Brettner, L., Eder, R., Schmidlin, K., & Geiler‐Samerotte, K. (2024). An ultra high‐throughput, massively multiplexable, single‐cell RNA‐seq platform in yeasts. Yeast, 41(4), 242-255.

Research article.

Butenko, A., Lukeš, J., Speijer, D., & Wideman, J. G. (2024). Mitochondrial genomes revisited: why do different lineages retain different genes?. BMC biology, 22(1), 15.

Research article.

Padilla, L. F. A., Murray, J. M., & Hu, K. (2024). The initiation and early development of the tubulin-containing cytoskeleton in the human parasite Toxoplasma gondii. Molecular Biology of the Cell, 35(3), ar37.

Research article.

Schmidlin, Apodaca, Newell, Sastokas, & Kinsler. (2024). Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs across hundreds of fluconazole-resistant yeast strains. eLife, 13, RP94144.

Research article.

Chung, C., Verheijen, B. M., Zhang, X., Huang, B., Coakley, A., McGann, E., Wade, E., Dinep-Schneider, O., LaGosh, J., Anagnostou, M.-E., Simpson, S., Thomas, K., Ernst, M., Rattray, A., Lynch, M., Kashlev, M., Benayoun, B. A., Li, Z., Strathern, J., … Vermulst, M. (2023). The fidelity of transcription in human cells. Proceedings of the National Academy of Sciences, 120(5).

Research article.

Devi, A., Speyer, G., & Lynch, M. (2023). The divergence of mean phenotypes under persistent directional selection. Genetics, 224(3), iyad091.

Research article.

Geiler-Samerotte, K., & Lang, G. I. (2023). Best Practices in Microbial Experimental Evolution. Journal of Molecular Evolution, 91(3), 237-240.

Research article.

Gout, J. F., Hao, Y., Johri, P., Arnaiz, O., Doak, T. G., Bhullar, S., … & Lynch, M. (2023). Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex. Molecular biology and evolution, 40(5), msad107.

Research article.

Hoelzel, A. R., & Lynch, M. (2023). The raw material of evolution. Science, 381(6661), 942-943.

Research article.

Kinsler, G., Schmidlin, K., Newell, D., Eder, R., Apodaca, S., Lam, G., … & Geiler-Samerotte, K. (2023). Extreme sensitivity of fitness to environmental conditions: Lessons from# 1BigBatch. Journal of Molecular Evolution, 91(3), 293-310.

Research article.

Kucukyildirim, S., Ozdemirel, H. O., & Lynch, M. (2023). Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea. G3: Genes, Genomes, Genetics, 13(3), jkac303.

Research article.

Kumar, A., Gok, M. O., Nguyen, K. N., Reese, M. L., Wideman, J. G., Muñoz-Gómez, S. A., & Friedman, J. R. (2023). A DRP-like pseudoenzyme coordinates with MICOS to promote cristae architecture. bioRxiv.

Research article.

Li, W., Baehr, S., Marasco, M., Reyes, L., Brister, D., Pikaard, C. S., … & Lynch, M. (2023). A Narrow Range of Transcript-error Rates Across the Tree of Life. bioRxiv, 2023-05.

Research article.

Long, H., Johri, P., Gout, J. F., Ni, J., Hao, Y., Licknack, T., … & Lynch, M. (2023). Paramecium Genetics, Genomics, and Evolution. Annual review of genetics, 57, 391-410.

Research article.

Lynch M. (2023). Mutation pressure, drift, and the pace of molecular coevolution. Proceedings of the National Academy of Sciences of the United States of America, 120(27), e2306741120.

Research article.

Lynch, M., Ali, F., Lin, T., Wang, Y., Ni, J., & Long, H. (2023). The divergence of mutation rates and spectra across the Tree of Life. EMBO reports, 24(10), e57561.

Research article.

Macher, J. N., Coots, N. L., Poh, Y. P., Girard, E. B., Langerak, A., Muñoz-Gómez, S. A., … & Wideman, J. G. (2023). Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria). Mbio, 14(2), e00302-23.

Research article.

Moger-Reischer, R. Z., Glass, J. I., Wise, K. S., Sun, L., Bittencourt, D. D. C., Lehmkuhl, B. K., … & Lennon, J. T. (2023). Evolution of a minimal cell. Nature, 620(7972), 122-127.

Research article.

Ni, J., Pan, J., Wang, Y., Chen, T., Feng, X., Li, Y., … & Li, W. (2023). An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. Marine Life Science & Technology, 5(4), 564-572.

Research article.

Quan, N., Eguchi, Y., & Geiler-Samerotte, K. (2023). Intra-FCY1: a novel system to identify mutations that cause protein misfolding. Frontiers in Genetics, 14, 1198203.

Research article.

Singh, R. P., Poh, Y. P., Sinha, S. D., & Wideman, J. G. (2023). Evolutionary History of Oxysterol-Binding Proteins Reveals Complex History of Duplication and Loss in Animals and Fungi. Contact, 6, 25152564221150428.

Research article.

Sinha, S. D., & Wideman, J. G. (2023). The persistent homology of mitochondrial ATP synthases. Iscience, 26(5).

Research article.

Sterner, B., Elliott, S., & Wideman, J. G. (2023). An account of conserved functions and how biologists use them to integrate cell and evolutionary biology. Biology & Philosophy, 38(5), 45.

Research article.

Suvorov, V., Saakian, D. B., & Lynch, M. (2023). A solution of the Crow-Kimura evolution model on fluctuating fitness landscape. Europhysics Letters, 142(5), 57003.

Research article.

Kucukyildirim, S., Ozdemirel, H. O., & Lynch, M. (2022). Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea. G3 Genes|Genomes|Genetics, 13(3).

Journal article.

Lynch, M., Schavemaker, P. E., Licknack, T. J., Hao, Y., & Pezzano, A. (2022). Evolutionary Bioenergetics of ciliates. Journal of Eukaryotic Microbiology, 69(5).

Review article.

Lynch, M., Trickovic, B., & Kempes, C. P. (2022). Evolutionary scaling of maximum growth rate with organism size. Scientific Reports, 12(1).

Journal article.

Schavemaker, P. E., & Lynch, M. (2022). Flagellar energy costs across the Tree of Life. eLife, 11.

Research article.

Brettner, L., Ho, W. C., Schmidlin, K., Apodaca, S., Eder, R., & Geiler-Samerotte, K. (2022). Challenges and potential solutions for studying the genetic and phenotypic architecture of adaptation in microbes. Current opinion in genetics & development, 75, 101951.

Research article.

Frasch, W. D., Bukhari, Z. A., & Yanagisawa, S. (2022). F1FO ATP synthase molecular motor mechanisms. Frontiers in microbiology, 13, 965620.

Research article.

Harrison, J. F., Biewener, A., Bernhardt, J. R., Burger, J. R., Brown, J. H., Coto, Z. N., … & Williams, T. M. (2022). White paper: an integrated perspective on the causes of hypometric metabolic scaling in animals. Integrative and Comparative Biology, 62(5), 1395-1418.

Research article.

Johri, P., Aquadro, C. F., Beaumont, M., Charlesworth, B., Excoffier, L., Eyre-Walker, A., … & Jensen, J. D. (2022). Recommendations for improving statistical inference in population genomics. PLoS biology, 20(5), e3001669.

Research article.

Johri, P., Gout, J. F., Doak, T. G., & Lynch, M. (2022). A population-genetic lens into the process of gene loss following whole-genome duplication. Molecular biology and evolution, 39(6), msac118.

Research article.

Lynch, M., Trickovic, B., & Kempes, C. P. (2022). Evolutionary scaling of maximum growth rate with organism size. Scientific reports, 12(1), 22586.

Research article.

Pan, J., Li, W., Ni, J., Wu, K., Konigsberg, I., Rivera, C. E., … & Long, H. (2022). Rates of mutations and transcript errors in the foodborne pathogen Salmonella enterica subsp. enterica. Molecular biology and evolution, 39(4), msac081.

Research article.

Richter, D. J., Berney, C., Strassert, J. F., Poh, Y. P., Herman, E. K., Muñoz-Gómez, S. A., … & de Vargas, C. (2022). EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community Journal, 2.

Research article.

Yanagisawa, S., & Frasch, W. D. (2021). pH-dependent 11 F1FO ATP synthase sub-steps reveal insight into the FO torque generating mechanism. Elife, 10, e70016.

Research article.