2024.12.25 Journal Club
Presenter: Danqi
Article: Gao, Z., Moorjani, P., Sasani, T. A., Pedersen, B. S., Quinlan, A. R., Jorde, L. B., … & Przeworski, M. (2019). Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proceedings of the National Academy of Sciences, 116(19), 9491-9500.
2024.12.11 Journal Club
Presenter: Yutong
Article: Kim, S., Lieberman, T. D., & Kishony, R. (2014). Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance. Proceedings of the National Academy of Sciences, 111(40), 14494-14499.
2024.12.4 Journal Club
Presenter: Haichao
Article: Zhou, C., Wang, Y., Huang, Y., An, Y., Fu, X., Yang, D., … & Huang, W. (2024). The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging. Nature Communications, 15(1), 10139.
2024.11.27 Journal Club
Presenter: Shichun
Article: Rix, G., Williams, R. L., Hu, V. J., Spinner, A., Pisera, A., Marks, D. S., & Liu, C. C. (2024). Continuous evolution of user-defined genes at 1 million times the genomic mutation rate. Science, 386(6722), eadm9073.
2024.11.20 Journal Club
Presenter: Qian Yang
Article: Siddiq, M.A., Duveau, F. & Wittkopp, P.J. Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae. Nat Ecol Evol 8, 2184–2194 (2024).
2024.11.7 Journal Club
Presenter: Wu Kun
Article: Lu, Z., Mo, S., Xie, D., Zhai, X., Deng, S., Zhou, K., … & Hu, Z. (2024). Polyclonal-to-monoclonal transition in colorectal precancerous evolution. Nature, 1-8.
2024.10.31 Journal Club
Presenter: Haoxuan
Article: Joyce, W., He, K., Zhang, M., Ogunsola, S., Wu, X., Joseph, K. T., … & Campbell, K. L. (2024). Genetic excision of the regulatory cardiac troponin I extension in high–heart rate mammal clades. Science, 385(6716), 1466-1471.
2024.10.17 Journal Club
Presenter: Danyang
Article: Rodriguez, A., Diehl, J. D., Wright, G. S., Bonar, C. D., Lundgren, T. J., Moss, M. J., … & Clark, P. L. (2024). Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production. Proceedings of the National Academy of Sciences, 121(36), e2405510121.
2024.10.10 Journal Club
Presenter: Shukun
Article: Wu, Z., Waneka, G., Broz, A. K., King, C. R., & Sloan, D. B. (2020). MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Proceedings of the National Academy of Sciences, 117(28), 16448-16455.
2024.9.19 Journal Club
Presenter: Danqi
Article: Armakolas, A., & Klar, A. J. (2006). Cell type regulates selective segregation of mouse chromosome 7 DNA strands in mitosis. Science, 311(5764), 1146-1149.
2024.9.12 Journal Club
Presenter: Qian Yang
Article: Balogun, E. J., & Ness, R. W. (2024). The effects of de novo mutation on gene expression and the consequences for fitness in Chlamydomonas reinhardtii. Molecular Biology and Evolution, 41(3), msae035.
2024.9.5 Journal Club
Presenter: Haichao
Article: Berra Erkosar, Cindy Dupuis, Fanny Cavigliasso, Loriane Savary, Laurent Kremmer, Hector Gallart-Ayala, Julijana Ivanisevic, Tadeusz J Kawecki (2023) Evolutionary adaptation to juvenile malnutrition impacts adult metabolism and impairs adult fitness in Drosophila. eLife 12:e92465
2024.8.29 Journal Club
Presenter: Wu Kun
Article: Gordon, J. L., Byrne, K. P., & Wolfe, K. H. (2011). Mechanisms of chromosome number evolution in yeast. PLoS Genetics, 7(7), e1002190.
2024.8.22 Journal Club
Presenter: Haoxuan
Article: Timasheva, Y., Lepik, K., Liska, O., Papp, B., & Kutalik, Z. (2024). Widespread natural selection on metabolite levels in humans. Genome Research, 34(8), 1121-1129.
2024.7.25 Journal Club
Presenter: Danyang
Article: Huang, Z., Whelan, C. V., Foley, N. M., Jebb, D., Touzalin, F., Petit, E. J., … & Teeling, E. C. (2019). Longitudinal comparative transcriptomics reveals unique mechanisms underlying extended healthspan in bats. Nature Ecology & Evolution, 3(7), 1110-1120.
2024.7.18 Journal Club
Presenter: Qian Yang
Article: Weimann, A., Dinan, A. M., Ruis, C., Bernut, A., Pont, S., Brown, K., … & Floto, R. A. (2024). Evolution and host-specific adaptation of Pseudomonas aeruginosa. Science, 385(6704), eadi0908.
2024.7.11 Journal Club
Presenter: Shukun
Article: Peterson, A., Baskett, C., Ratcliff, W. C., & Burnetti, A. (2024). Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Current Biology, 34(3), 648-654.
2024.7.8 Journal Club
Presenter: Haichao
Article: Tengölics, R., Szappanos, B., Mülleder, M., Kalapis, D., Grézal, G., Sajben, C., … & Papp, B. (2024). The metabolic domestication syndrome of budding yeast. Proceedings of the National Academy of Sciences, 121(11), e2313354121.
2024.6.27 Journal Club
Presenter: Danqi
Article: Anderson, C. J., Talmane, L., Luft, J., Connelly, J., Nicholson, M. D., Verburg, J. C., … & Taylor, M. S. (2024). Strand-resolved mutagenicity of DNA damage and repair. Nature, 1-8.
2024.6.20 Journal Club
Presenter: Wu Kun
Article: Rudman, S. M., Greenblum, S. I., Rajpurohit, S., Betancourt, N. J., Hanna, J., Tilk, S., … & Schmidt, P. (2022). Direct observation of adaptive tracking on ecological time scales in Drosophila. Science, 375(6586), eabj7484.
2024.6.13 Journal Club
Presenter: Haoxuan
Article: Zhang, T., Tan, S., Tang, N., Li, Y., Zhang, C., Sun, J., … & Zhang, Y. E. (2024). Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox. Cell.
2024.6.6 Journal Club
Presenter: Liu Lei
Article: Puddu, F., Herzog, M., Selivanova, A., Wang, S., Zhu, J., Klein-Lavi, S., … & Jackson, S. P. (2019). Genome architecture and stability in the Saccharomyces cerevisiae knockout collection. Nature, 573(7774), 416-420.
2024.5.30 Journal Club
Presenter: Yiping
Article: Strauss, S. K., Liti, G., Dahan, O., & Pilpel, Y. (2024). Adaptive Mating Among Natural Strains of S. cerevisiae. bioRxiv, 2024-02.
2024.5.23 Journal Club
Presenter: Haichao
Article: Campbell-Staton, S. C., Velotta, J. P., & Winchell, K. M. (2021). Selection on adaptive and maladaptive gene expression plasticity during thermal adaptation to urban heat islands. Nature Communications, 12(1), 6195.
2024.5.16 Journal Club
Presenter: Qian Yang
Article: Field, Y., Fondufe-Mittendorf, Y., Moore, I. K., Mieczkowski, P., Kaplan, N., Lubling, Y., … & Segal, E. (2009). Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nature Genetics, 41(4), 438-445.
2024.4.25 Journal Club
Presenter: Shukun
Article: Bing, J., Guan, Z., Zheng, T., Ennis, C. L., Nobile, C. J., Chen, C., … & Huang, G. (2024). Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection. Nature Communications, 15(1), 2381.
2024.4.18 Journal Club
Presenter: Danqi
Article: Glass, D. S., Bren, A., Vaisbourd, E., Mayo, A., & Alon, U. (2024). A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover. Cell, 187(4), 931-944.
2024.4.11 Journal Club
Presenter: Wu Kun
Article: Fabre, M. A., de Almeida, J. G., Fiorillo, E., Mitchell, E., Damaskou, A., Rak, J., … & Vassiliou, G. S. (2022). The longitudinal dynamics and natural history of clonal haematopoiesis. Nature, 606(7913), 335-342.
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