2024.4.7 Journal Club
Presenter: Haoxuan
Article: Ellis, S., Franks, D. W., Nielsen, M. L. K., Weiss, M. N., & Croft, D. P. (2024). The evolution of menopause in toothed whales. Nature, 1-7.
2024.3.28 Journal Club
Presenter: Liu Lei
Article: Freeland, S. J., & Hurst, L. D. (1998). The genetic code is one in a million. Journal of molecular evolution, 47, 238-248.
2024.3.21 Journal Club
Presenter: Yiping
Article: Serrano, I. M., Hirose, M., Valentine, C. C., Roesner, S., Schmidt, E., Pratt, G., … & Sudmant, P. H. (2024). Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing. Nature Ecology & Evolution, 1-14.
2024.3.14 Journal Club
Presenter: Zhixuan
Article: Li, R., Di, L., Li, J., Fan, W., Liu, Y., Guo, W., … & Wu, C. (2021). A body map of somatic mutagenesis in morphologically normal human tissues. Nature, 597 (7876), 398-403.
2024.3.7 Journal Club
Presenter: Qian Yang
Article: Abreu, C. I., Mathur, S., & Petrov, D. A. (2023). Strong environmental memory revealed by experimental evolution in static and fluctuating environments. bioRxiv.
2024.2.29 Journal Club
Presenter: Danyang
Article: Ölmez, T. T., Moreno, D. F., Liu, P., Johnson, Z. M., McGinnis, M. M., Tu, B. P., … & Acar, M. (2023). Sis2 regulates yeast replicative lifespan in a dose-dependent manner. Nature communications, 14 (1), 7719.
2024.2.22 Journal Club
Presenter: Shukun
Article: Nguyen, A. N., Gorrell, R., Kwok, T., Connallon, T., & McDonald, M. J. (2024). Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori. Nature Ecology & Evolution, 1-10.
2024.1.25 Journal Club
Presenter: Danqi
Article: Hinch, R., Donnelly, P., & Hinch, A. G. (2023). Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science, 382(6674), eadh2531.
2024.1.18 Journal Club
Presenter: Qian Yang
Articles: Song, S., & Zhang, J. (2024). Genetic variants underlying human bisexual behavior are reproductively advantageous. Science Advances, 10 (1), eadj6958.
Long, E., & Zhang, J. (2023). Evidence for the role of selection for reproductively advantageous alleles in human aging. Science Advances, 9 (49), eadh4990.
2024.1.11 Journal Club
Presenter: Haoxuan
Article: Vlková, M., & Silander, O. K. (2022). Gene regulation in Escherichia coli is commonly selected for both high plasticity and low noise. Nature Ecology & Evolution, 6 (8), 1165-1179.
2023.12.25 Journal Club
Presenter: Qian Yang
Article: Ng, A. W., Poon, S. L., Huang, M. N., Lim, J. Q., Boot, A., Yu, W., … & Rozen, S. G. (2017). Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia. Science translational medicine, 9 (412), eaan6446.
2023.12.15 Journal Club
Presenter: Shukun
Article: Jiang, P., Ollodart, A. R., Sudhesh, V., Herr, A. J., Dunham, M. J., & Harris, K. (2021). A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae. elife, 10, e68285.
2023.12.8 Journal Club
Presenter: Danyang
Article: Wei, W., Ho, W. C., Behringer, M. G., Miller, S. F., Bcharah, G., & Lynch, M. (2022). Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges. Nature communications, 13 (1), 4752.
2023.12.1 Journal Club
Presenter: Wu Kun
Article: Gao, H., Hamp, T., Ede, J., Schraiber, J. G., McRae, J., Singer-Berk, M., … & Farh, K. K. H. (2023). The landscape of tolerated genetic variation in humans and primates. Science, 380 (6648), eabn8153.
2023.11.25 Journal Club
Presenter: Danqi
Article: Witt, E., Langer, C. B., Svetec, N., & Zhao, L. (2023). Transcriptional and mutational signatures of the Drosophila ageing germline. Nature ecology & evolution, 7(3), 440-449.
2023.11.10 Journal Club
Presenter: Haoxuan
Article: Aguirre, L., Hendelman, A., Hutton, S. F., McCandlish, D. M., & Lippman, Z. B. (2023). Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382(6668), 315-320.
2023.11.3 Journal Club
Presenter: Yiping
Article: Xia, B., Zhang, W., Wudzinska, A., Huang, E., Brosh, R., Pour, M., … & Yanai, I. (2021). The genetic basis of tail-loss evolution in humans and apes. BioRxiv, 2021-09.
2023.10.26 Journal Club
Presenter: Zhixuan
Article: Keren, L., Hausser, J., Lotan-Pompan, M., Slutskin, I. V., Alisar, H., Kaminski, S., … & Segal, E. (2016). Massively parallel interrogation of the effects of gene expression levels on fitness. Cell, 166(5), 1282-1294.
2023.10.20 Journal Club
Presenter: QianYang
Article: Vaishnav, E. D., de Boer, C. G., Molinet, J., Yassour, M., Fan, L., Adiconis, X., … & Regev, A. (2022). The evolution, evolvability and engineering of gene regulatory DNA. Nature, 603(7901), 455-463.
2023.10.12 Journal Club
Presenter: Danyang
Article: Moore, L., Cagan, A., Coorens, T. H., Neville, M. D., Sanghvi, R., Sanders, M. A., … & Rahbari, R. (2021). The mutational landscape of human somatic and germline cells. Nature, 597(7876), 381-386.Karlsson, K., Przybilla, M. J., Kotler, E., Khan, A., Xu, H., Karagyozova, K., … & Curtis, C. (2023). Deterministic evolution and stringent selection during preneoplasia. Nature, 1-11.
2023.9.21 Journal Club
Presenter: Shukun
Article: Moore, L., Cagan, A., Coorens, T. H., Neville, M. D., Sanghvi, R., Sanders, M. A., … & Rahbari, R. (2021). The mutational landscape of human somatic and germline cells. Nature, 597(7876), 381-386.
2023.9.15 Journal Club
Presenter: Danqi
Article: Cagan, A., Baez-Ortega, A., Brzozowska, N., Abascal, F., Coorens, T. H., Sanders, M. A., … & Martincorena, I. (2022). Somatic mutation rates scale with lifespan across mammals. Nature, 604(7906), 517-524.
2023.8.31 Journal Club
Presenter: Haoxuan
Article: Nalabothu, R. L., Fisher, K. J., LaBella, A. L., Meyer, T. A., Opulente, D. A., Wolters, J. F., … & Hittinger, C. T. (2023). Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Molecular Biology and Evolution, msad111.
2023.8.17 Journal Club
Presenter: Shukun
Article: Farkas, Z., Kovács, K., Sarkadi, Z., Kalapis, D., Fekete, G., Birtyik, F., … & Papp, B. (2022). Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast. Nature Ecology & Evolution, 6(6), 763-773.
2023.8.24 Journal Club
Presenter: QianYang
Article: Russo, M., Crisafulli, G., Sogari, A., Reilly, N. M., Arena, S., Lamba, S., … & Bardelli, A. (2019). Adaptive mutability of colorectal cancers in response to targeted therapies. Science, 366(6472), 1473-1480.
2023.8.10 Journal Club
Presenter: Danyang
Article: Guillemet, M., Chabas, H., Nicot, A., Gatchich, F., Ortega-Abboud, E., Buus, C., … & Gandon, S. (2022). Competition and coevolution drive the evolution and the diversification of CRISPR immunity. Nature Ecology & Evolution, 6(10), 1480-1488.
2023.8.3 Journal Club
Presenter: Danqi
Article: Venkataram, S., Kuo, H. Y., Hom, E. F., & Kryazhimskiy, S. (2023). Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community. Nature Ecology & Evolution, 7(1), 143-154.
2023.7.27 Journal Club
Presenter: Haoxuan
Article: Zhai, Y., Pribis, J. P., Dooling, S. W., Garcia-Villada, L., Minnick, P. J., Xia, J., … & Rosenberg, S. M. (2023). Drugging evolution of antibiotic resistance at a regulatory network hub. Science Advances, 9(25), eadg0188.
2023.7.21 Journal Club
Presenter: Shukun
Article: Rolland, J., Henao-Diaz, L. F., Doebeli, M., Germain, R., Harmon, L. J., Knowles, L. L., … & Schluter, D. (2023). Conceptual and empirical bridges between micro-and macroevolution. Nature Ecology & Evolution, 1-13.
2023.6.23 Journal Club
Presenter: Danqi
Article: Bozdag, G. O., Zamani-Dahaj, S. A., Day, T. C., Kahn, P. C., Burnetti, A. J., Lac, D. T., … & Ratcliff, W. C. (2023). De novo evolution of macroscopic multicellularity. Nature, 1-8.
2023.6.16 Journal Club
Presenter: Haoxuan
Article: Nam, C. H., Youk, J., Kim, J. Y., Lim, J., Park, J. W., Oh, S. A., … & Ju, Y. S. (2023). Widespread somatic L1 retrotransposition in normal colorectal epithelium. Nature, 1-8.
2023.8.17 Journal Club
Presenter: Shukun
Article: Farkas, Z., Kovács, K., Sarkadi, Z., Kalapis, D., Fekete, G., Birtyik, F., … & Papp, B. (2022). Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast. Nature Ecology & Evolution, 6(6), 763-773.
2023.8.10 Journal Club
Presenter: Danyang
Article: Guillemet, M., Chabas, H., Nicot, A., Gatchich, F., Ortega-Abboud, E., Buus, C., … & Gandon, S. (2022). Competition and coevolution drive the evolution and the diversification of CRISPR immunity. Nature Ecology & Evolution, 6(10), 1480-1488.
2023.8.3 Journal Club
Presenter: Danqi
Article: Venkataram, S., Kuo, H. Y., Hom, E. F., & Kryazhimskiy, S. (2023). Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community. Nature Ecology & Evolution, 7(1), 143-154.
2023.7.27 Journal Club
Presenter: Haoxuan
Article: Zhai, Y., Pribis, J. P., Dooling, S. W., Garcia-Villada, L., Minnick, P. J., Xia, J., … & Rosenberg, S. M. (2023). Drugging evolution of antibiotic resistance at a regulatory network hub. Science Advances, 9(25), eadg0188.
2023.7.21 Journal Club
Presenter: Shukun
Article: Rolland, J., Henao-Diaz, L. F., Doebeli, M., Germain, R., Harmon, L. J., Knowles, L. L., … & Schluter, D. (2023). Conceptual and empirical bridges between micro-and macroevolution. Nature Ecology & Evolution, 1-13.
2023.6.23 Journal Club
Presenter: Danqi
Article: Bozdag, G. O., Zamani-Dahaj, S. A., Day, T. C., Kahn, P. C., Burnetti, A. J., Lac, D. T., … & Ratcliff, W. C. (2023). De novo evolution of macroscopic multicellularity. Nature, 1-8.
2023.6.16 Journal Club
Presenter: Haoxuan
Article: Nam, C. H., Youk, J., Kim, J. Y., Lim, J., Park, J. W., Oh, S. A., … & Ju, Y. S. (2023). Widespread somatic L1 retrotransposition in normal colorectal epithelium. Nature, 1-8.
2022.10.19 Start up of the Liu Lab