom.2020.10.011

• PRE-PRINT Analysis for McCrone et. al., 2020: The effective population size and mutation rate of influenza A virus in acutely infected individuals. John T. McCrone, Robert J. Woods, Arnold S. Monto, Emily T. Martin, Adam S. Lauring. bioRxiv 2020.10.24.353748; doi: https://doi.org/10.1101/2020.10.24.353748

• Analysis for Valesano et. al., 2020: Valesano, A. L., Fitzsimmons, W. J., McCrone, J. T., Petrie, J. G., Monto, A. S., Martin, E. T., & Lauring, A. S. (2020). Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts. Journal of virology, 94(5), e01710-19. https://doi.org/10.1128/JVI.01710-19

• Analysis for McCrone et. al., 2018: McCrone, J. T., Woods, R. J., Martin, E. T., Malosh, R. E., Monto, A. S., & Lauring, A. S. (2018). Stochastic processes constrain the within and between host evolution of influenza virus. eLife, 7, e35962. https://doi.org/10.7554/eLife.35962

• Analysis for Fitzsimmons et. al., 2018: Fitzsimmons, W. J., Woods, R. J., McCrone, J. T., Woodman, A., Arnold, J. J., Yennawar, M., Evans, R., Cameron, C. E., & Lauring, A. S. (2018). A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. PLoS biology, 16(6), e2006459. https://doi.org/10.1371/journal.pbio.2006459

• Figure Generation for Peck & Lauring, 2018: Peck, Kayla & Lauring, Adam. (2018). The complexities of viral mutation rates. Journal of virology. 92. 10.1128/JVI.01031-17.

• Analysis for Lyons et. al, 2017: Lyons, D. M., & Lauring, A. S. (2017). Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses. Molecular biology and evolution, 34(12), 3205–3215. https://doi.org/10.1093/molbev/msx251

• Analysis for Debbink et. al., 2017: Debbink, K., McCrone, J. T., Petrie, J. G., Truscon, R., Johnson, E., Mantlo, E. K., Monto, A. S., & Lauring, A. S. (2017). Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses. PLoS pathogens, 13(1), e1006194. https://doi.org/10.1371/journal.ppat.1006194

• Analysis for Visher et. al., 2016: Visher, E., Whitefield, S. E., McCrone, J. T., Fitzsimmons, W., & Lauring, A. S. (2016). The Mutational Robustness of Influenza A Virus. PLoS pathogens, 12(8), e1005856. https://doi.org/10.1371/journal.ppat.1005856

• Analysis for McCrone & Lauring, 2016: McCrone, J. T., & Lauring, A. S. (2016). Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling. Journal of virology, 90(15), 6884–6895. https://doi.org/10.1128/JVI.00667-16

• Variant Pipeline

• Codon Shuffle Package: Jorge D M M, Mills R E, Lauring A S, CodonShuffle: a tool for generating and analyzing synonymously mutated sequences. Virus Evolution, 2015, 1(1): vev012

• Post- Consensus Genome Creation Pipeline

• Using Slack for Alerts & Updates

• Report Generation & Visualization - SARS-CoV-2

• Displaying Zip Code and County Level SARS-CoV-2 Data

• Processing SARS-CoV-2 Data Post-Testing

• Validation Analysis for McCrone & Lauring, 2016: McCrone, J. T., & Lauring, A. S. (2016). Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling. Journal of virology, 90(15), 6884–6895. https://doi.org/10.1128/JVI.00667-16

• Exploring iSNV, Particularly Tranmission Pairs

• Assay Analysis - Illumina, Influenza A; Assay used in Pauly, M. D., Procario, M. C., & Lauring, A. S. (2017). A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. eLife, 6, e26437. https://doi.org/10.7554/eLife.26437