Publications
(*Equal contribution, ** mentee, T corresponding author, bolded names are members of the Weber Lab)
Abels, J. R.**T and J. N. Weber (2025). A call for phylogenetic context to understand geographic variation and host specificity in the parasitic copepod genus Salmincola. Parasitology, 1–13. https://doi.org/10.1017/S0031182025100954
Malinsky, M., Talbi, M., Zhou, C., Maurer, N., Sacco, S., Shapiro, B., Peichel, C. L., Seehausen, O., Salzburger, W., Weber, J. N., Bolnick, D. I., Green, R. E., & Durbin, R. (2025). Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing. Genetics, iyaf150. https://doi.org/10.1093/genetics/iyaf150
Fouilloux, C. A., Neeno-Eckwall, E., Srinivas, I., Compton, J. S., Sampson, J., Weber, J. N., Wolf, C.**, Hund, A. K., Berini, J., III, Alexander, H., Choi, E., Bolnick, D. I., & Hite, J. L. (2025). Needle in a haystack: A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations. Mol Ecol Res, e14131. https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.14131
Hu, J., Weber, J. N., Fuess, L. E., Steinel, N. C., Bolnick, D. I., & Wang, M. (2025). A spectral framework to map QTLs affecting joint differential networks of gene co-expression. PLoS Computational Biology, 21(4), e1012953.https://doi.org/10.1371/journal.pcbi.1012953
Hendry, A. P., Barrett, R. D. H., Bell, A. M., Bell, M. A., Bolnick, D. I., Gotanda, K. M., Haines, G. E., Lind, Å. J., Packer, M., Peichel, C. L., Peterson, C. R., Poore, H. A., Massengill, R. L., Milligan-McClellan, K., Steinel, N. C., Sanderson, S., Walsh, M. R., Weber, J. N., & Derry, A. M. (2024). Designing eco-evolutionary experiments for restoration projects: Opportunities and constraints revealed during stickleback introductions. Ecology and Evolution, 14(6), e11503. https://doi.org/10.1002/ece3.11503
Weber, J. N.T*, Kojima, W.*, Boisseau, R. P.*, Niimi, T., Morita, S., Shigenobu, S., Gotoh, H., Araya, K., Lin, C.-P., Thomas-Bulle, C., Allen, C. E., Tong, W., Lavine, L. C., Swanson, B. O., & Emlen, D. J.T (2023). Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus. Current Biology: CB, 33(20), 4285–4297.e5. https://doi.org/10.1016/j.cub.2023.08.066
Claar, D. C., Faiad, S. M., Mastick, N. C., Welicky, R. L., Williams, M. A., Sasser, K. T.**, Weber, J. N., & Wood, C. L. (2023). Estimating the magnitude and sensitivity of energy fluxes for stickleback hosts and Schistocephalus solidus parasites using the metabolic theory of ecology. Ecology and Evolution, 13(12), e10755. https://doi.org/10.1002/ece3.10755
Morita, S., Shibata, T. F., Nishiyama, T., Kobayashi, Y., Yamaguchi, K., Toga, K., Ohde, T., Gotoh, H., Kojima, T., Weber, J. N., Salvemini, M., Bino, T., Mase, M., Nakata, M., Mori, T., Mori, S., Cornette, R., Sakura, K., Lavine, L. C., … Shigenobu, S. (2023). The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation. Scientific Reports, 13(1), 8735.
Sasser, K**. and J.N. Weber. A call for more ecologically relevant studies of immune costs. (2022). Evolutionary Ecology. doi: 10.1007/s10682-022-10213-5
Weber, J.N.T,*, Steinel, N.C.T,*, Peng, F., Shim, K.C., Lohman, B.K., Fuess, L.E., Subramanian, S., De Lisle, S.P., Bolnick, D.I.T,* (2022) Evolutionary Gain and Loss of a Pathological Immune Response to Parasitism. Science 377 (6611): 1206–11. doi: 10.1126/science.abo3411
Bedford, N.L.*, Weber, J.N.*, Tong, W., Baier, F., Kam, A., Greenberg, R.A., & Hoekstra, H.E. (2022) Interspecific variation in cooperative burrowing behavior by Peromyscus mice. Evolution Letters. doi: 10.1002/evl3.293
Fuess, Lauren E., Jesse N. Weber, Stijn den Haan, Natalie C. Steinel, Kum Chuan Shim, and Daniel I. Bolnick. 2021. “Between-Population Differences in Constitutive and Infection-Induced Gene Expression in Threespine Stickleback.” Molecular Ecology 30 (24): 6791–6805. doi: 10.1111/mec.16197.
Lauren E Fuess, Stijn Den Haan, Fei Ling, Jesse N Weber, Natalie C Steinel, Daniel I Bolnick (2021). Immune gene expression covaries with gut microbiome composition in stickleback. mBio doi: 10.1128/mBio.00145-21.
Katie Hinde, Carlos Eduardo G. Amorim, Alyson F. Brokaw, Nicole Burt, Mary Casillas, Albert Chen, Tara Chestnut, Patrice K. Connors, Mauna Dasari, Connor Fox Ditelberg, Jeanne Dietrick, Josh Drew, Lara Durgavich, Brian Easterling, Charon Henning, Anne Hilborn, Elinor K. Karlsson, Marc Kissel, Jennifer Kobylecky, Jason Krell, Danielle N. Lee, Kate M Lesciotto, Kristi L. Lewton, Jessica E. Light, Jessica Martin, Asia Murphy, William Nickley, Alejandra Núñez-de la Mora, Olivia Pellicer, Valeria Pellicer, Anali Maughan Perry, Stephanie G. Schuttler, Anne C. Stone, Brian Tanis, Jesse N. Weber, Melissa Wilson, Emma Willcocks, Christopher N. Anderson (2021). March Mammal Madness and the power of narrative in science outreach. eLife 10:e65066. doi: 10.7554/eLife.65066
Ling, F., Steinel, N.C., Weber, J.N., Ma, L., Smith, C., Correa, D., Zhu, B., Bolnick, D.I. and G.Wang (2020). The gut microbiota response to helminth infection depends on host sex and genotype. The ISME Journal 14 (5), 1141-1153. doi: 10.1038/s41396-020-0589-3
Smith C.C., Weber J.N., Mikheyev A.S., Roces F., Bollazzi M., Kellner K., Seal J.N., and U.G. Mueller (2019). Landscape genomics of an obligate mutualism: Concordant and discordant population structures between the leafcutter ant Atta texana and its two main fungal symbiont types. Molecular Ecology. doi: 10.1111/mec.15111
Vasconcellos, M.M., Colli, G.R., Weber, J.N., Ortiz, E.O., Rodrigues, M.T., and D.C. Cannatella (2019). Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna. Molecular Ecology 28 (7): 1748–64. doi: 10.1111/mec.15045.
Weber, J.NT., Steinel, N.C., Shim, K.C. and D.I. Bolnick (2017). Recent evolution of extreme cestode growth suppression by a vertebrate host. PNAS 114: 6575–6580. doi: 10.1073/pnas.1620095114
Weber, J.NT., Kalbe, M., Shim, K.C., Erin, N.I., Steinel, N.C., Ma, L. and D.I. Bolnick (2017) Resist globally, infect locally: a trans-continental test of adaptation by stickleback and their tapeworm parasite. American Naturalist 189: 43-57. doi: 10.1086/689597
Weber, J.N., Bradburd, G.S., Stuart, Y.E., Stutz, W.E. and D.I. Bolnick (2017) Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback. Evolution 71: 342–356. doi: 10.1111/evo.13110
Lohman, B., N. Steinel, J.N. Weber and D.I. Bolnick (2017). Gene expression contributes to the recent evolution of host resistance in a model host parasite system.Frontiers in Immunology doi: 10.3389/fimmu.2017.01071
Stuart, Y.E., T. Veen, J.N. Weber, D. Hanson, M. Ravinet, B.K. Lohman, C.J. Thompson, T. Tasneem, A. Doggett, R. Izen, N. Ahmed, R.D.H. Barrett, A.P. Hendry, C.L. Peichel, and D.I. Bolnick. (2017). Contrasting effects of environment and genetics generate a continuum of parallel evolution.Nature Ecology and Evolution. 1:0158. doi: 10.1038/s41559-017-0158
Lohman, B.K., Weber, J.N. and D.I. Bolnick (2016). Evaluation of TagSeq, a reliable low-cost alternative for RNAseq. Molecular Ecology Resources. doi: 10.1111/1755-0998.12529
Puritz, J.B., Matz, M.V., Toonen, R.J., Weber, J.N., Bolnick, D.I. and C.E. Bird (2014). Comment:Demystifying the RAD fad. Molecular Ecology 23: 5937-5942. doi: 10.1111/mec.12965
Kowalko, J.E., Rohner, N., Rompani, S.B., Peterson, B.K., Linden, T.A., Yoshizawa, M., Kay, E.H.,Weber, J.N., Hoekstra, H.E., Jeffery, W.R., Borowsky, R. and C.J. Tabin (2013). Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms. Current Biology 23,1874-1883. doi: 10.1016/j.cub.2013.07.056
Weber, J.N., Peterson, B.K. and H.E. Hoekstra (2013). Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Nature 493: 402-405. doi: 10.1038/nature11816
Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S. and H.E. Hoekstra (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7: e37135. doi: 10.1371/journal.pone.0037135
Weber, J.N., Peters, M.B., Tsyusko, O.V., Linnen, C.R., Hagen, C., Schable, N.A., Tuberville, T.D., McKee, A.M., Lance, K.L., Fisher, H.S., Dewey, M.J., Hoekstra, H.E. and T.C. Glenn (2010). Five hundred microsatellite loci for Peromyscus. Conservation Genetics 11: 1243-1246. doi: 10.1007/s10592-009-9941-x
Weber, J.N.T and H.E. Hoekstra (2009). The evolution of burrowing behaviour in deer mice (genus Peromyscus). Animal Behaviour 77: 603-609. doi: 10.1016/j.anbehav.2008.10.031
Steiner, C.C., Weber, J.N. and H.E. Hoekstra (2007). Adaptive variation in beach mice caused by two interacting pigmentation genes. PLoS Biology 5: 1880-1889. doi: 10.1371/journal.pbio.0050219
Allen, D.L., Weber, J.N., Sycuro, L.K. and L.A. Leinwand (2005). Myocyte enhancer factor-2 and serum response factor binding elements regulate fast myosin heavy chain transcription in vivo. Journal of Biological Chemistry 280: 17126-17134. doi: 10.1074/jbc.M501207200