2026.6.15 Journal Club
Presenter: Chen lab
Article: Ravasio, R., Husain, K., Evans, C. G., Phillips, R., Ribezzi-Crivellari, M., Szostak, J. W., & Murugan, A. (2026). Evolution of error correction through a need for speed. Science, 391(6787), 818–824. https://doi.org/10.1126/science.adt1275
2026.6.8 Journal Club
Presenter: Lei Liu
Article: Lisowski, C., Quetting, M., Klaus, D., Lazarevski, L., Seep, L., Germer, M., Li, J., Müller, I., Zuniga, D., Fiedler, W., Dechmann, D. K. N., Thorup, K., Hasenauer, J., Fester, L., Kuerten, S., Farle, M., Wiedwald, U., Wikelski, M., & Kurts, C. (2026). Homing pigeon navigation relies on superparamagnetic macrophages under overcast conditions. Science, 392(6801), 985–991. https://doi.org/10.1126/science.ady2486
2026.6.1 Journal Club
Presenter: Chen lab
Article: Xu, M. M., Huang, Y., Zhang, Y. P., & Peng, M. S. (2026). Restoration of ancestral transcriptional plasticity contributes to plastic heterosis in fatty liver of hybrid ducks. Communications biology, 10.1038/s42003-026-10049-7. https://doi.org/10.1038/s42003-026-10049-7
2026.5.25 Journal Club
Presenter: Haoxuan Liu
Article: Ricemeyer, E. S., Schaefer, N. K., Du, K., da Cruz, I., Kneitz, S., Acemel, R. D., Lupiáñez, D. G., Carroll, R. A., Drinkwater, R., Schartl, M., & Warren, W. C. (2026). Gene conversion empowers natural selection in a clonal fish species. Nature, 652(8109), 398–404. https://doi.org/10.1038/s41586-026-10180-9
2026.5.18 Journal Club
Presenter: Chen lab
Article: Pai, S. V., Humphrey, P. T., Simonet, C., Kosheleva, K., Limdi, A., & Desai, M. M. (2026). Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load. Science, 392(6796), 415–420. https://doi.org/10.1126/science.aec9708
2026.5.11 Journal Club
Presenter: Hanchi Yu
Article: Ciucci, G., Lorizio, D., Bartoloni, N., Budini, M., Colliva, A., Vodret, S., Nguyen, A. V., Ciacci, L., Texler, B., Cardini, B., Oberhuber, R., Bindelli, S., Del Giudice, I. L. C., Vuerich, R., Riccitelli, F., Zago, E., Finsberg, H. N., Chiesa, M., Perrucci, G. L., Bussani, R., … Zacchigna, S. (2026). Mechanical load inhibits cancer growth in mouse and human hearts. Science, 392(6796), eads9412. https://doi.org/10.1126/science.ads9412
2026.4.27 Journal Club
Presenter: Chenggen Qiang
Article: Wu, X., Bellagio, T., Peng, Y., Czech, L., Lin, M., Lang, P., Epstein, R., Abdelaziz, M., Alexander, J., Alonso-Blanco, C., Andersen, H. L., Berbel, M., Bergelson, J., Bossdorf, O., Burghardt, L., Caton-Darby, M., Colautti, R., Delker, C., Dimitrakopoulos, P. G., Donohue, K., … Exposito-Alonso, M. (2026). Rapid adaptation and extinction in synchronized outdoor evolution experiments of Arabidopsis. Science, 391(6792), eadz0777. https://doi.org/10.1126/science.adz0777
2026.4.20 Journal Club
Presenter: Ti Qin
Article: Deng, P., Lee, H., Armijo, C., Wang, H., & Gao, A. (2026). Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase. Science, eaed1656. https://doi.org/10.1126/science.aed1656
2026.4.13 Journal Club
Presenter: Shichun Wang
Article: Tran, V. Q., Nemeth, M., Bartie, L. J., Chandrasekaran, S. S., Fanton, A., Moon, H. C., Hie, B. L., Konermann, S., & Hsu, P. D. (2026). Rapid directed evolution guided by protein language models and epistatic interactions. Science, 392(6798), eaea1820. https://doi.org/10.1126/science.aea1820
2026.4.6 Journal Club
Presenter: Danqi Qin
Article: Bou Sleiman, M., Roy, S., Gao, A. W., Sadler, M. C., von Alvensleben, G. V. G., Li, H., Sen, S., Harrison, D. E., Nelson, J. F., Strong, R., Miller, R. A., Kutalik, Z., Williams, R. W., & Auwerx, J. (2022). Sex- and age-dependent genetics of longevity in a heterogeneous mouse population. Science, 377(6614), eabo3191. https://doi.org/10.1126/science.abo3191
2026.3.30 Journal Club
Presenter: Chen lab
Article: Tarkington, J., Mahadevan, A., Chan, A. G., & Sherlock, G. (2026). Experimental Evolution of Yeast Reveals Trade-offs Between Early and Late Stationary Phase. bioRxiv : the preprint server for biology, 2026.03.12.711341. https://doi.org/10.64898/2026.03.12.711341
2026.3.23 Journal Club
Presenter: Yang Qian
Article: Anstett, D. N., Anstett, J., Sheth, S. N., Moxley, D. R., Branch, H. A., Jahani, M., Huang, K., Todesco, M., Jordan, R., Lazaro-Guevara, J. M., Rieseberg, L. H., & Angert, A. L. (2026). Rapid evolution predicts demographic recovery after extreme drought. Science, 391(6790), 1172–1176. https://doi.org/10.1126/science.adu0995
2026.3.16 Journal Club
Presenter: Chen lab
Article: Robertson, A. J., Kerr, B., & Feder, A. F. (2026). Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback. Nature ecology & evolution, 10(3), 429–438. https://doi.org/10.1038/s41559-025-02926-x
2026.3.9 Journal Club
Presenter: Haichao Li
Article: Uller, T., Feiner, N., Sacchi, R., Zuffi, M., Scali, S., Pafilis, P., Plavos, K., Abalos, J., Andrade, P., Aguilar, P., Salvi, D., & While, G. M. (2026). Adaptive spread of a sexually selected syndrome eliminates an ancient color polymorphism in wall lizards. Science, 391(6780), 64–68. https://doi.org/10.1126/science.adx3708
Corl, A., Guzman, A., Bi, K., Vazquez, J. M., Smith, L. L., Blaimont, P., Spranger, R., Cooper, R. D., Miles, D., Goldberg, A., Gao, J., Xiang, X., Zhou, Y., Li, Q., Zhang, G., Sudmant, P. H., Bowie, R. C. K., McGuire, J. A., Sinervo, B., & Nielsen, R. (2026). The genetics, evolution, and maintenance of a biological rock-paper-scissors game. Science, 391(6780), 69–74. https://doi.org/10.1126/science.adw8265
2026.2.2 Journal Club
Presenter: Chen lab
Article: Pisera, A., & Liu, C. C. (2025). The role of plasmid copy number and mutation rate in evolutionary outcomes. Nature ecology & evolution, 9(9), 1694–1704. https://doi.org/10.1038/s41559-025-02792-7
2026.1.26 Journal Club
Presenter: Kun Wu
Article: Aguilar, R. R., Khan, L. F., Cummins, C. K., Arslanovic, N., Grauer, T., Birmingham, K., Kasliwal, K., Posnikoff, S. D. L., Chakraborty, U., Hickman, A. R., Watson, R., Ezell, R. J., Hunt, S. R., Mukhsinova, L., Willis, H. E., Cowles, M. W., Garner, R., Shim, A., Gutierrez, J. I., Venters, B. J., … Tyler, J. K. (2025). Multivalent binding of the tardigrade Dsup protein to chromatin promotes yeast survival and longevity upon exposure to oxidative damage. Nature communications, 16(1), 8617. https://doi.org/10.1038/s41467-025-63652-3
2026.1.19 Journal Club
Presenter: Chen lab
Article: Wu, D., Wang, Z., Huang, J., Huang, L., Zhang, S., Zhao, R., Li, W., Chen, D., & Ou, G. (2022). An antagonistic pleiotropic gene regulates the reproduction and longevity tradeoff. PNAS, 119(18), e2120311119. https://doi.org/10.1073/pnas.2120311119
2026.1.12 Journal Club
Presenter: Haoxuan Liu
Article: Tian, S., Lee, B., Banerjee, T. D., Murugesan, S. N., & Monteiro, A. (2025). A novel Hox gene promoter fuels the evolution of adaptive phenotypic plasticity in wing eyespots of satyrid butterflies. Nature ecology & evolution, 9(12), 2391–2403. https://doi.org/10.1038/s41559-025-02891-5
2025.12.29 Journal Club
Presenter: Shichun Wang
Article: Lin, S. Y., Futeran, H. R., Cruga, B. N., Santiago-Frangos, A., & Levine, M. T. (2025). Rapid compensatory evolution within a multiprotein complex preserves telomere integrity. Science, 390(6776), 918–924. https://doi.org/10.1126/science.adv0657
2025.12.22 Journal Club
Presenter: Danqi Qin
Article: Chen, Y., Chen, Z., Wang, H., Cui, Z., Li, K. L., Song, Z., Chen, L., Sun, X., Xu, X., Zhang, Y., Tan, L., Yuan, J., Tan, R., Luo, M. H., Sun, F. L., Liu, H., Jiang, Y., & Mao, Z. (2025). A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging. Science, 390(6769), eadp5056. https://doi.org/10.1126/science.adp5056
2025.12.1 Journal Club
Presenter: Yang Qian
Article: Parée, T., Noble, L., Roze, D., & Teotónio, H. (2025). Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation. Molecular biology and evolution, 42(1), msae273. https://doi.org/10.1093/molbev/msae273
2025.11.24 Journal Club
Presenter: Chen lab
Article: Zik, J. J., Price, M. N., Mayra, K. H. A., Santoso, A. A., Arkin, A. P., Deutschbauer, A. M., & Sham, L. T. (2025). Dual transposon sequencing profiles the genetic interaction landscape in bacteria. Science, 389(6767), eadt7685. https://doi.org/10.1126/science.adt7685
2025.11.12 Journal Club
Presenter: Ti Qin
Article: Firsanov, D., Zacher, M., Tian, X., Sformo, T. L., Zhao, Y., Tombline, G., Lu, J. Y., Zheng, Z., Perelli, L., Gurreri, E., Zhang, L., Guo, J., Korotkov, A., Volobaev, V., Biashad, S. A., Zhang, Z., Heid, J., Maslov, A. Y., Sun, S., Wu, Z., … Gorbunova, V. (2025). Evidence for improved DNA repair in the long-lived bowhead whale. Nature, 648(8094), 717–725. https://doi.org/10.1038/s41586-025-09694-5
2025.11.7 Journal Club
Presenter: Chen lab
Article: Wood, D. P., Holmberg, J. A., Osborne, O. G., Helmstetter, A. J., Dunning, L. T., Ellison, A. R., Smith, R. J., Lighten, J., & Papadopulos, A. S. T. (2023). Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora. Nature ecology & evolution, 7(3), 414–423. https://doi.org/10.1038/s41559-022-01975-w
2025.10.24 Journal Club
Presenter: Lei Liu
Article: Jakobson, C. M., Hartl, J., Trébulle, P., Mülleder, M., Jarosz, D. F., & Ralser, M. (2025). A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness. Science, 390(6769), eadu3198.
2025.10.17 Journal Club
Presenter: Chen lab
Article: Sane, M., Parveen, S., & Agashe, D. (2025). Mutation bias alters the distribution of fitness effects of mutations. Plos Biology, 23(7), e3003282.
2025.10.10 Journal Club
Presenter: Haichao
Article: Gardner, C., Chen, J., Hadfield, C., Lu, Z., Debruin, D., Zhan, Y., … & Lin, Z. (2024). Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization. Genome Research, 34(11), 2133-2146.
2025.09.19 Journal Club
Presenter: Kun Wu
Article: Li W, Baehr S, Marasco M, Reyes L, Brister D, Pikaard CS, Gout JF, Vermulst M, Lynch M. A narrow range of transcript-error rates across the Tree of Life. Sci Adv. 2025 Jul 11;11(28):eadv9898. doi: 10.1126/sciadv.adv9898.
2025.09.12 Journal Club
Presenter: Chen lab
Article: Karageorgi, M., Lyulina, A.S., Bitter, M.C. et al. Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection. Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02853-x
2025.09.05 Journal Club
Presenter: Lan Mi
Article: Zheng, B., Zhang, W., Yu, G., Shi, W., Deng, S., Zhang, X., … & Yang, J. R. (2025). Translational fidelity and longevity are genetically linked. Nature Communications, 16(1), 7521.
2025.08.26 Journal Club
Presenter: Chen lab
Article: Sastre-Dominguez, J., DelaFuente, J., Toribio-Celestino, L., Herencias, C., Herrador-Gomez, P., Costas, C., … & San Millan, A. (2024). Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria. Nature ecology & evolution, 8(11), 2097-2112.
2025.07.08 Journal Club
Presenter: Haichao
Article: Chen, Y., & Nielsen, J. (2022). Yeast has evolved to minimize protein resource cost for synthesizing amino acids. Proceedings of the National Academy of Sciences, 119(4), e2114622119.
2025.07.01 Journal Club
Presenter: Chen lab
Article: Maeda, T., Iwasawa, J., Kotani, H., Sakata, N., Kawada, M., Horinouchi, T., … & Furusawa, C. (2020). High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli. Nature communications, 11(1), 5970.
2025.06.24 Journal Club
Presenter: Haoxuan
Article: Zhu, L., Beichman, A., & Harris, K. (2025). Population size interacts with reproductive longevity to shape the germline mutation rate. Proceedings of the National Academy of Sciences, 122(21), e2423311122.
2025.06.10 Journal Club
Presenter: Chen lab
Article: Liu, J., Gefen, O., Ronin, I., Bar-Meir, M., & Balaban, N. Q. (2020). Effect of tolerance on the evolution of antibiotic resistance under drug combinations. Science, 367(6474), 200-204.
2025.05.27 Journal Club
Presenter: Chen lab
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.
2025.05.13 Journal Club
Presenter: Chen lab
Article: Pokusaeva, V. O., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K. S., Mishin, A. S., … & Kondrashov, F. A. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS genetics, 15(4), e1008079.
2025.04.22 Journal Club
Presenter: Yang Qian
Article: Brixi, G., Durrant, M. G., Ku, J., Poli, M., Brockman, G., Chang, D., … & Hie, B. L. (2025). Genome modeling and design across all domains of life with Evo 2. BioRxiv, 2025-02.
2025.04.15 Journal Club
Presenter: Chen lab
Article: Jiang, W., Yin, H., Khan, S. S., & Yiparemu. (2025). Super-compensator alleles rescue diverse deleterious substitutions and buffer the effects of mutations. bioRxiv, 2025-01.
2025.04.08 Journal Club
Presenter: Danqi
Article: Spisak, N., de Manuel, M., Milligan, W., Sella, G., & Przeworski, M. (2024). The clock-like accumulation of germline and somatic mutations can arise from the interplay of DNA damage and repair. PLoS biology, 22(6), e3002678.
2025.03.18 Journal Club
Presenter: Haichao
Article: Cope, A. L., Schraiber, J. G., & Pennell, M. (2025). Macroevolutionary divergence of gene expression driven by selection on protein abundance. Science, 387(6738), 1063-1068.
2025.03.11 Journal Club
Presenter: Chen lab
Article: Rohwer, R. R., Kirkpatrick, M., Garcia, S. L., Kellom, M., McMahon, K. D., & Baker, B. J. (2025). Two decades of bacterial ecology and evolution in a freshwater lake. Nature Microbiology, 10(1), 246-257.
2025.03.04 Journal Club
Presenter: Kun Wu
Article: Barnett, M., Meister, L., & Rainey, P. B. (2025). Experimental evolution of evolvability. Science, 387(6736), eadr2756.
2025.02.25 Journal Club
Presenter: Chen lab
Article: Matsui, T., Mullis, M. N., Roy, K. R., Hale, J. J., Schell, R., Levy, S. F., & Ehrenreich, I. M. (2022). The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross. Nature Communications, 13(1), 1463.
2025.02.19 Journal Club
Presenter: Haoxuan
Article: Vaisvila, R., Johnson, S. R., Yan, B., Dai, N., Bourkia, B. M., Chen, M., … & Sun, Z. (2024). Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme. Molecular Cell, 84(5), 854-866.
2025.01.17 Journal Club
Presenter: Chen lab
Article: Beltran, A., Jiang, X. E., Shen, Y., & Lehner, B. (2025). Site-saturation mutagenesis of 500 human protein domains. Nature, 637(8047), 885-894.
2025.01.10 Journal Club
Presenter: Ti Qin
Article: Liu, G., Pan, Q., Zhu, P., Guo, X., Zhang, Z., Li, Z., … & Zhou, X. (2024). Comparative genomics provides insights into adaptive evolution and demographics of bats. Molecular Biology and Evolution, 41(12), msae208.
2025.01.02 Journal Club
Presenter: Chen lab
Article: Brandes, N., Goldman, G., Wang, C. H., Ye, C. J., & Ntranos, V. (2023). Genome-wide prediction of disease variant effects with a deep protein language model. Nature Genetics, 55(9), 1512-1522.
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