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Daniel Weissman

Assistant Professor

Education

Affiliations

Bio

I build and analyze models of biological populations to predict their future evolution. Ultimately, we would like to understand evolution well enough that when, for example, a new antibiotic is developed, a reasonable number of experiments would be enough to learn how long it would take for bacteria to become resistant. This goal is just starting to become realistic due to rapid advances in sequencing technology. Now we need to solve a pair of theoretical problems in order to translate this sequence data into evolutionary predictions. First, we need to understand how to infer prevailing population dynamics from population genomic data — given a set of sequenced individuals, what can we learn about patterns of reproduction, migration, and adaptation in the population that they came from? Second, given these patterns, what do we expect the population to do in the future, and how can we test our predictions in scaled-down lab populations? A particular focus of my work on this second problem has been on understanding the likelihood and dynamics of complex adaptations whose benefits require combinations of multiple mutations.

Preferred Pronouns

He/him/his

Personal Academic Website

Research/Topics of Interest

Agent-based models
Antibiotic resistance
Between-host modeling
Forecasting
Geospatial models
Intra-host modeling
Mobility
New methods development
Phylogenetic models
Phylogenetics
Spatial transmission patterns
Statistical models
Time-series models
Zoonosis

Pathogens/Diseases of Main Interest/Expertise

Polio
Season influenza
Staphylococcus aureus

Countries of Work/Collaboration

United States

Projects

Papers

Allman B, Koelle K, Weissman D. (2022). Heterogeneity in viral populations increases the rate of deleterious mutation accumulation. Genetics

Min J, Gupta M, Desai MM, Weissman DB. (2022). Spatial structure alters the site frequency spectrum produced by hitchhiking. Genetics

Scherer EM, Babiker A, Adelman MW, Allman B, Key A, Kleinhenz JM, Langsjoen RM, Nguyen PV, Onyechi I, Sherman JD, Simon TW, Soloff H, Tarabay J, Varkey J, Webster AS, Weiskopf D, Weissman DB, Xu Y, Waggoner JJ, Koelle K, Rouphael N, Pouch SM, Piantadosi A. (2022). SARS-CoV-2 Evolution and Immune Escape in Immunocompromised Patients. The New England journal of medicine

Rybnikov S, Weissman DB, Hübner S, Korol AB. (2021). Fitness dependence preserves selection for recombination across diverse mixed mating strategies. Journal of theoretical biology

Ghafari M, Lumby CK, Weissman DB, Illingworth CJR. (2020). Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method. Journal of virology, 94(13)

Tusting LS, Bisanzio D, Alabaster G, Cameron E, Cibulskis R, Davies M, Flaxman S, Gibson HS, Knudsen J, Mbogo C, Okumu FO, von Seidlein L, Weiss DJ, Lindsay SW, Gething PW, Bhatt S. (2019). Mapping changes in housing in sub-Saharan Africa from 2000 to 2015. Nature, 568(7752)

Battle KE, Lucas TCD, Nguyen M, Howes RE, Nandi AK, Twohig KA, Pfeffer DA, Cameron E, Rao PC, Casey D, Gibson HS, Rozier JA, Dalrymple U, Keddie SH, Collins EL, Harris JR, Guerra CA, Thorn MP, Bisanzio D, Fullman N, Huynh CK, Kulikoff X, Kutz MJ, Lopez AD, Mokdad AH, Naghavi M, Nguyen G, Shackelford KA, Vos T, Wang H, Lim SS, Murray CJL, Price RN, Baird JK, Smith DL, Bhatt S, Weiss DJ, Hay SI, Gething PW. (2019). Mapping the global endemicity and clinical burden of Plasmodium vivax, 2000-17: a spatial and temporal modelling study. Lancet, 394(10195)

Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K. (2019). Correction for Sobel Leonard et al., "Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus". Journal of virology, 93(17)

Li ZT, Zarnitsyna VI, Lowen AC, Weissman D, Koelle K, Kohlmeier JE, Antia R. (2019). Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?. Journal of virology, 93(6)

Ghafari M, Weissman DB. (2019). The expected time to cross extended fitness plateaus. Theoretical population biology, (129)

Allman BE, Weissman DB. (2018). Hitchhiking in space: Ancestry in adapting, spatially extended populations. Evolution; international journal of organic evolution, 72(4)

Delarue M, Weissman D, Hallatschek O. (2017). A simple molecular mechanism explains multiple patterns of cell-size regulation. PloS one, 12(8)

Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K. (2017). Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus. Journal of virology, 91(14)

Weissman DB, Hallatschek O. (2017). Minimal-assumption inference from population-genomic data. eLife, (6)

Pigott DM, Millear AI, Earl L, Morozoff C, Han BA, Shearer FM, Weiss DJ, Brady OJ, Kraemer MU, Moyes CL, Bhatt S, Gething PW, Golding N, Hay SI. (2016). Updates to the zoonotic niche map of Ebola virus disease in Africa. eLife, (5)

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