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Publications
Open access to ‘The Origins of Cellular Architecture’
We have taken on one of the last uncharted fields in evolution: integrating evolutionary biology with cell biology. This sequel to The Origins of Genome Architecture brings evolutionary theory to bear on a diversity of observations on the functional and structural features of cells.
Explore our other publications
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2024
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.
https://doi.org/10.1002/yea.3927.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.
https://doi.org/10.1186/s12915-024-01824-1.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.
https://doi.org/10.1091/mbc.E23-11-0418.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.
https://doi.org/10.7554/eLife.94144.1.Research article.
2023
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).
https://doi.org/10.1073/pnas.2210038120.Research article.
Devi, A., Speyer, G., & Lynch, M. (2023). The divergence of mean phenotypes under persistent directional selection. Genetics, 224(3), iyad091.
https://doi.org/10.1093/genetics/iyad091.Research article.
Geiler-Samerotte, K., & Lang, G. I. (2023). Best Practices in Microbial Experimental Evolution. Journal of Molecular Evolution, 91(3), 237-240.
https://doi.org/10.1007/s00239-023-10119-y.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.
https://doi.org/10.1093/molbev/msad107.Research article.
Hoelzel, A. R., & Lynch, M. (2023). The raw material of evolution. Science, 381(6661), 942-943.
https://doi.org/10.1126/science.adk0121.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.
https://doi.org/10.1007/s00239-023-10114-3.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.
https://doi.org/10.1093/g3journal/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.
https://doi.org/10.1101%2F2023.10.03.560745.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.
https://doi.org/10.1101/2023.05.02.538944.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.
https://doi.org/10.1146/annurev-genet-071819-104035.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.
https://doi.org/10.1073/pnas.2306741120.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.
https://doi.org/10.15252/embr.202357561.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.
https://doi.org/10.1128/mbio.00302-23.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.
https://doi.org/10.1038/s41586-023-06288-x.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.
https://doi.org/10.1007/s42995-023-00182-1.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.
https://doi.org/10.3389/fgene.2023.1198203.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.
https://doi.org/10.1177/25152564221150428.Research article.
Sinha, S. D., & Wideman, J. G. (2023). The persistent homology of mitochondrial ATP synthases. Iscience, 26(5).
https://doi.org/10.1016/ j.isci.2023.106700.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.
https://doi.org/10.1007/s10539-023-09933-x.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.
https://doi.org/10.1209/0295-5075/acd65b.Research article.
2022
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).
https://doi.org/10.1093/g3journal/jkac303.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).
https://doi.org/10.1111/jeu.12934.Review article.
Lynch, M., Trickovic, B., & Kempes, C. P. (2022). Evolutionary scaling of maximum growth rate with organism size. Scientific Reports, 12(1).
https://doi.org/10.1038/s41598-022-23626-7.Journal article.
Schavemaker, P. E., & Lynch, M. (2022). Flagellar energy costs across the Tree of Life. eLife, 11.
https://doi.org/10.7554/eLife.77266.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.
https://doi.org/10.1016/j.gde.2022.101951.Research article.
Frasch, W. D., Bukhari, Z. A., & Yanagisawa, S. (2022). F1FO ATP synthase molecular motor mechanisms. Frontiers in microbiology, 13, 965620.
https://doi.org/10.3389/fmicb.2022.965620.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.
https://doi.org/10.1093/icb/icac136.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.
https://doi.org/10.1371/journal.pbio.3001669.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.
https://doi.org/10.1093/molbev/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.
https://doi.org/10.1038/s41598-022-23626-7.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.
https://doi.org/10.1093/molbev/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.
https://doi.org/10.24072/pcjournal.173.Research article.
2021
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.
https://doi.org/10.7554/eLife.70016.Research article.