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Date: 06/11/2018 Presenter: N. A. Reference: Kern AD, Hahn MW. The neutral theory in light of natural selection. Mol Biol Evol, 35:1366-1371. doi: https://doi.org/10.1093/molbev/msy092 (2018). [PDF] |
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| 2018 | |
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Date: 04/09/2018 Presenter: Haoxuan Reference: Carey JN, Mettert EL, Roggiani M, Myers KS, Kiley PJ, Goulian M. Regulated stochasticity in a bacterial signaling network permits tolerance to a rapid environmental change. Cell, 173:196-207. doi: https://doi.org/10.1016/j.cell.2018.02.005 (2018). [PDF] |
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Date: 04/02/2018 Presenter: Haiqing Reference: Lalanne J, Taggart JC, Guo MS, Herzel L, Schieler A, Li G. Evolutionary convergence of pathway-specific enzyme expression stoichiometry. Cell, 173:1-13. doi: https://doi.org/10.1016/j.cell.2018.03.007 (2018). [PDF] |
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Date: 03/26/2018 Presenter: Danny Reference: Otwinowski J, McCandlish DM, Plotkin J. Inferring the shape of global epistasis. bioRxiv, doi: https://doi.org/10.1101/278630 (2018). [PDF] |
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Date: 03/19/2018 Presenter: Guiliang Reference: Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, doi: 10.1038/nature26155 (2018). [PDF] |
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Date: 03/12/2018 Presenter: Xukang Reference: Nosil P, Villoutreix R, de Carvalho CF, Farkas TE, Soria-Carrasco V, Feder JL, et al. Natural selection and the predictability of evolution in Timema stick insects. Science, 359:765-770 (2018). [PDF] |
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Date: 03/02/2018 Presenter: Daohan Reference: Long H, Sung W, Kucukyildirim S, Williams E, Miller SF, Guo W, et al. Evolutionary determinants of genome-wide nucleotide composition. Nat Ecol Evol, 2:237-240 (2018). [PDF] |
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Date: 02/26/2018 Presenter: Minhan Reference: Xiang JF, Yang Q, Liu CX, Wu M, Chen LL, Yang L. N6-Methyladenosines Modulate A-to-I RNA Editing. Mol Cell, 69:126-135 (2018). [PDF] |
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Date: 02/19/2018 Presenter: Jason Reference: Diaz de Arce AJ, Noderer WL, Wang CL. Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons. Nucleic Acids Res, 46:985-994 (2018). [PDF] |
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Date: 02/12/2018 Presenter: Andrea Reference: Collet JM, McGuigan K, Allen SL, Chenoweth SF, Blows MW. Mutational pleiotropy and the strength of stabilizing selection within and between functional modules of gene expression. Genetics, doi: 10.1534/genetics.118.300776 (2018). [PDF] |
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Date: 02/05/2018 Presenter: Piaopiao Reference: Truong DM, Boeke JD. Resetting the yeast epigenome with human nucleosomes. Cell, 171:1508-1519 (2017). [PDF] |
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Date: 01/29/2018 Presenter: Xinzhu Reference: Sun L, Alexander HK, Bogos B, Kiviet DJ, Ackermann M, Bonhoeffer S. Effective polyploidy causes phenotypic delay and influences bacterial evolvability. bioRxiv, doi: https://doi.org/10.1101/226654 (2018). [PDF] |
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Date: 01/22/2018 Presenter: Mengyi Reference: Reuveni S, Ehrenberg M, Paulsson J. Ribosomes are optimized for autocatalytic production. Nature, 547:293-297 (2017). [PDF] |
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Date: 01/15/2018 Presenter: Zhengting Reference: Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. eLife, pii: e29005. doi: 10.7554/eLife.29005 (2017). [PDF] |
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| 2017 | |
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Date: 12/13/2017 Presenter: George Reference: de Boer CG, Sadeh R, Friedman N, Regev A. Deciphering cis-regulatory logic with 100 million synthetic promoters. bioRxiv, doi: https://doi.org/10.1101/224907 (2017). [PDF] |
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Date: 12/06/2017 Presenter: Haiqing Reference: Zhang Y, Ptacin JL, Fischer EC, Aerni HR, Caffaro CE, San Jose K, et al. A semi-synthetic organism that stores and retrieves increased genetic information. Nature, 551:644-647 (2017). [PDF] |
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Date: 11/29/2017 Presenter: Haoxuan Reference: Neme R, Amador C, Yildirim B, McConnell E, Tautz D. Random sequences are an abundant source of bioactive RNAs or peptides. Nat Ecol Evol, 6:0217 (2017). [PDF] |
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Date: 11/22/2017 Presenter: Yifan Reference: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife, 6:e28921, DOI: 10.7554/eLife.28921 (2017). [PDF] |
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Date: 11/15/2017 Presenter: Rex Reference: Chen Y, Tong D, Wu CI. A new formulation of random genetic drift and its application to the evolution of cell populations. Mol Biol Evol, 34:2057-2064 (2017). [PDF] |
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Date: 11/03/2017 Presenter: Xukang Reference: Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. The dynamics of molecular evolution over 60,000 generations. Nature, 551:45-50 (2017). [PDF] |
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Date: 11/01/2017 Presenter: Andrea Reference: Starr TN, Flynn JM, Mishra P, Bolon DNA, Thornton JW. Pervasive contingency and entrenchment in a billion years of Hsp90 evolution. bioRxiv, https://doi.org/10.1101/189803 (2017). [PDF] |
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Date: 10/25/2017 Presenter: Jason Reference: Sarda S, Das A, Vinson C, Hannenhalli S. Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters. Genome Res, 27:553-566 (2017). [PDF] |
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Date: 10/18/2017 Presenter: Xinzhu Reference: Reding-Roman C, Hewlett M, Duxbury S, Gori F, Gudelj I, Beardmore R. The unconstrained evolution of fast and efficient antibiotic-resistant bacterial genomes. Nat Ecol Evol, doi:10.1038/s41559-016-0050 (2017). [PDF] |
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Date: 10/11/2017 Presenter: Piaopiao Reference: Michel AH, Hatakeyama R, Kimmig P, Arter M, Peter M, Matos J, et al. Functional mapping of yeast genomes by saturated transposition. eLife, 6:e23570, doi: 10.7554/eLife.23570 (2016). [PDF] |
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Date: 10/04/2017 Presenter: Zhengting Reference: Hu H, Uesaka M, Guo S, Shimai K, Lu TM, Li F, et al. Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol, doi:10.1038/s41559-017-0318-0 (2017). [PDF] |
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Date: 09/27/2017 Presenter: Minhan Reference: Natarajan C, Hoffmann FG, Weber RE, Fago A, Witt CC, Storz JF. Predictable convergence in hemoglobin function has unpredictable molecular underpinnings. Science, 354:336-339 (2016). [PDF] |
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Date: 09/20/2017 Presenter: Zhen Reference: Starr TN, Picton LK, Thornton JW. Alternative evolutionary histories in the sequence space of an ancient protein. Nature, doi: 10.1038/nature23902 (2017). [PDF] |
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Date: 09/13/2017 Presenter: Mengyi Reference: Csárdi G, Franks A, Choi DS, Airoldi EM, Drummond DA. Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast. PLoS Genet, 11:e1005206 (2015). [PDF] |
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Date: 09/01/2017 Presenter: Jen Reference: Houle D, Bolstad GH, van der Linde K, Hansen TF. Mutation predicts 40 million years of fly wing evolution. Nature, 548:447-450 (2017). [PDF] |
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Date: 08/25/2017 Presenter: Jason Reference: Jin Y, Eser U, Struhl K, Churchman LS. The ground state and evolution of promoter region directionality. Cell, 170:889-898 (2017). [PDF] |
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Date: 08/11/2017 Presenter: Zhen Reference: Steinrueck M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife, 6:e25100 (2017). [PDF] |
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Date: 08/04/2017 Presenter: Xinzhu Reference: Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones L, Yengo L, et al. Widespread signatures of negative selection in the genetic architecture of human complex traits. bioRxiv, 145755 (2017). [PDF] |
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Date: 07/28/2017 Presenter: Piaopiao Reference: Swings T, Van den Bergh B, Wuyts S, Oeyen E, Voordeckers K, Verstrepen KJ, et al. Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli. eLife, 6:e22939 (2017). [PDF] |
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Date: 07/21/2017 Presenter: Andrea Reference: Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, et al. The dynamic three-dimensional organization of the diploid yeast genome. eLife, 6:e23623 (2017). [PDF] |
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Date: 07/14/2017 Presenter: Minhan Reference: Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, et al. Functional segregation of overlapping genes in HIV. Cell, 167:1762-1773 (2017). [PDF] |
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Date: 06/30/2017 Presenter: Zhengting Reference: Mazel F, Wüest RO, Gueguen M, Renaud J, Ficetola GF, Lavergne S, Thuiller W. The geography of ecological niche evolution in mammals. Curr Biol, 27:1369-1374 (2017). [PDF] |
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Date: 06/21/2017 Presenter: Haiqing Reference: Bódi Z, Farkas Z, Nevozhay D, Kalapis D, Lázár V, Csörgő B, et al. Phenotypic heterogeneity promotes adaptive evolution. PLoS Biol, 15:e2000644 (2017). [PDF] |
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Date: 06/16/2017 Presenter: Chuan Reference: Rego EH, Audette RE, Rubin EJ. Deletion of a mycobacterial divisome factor collapses single-cell phenotypic heterogeneity. Nature, 546:153-157 (2017). [PDF] |
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Date: 06/09/2017 Presenter: Wei-Chin Reference: Plech M, Tomala K, Tutaj H, Piwcewicz DE, de Visser JAGM, Korona R. Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy. PLoS Genet, 13:e1006768 (2017). [PDF] |
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Date: 06/02/2017 Presenter: Mengyi Reference: Tsochatzidou M, Malliarou M, Papanikolaou N, Roca J, Nikolaou C. Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae. Nucleic Acids Res, doi: 10.1093/nar/gkx19 (2017). [PDF] |
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Date: 04/26/2017 Presenter: George Reference: Meyer JR, Dobias DT, Medina SJ, Servilio L, Gupta A, Lenski RE. Ecological speciation of bacteriophage lambda in allopatry and sympatry. Science, 354:1301-1304 (2016). [PDF] |
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Date: 04/12/2017 Presenter: Piaopiao Reference: Nocedal I, Mancera E, Johnson AD. Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator. Elife, 6. pii: e23250 (2017). [PDF] |
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Date: 04/05/2017 Presenter: Minhan Reference: Cassan E, Arigon-Chifolleau AM, Mesnard JM, Gross A, Gascuel O. Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic. PNAS, 113:11537-11542 (2016). [PDF] |
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Date: 03/29/2017 Presenter: Trevor Reference: Wang S, Wang S, Luo Y, Xiao L, Luo X, Gao S, et al. Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host. Nat Commun, 7:12845 (2016). [PDF] |
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Date: 03/22/2017 Presenter: Zhen Reference: Kapusta A, Suh A, Feschotte C. Dynamics of genome size evolution in birds and mammals. PNAS, 114:E1460-E1469 (2017). [PDF] |
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Date: 03/15/2017 Presenter: Jen Reference: Diss G, Gagnon-Arsenault I, Dion-Coté AM, Vignaud H, Ascencio DI, Berger CM, Landry CR. Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science, 355:630-634 (2017). [PDF] |
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Date: 03/08/2017 Presenter: Andrea Reference: Katz Y, Springer M. Probabilistic adaptation in changing microbial environments. PeerJ, 4:e2716 (2017). [PDF] |
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Date: 02/22/2017 Presenter: Zhengting Reference: Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nat Biotechnol, 35:128-135 (2017). [PDF] |
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Date: 02/15/2017 Presenter: Xinzhu Reference: Yaakov G, Lerner D, Bentele K, Steinberger J, Barkai N. Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress. Nat Ecol Evol, 1:0016 (2017). [PDF] |
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Date: 02/08/2017 Presenter: Haiqing Reference: Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, et al. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science, 354:769-773 (2016). [PDF] |
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Date: 02/01/2017 Presenter: Chuan Reference: Frieda KL, Linton JM, Hormoz S, Choi J, Chow KK, et al. Synthetic recording and in situ readout of lineage information in single cells. Nature, 541:107-111 (2017). [PDF] |
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Date: 01/25/2017 Presenter: Mengyi Reference: Bintu L, Yong J, Antebi YE, McCue K, Kazuki Y, Uno N. Dynamics of epigenetic regulation at the single-cell level. Science, 351:720-724 (2016). [PDF] |
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Date: 01/18/2017 Presenter: Nagarjun Reference: Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L. Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell, 167:1853-1866 (2016). [PDF] |
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Date: 01/11/2017 Presenter: Wei-Chin Reference: Bank C, Matuszewski S, Hietpas RT, Jensen JD. On the (un)predictability of a large intragenic fitness landscape. Proc Natl Acad Sci U S A, 113:14085-14090 (2016). [PDF] |
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| 2016 | |
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Date: 12/01/2016 Presenter: Andrea Reference: Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. Elife, 5:e19027 (2016). [PDF] |
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Date: 11/17/2016 Presenter: Jen Reference: Lu YJ, Swamy KB, Leu JY. Experimental evolution reveals interplay between Sch9 and polyploid stability in yeast. PLoS Genet, 12:e1006409 (2016). [PDF] |
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Date: 11/03/2016 Presenter: Zhengting Reference: Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature, doi: 10.1038/nature20149 (2016). [PDF] |
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Date: 10/27/2016 Presenter: Haiqing Reference: Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. eLife, 5:e18981 (2016). [PDF] |
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Date: 10/20/2016 Presenter: Xinzhu Reference: Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, et al. Defining the consequences of genetic variation on a proteome-wide scale. Nature, 534: 500-505 (2016). [PDF] |
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Date: 10/13/2016 Presenter: Chuan Reference: Venkataram S, Dunn B, Li Y, Agarwala A, Chang J, Ebel ER, et al. Development of a comprehensive genotype-to-fitness map of adaptation-driving mutations in yeast. Cell, 166:1585-1596 (2016). [PDF] |
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Date: 10/06/2016 Presenter: Mengyi Reference: Chakrabortee S, Byers JS, Jones S, Garcia DM, Bhullar B, Chang A. Intrinsically disordered proteins drive emergence and inheritance of biological traits. Cell, pii: S0092-8674(16)31250-8 (2016). [PDF] |
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Date: 09/29/2016 Presenter: Bryan Reference: Wijaya E, Frith MC, Horton P, Asai K. Finding protein-coding genes through human polymorphisms. PLoS One, 8:e54210 (2013). [PDF] |
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Date: 09/22/2016 Presenter: Nagarjun Reference: Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L, Mosberg JA, et al. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli. PNAS, pii: 201605856 (2016). [PDF] |
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Date: 09/15/2016 Presenter: Wei-Chin Reference: Keren L, Hausser J, Lotan-Pompan M, Vainberg Slutskin I, Alisar H, Kaminski S, et al. Massively parallel interrogation of the effects of gene expression levels on fitness. Cell, 166:1282-1294 (2016). [PDF] |
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Date: 08/30/2016 Presenter: Chuan Reference: Arribere JA, Cenik ES, Jain N, Hess GT, Lee CH, Bassik MC, Fire AZ. Translation readthrough mitigation. Nature, 534: 719-723 (2016). [PDF] |
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Date: 08/23/2016 Presenter: Xinzhu Reference: Wang Y, Diaz Arenas C, Stoebel DM, Flynn K, Knapp E, Dillon MM. Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness. PNAS, 113:5047-5052 (2016). [PDF] |
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Date: 08/16/2016 Presenter: Zhengting Reference: Chikina M, Robinson JD, Clark NL. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Mol Biol Evol, pii: msw112 (2016). [PDF] |
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Date: 08/09/2016 Presenter: Nagarjun Reference: Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, et al. Tempo and mode of genome evolution in a 50,000-generation experiment. Nature, doi: 10.1038/nature18959 (2016). [PDF] |
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Date: 08/02/2016 Presenter: Jason Reference: Szappanos B, Fritzemeier J, Csörgő B, Lázár V, Lu X, Fekete G, et al. Adaptive evolution of complex innovations through stepwise metabolic niche expansion. Nat Commun, 7:11607 (2016). [PDF] |
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Date: 06/21/2016 Presenter: Mengyi Reference: Wang Q, Jiang C, Liu H, Xu JR. ADAR-Independent A-to-I RNA editing is generally adaptive for sexual reproduction in fungi. bioRxiv, 059725 (2016). [PDF] |
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Date: 06/14/2016 Presenter: Bryan Reference: Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R. Origins of de novo genes in human and chimpanzee. PLoS Genet., 11:e1005721 (2015). [PDF] |
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Date: 06/07/2016 Presenter: Wei-Chin Reference: Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S. Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol. Syst. Biol., 12: 857 (2016). [PDF] |
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Date: 05/31/2016 Presenter: Soochin Reference: Roop JI, Chang KC, Brem RB. Polygenic evolution of a sugar specialization trade-off in yeast. Nature, 530:336-339 (2015). [PDF] |
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Date: 05/24/2016 Presenter: Calum Reference: Sarkisyan KS, Bolotin DA, Meer MV, Usmanova DR, Mishin AS, Sharonov GV, et al. Local fitness landscape of the green fluorescent protein. Nature, 533: 397-401 (2016). [PDF] |
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Date: 05/03/2016 Presenter: Chuan Reference: Dar D, Shamir M, Mellin JR, Koutero M, Stern-Ginossar N, Cossart P, Sorek R. Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. Science, 352:aad9822 (2015). [PDF] |
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Date: 04/26/2016 Presenter: Nagajun Reference: McDonald MJ, Rice DP, Desai MM. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature, 531: 233-236 (2016). [PDF] |
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Date: 04/19/2016 Presenter: Andrea Reference: Cerulus B, New AM, Pougach K, Verstrepen KJ. Noise and Epigenetic Inheritance of Single-Cell Division Times Influence Population Fitness. Curr. Biol., 26:1-10 (2015). [PDF] |
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Date: 04/11/2016 Presenter: Xiaoshu Reference: Uphoff S, Lord ND, Okumus B, Potvin-Trottier L, Sherratt DJ, Paulsson J. Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation. Science, 351: 1094-1097 (2016). [PDF] |
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Date: 04/05/2016 Presenter: Jen Reference: Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ et al. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science, 351:1450-1454 (2015). [PDF] |
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Date: 03/29/2016 Presenter: Jason Reference: Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM et al. Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair. Cell, 164: 538-549 (2016). [PDF] |
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Date: 03/22/2016 Presenter: Fabien Reference: Agashe D, Sane M, Phalnikar K, Diwan GD, Habibullah A, Martinez-Gomez NC et al. Large-effect beneficial synonymous mutations mediate rapid and parallel adaptation in a bacterium. Mol. Biol. Evol. , msw035 (2015). [PDF] |
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Date: 03/15/2016 Presenter: Mengyi Reference: Clune J, Mouret JB, Lipson H. The evolutionary origins of modularity. Proc R Soc B, 280: 20122863 (2013). [PDF] |
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Date: 03/04/2016 Presenter: Bryan Reference: Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Evidence for a common evolutionary rate in metazoan transcriptional networks. Elife, 4: e11615 (2015). [PDF] |
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Date: 02/23/2016 Presenter: Zhengting Reference: Neme R, Tautz D. Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence. Elife, 5: e09977 (2016). [PDF] |
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Date: 02/16/2016 Presenter: Wei-Chin Reference: Kafri M, Metzl-Raz E, Jona G, Barkai N. The cost of protein production. Cell reports, 14: 22-31 (2016). [PDF] |
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Date: 02/09/2016 Presenter: Jian-Rong Reference: Tyler AL, Donahue LR, Churchill GA, Carter GW. Weak epistasis generally stabilizes phenotypes in a mouse intercross. PLoS Genet, 12: e1005805 (2016). [PDF] |
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Date: 02/02/2016 Presenter: Calum Reference: Boël G, Letso R, Neely H, Price WN, Wong KH, Su M, et al. Codon influence on protein expression in E. coli correlates with mRNA levels. Nature, 529: 358-363 (2016). [PDF] |
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Date: 01/26/2016 Presenter: Soochin Reference: Lenski RE, Wiser MJ, Ribeck N, Blount ZD, Nahum JR, Morris JJ, et al. Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli<\em>. Proc. R. Soc. B, 282:20152292 (2015). [PDF] |
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Date: 01/12/2016 Presenter: Xinzhu Reference: Liu G, Yong MYJ, Yurieva M, Srinivasan K G, Liu J, Lim JSY, et al. Gene essentiality is a quantitative property linked to cellular evolvability. Cell, 163: 1388-1399 (2016). [PDF] |
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| 2015 | |
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Date: 12/17/2015 Presenter: Xiaoshu Reference: Chen J, Coakley A, O’Connor M, Petrov A, O’Leary SE, Atkins JF, Puglisi JD. Coupling of mRNA structure rearrangement to ribosome movement during bypassing of non-coding regions. Cell, 163:1267-1280 (2015). [PDF] |
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Date: 12/10/2015 Presenter: Chuan Reference: de Vos MG, Dawid A, Sunderlikova V, Tans SJ. Breaking evolutionary constraint with a tradeoff ratchet. PNAS, 112: 14906-14911 (2015). [PDF] |
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Date: 12/03/2015 Presenter: Fabien Reference: Stoltzfus A, Norris RW. On the causes of evolutionary transition: transversion bias. Mol. Biol. Evol., msv274 (2015). [PDF] |
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Date: 11/19/2015 Presenter: Calum Reference: Kalapis D, Bezerra AR, Farkas Z, Horvath P, Bódi Z, Daraba A. Evolution of robustness to protein mistranslation by accelerated protein turnover. PLoS Biol, 13: e1002291 (2015). [PDF] |
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Date: 11/12/2015 Presenter: Jennifer Reference: Rodríguez-Verdugo A, Tenaillon O, Gaut BS. First-step mutations during adaptation restore the expression of hundreds of genes. Mol. Biol. Evol., msv228 (2015). [PDF] |
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Date: 11/05/2015 Presenter: Mengyi Reference: Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, GuhaThakurta D, et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics, 37: 710-717 (2015). [PDF] |
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Date: 10/29/2015 Presenter: Bryan Reference: Yang H, He BZ, Ma H, Tsaur SC, Ma C, Wu Y, et al. Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population. Mol. Biol. Evol., 32: 216-228 (2015). [PDF] |
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Date: 10/22/2015 Presenter: Zhengting Reference: Aakre CD, Herrou J, Phung TN, Perchuk BS, Crosson S, Laub MT. Evolving new protein-protein interaction specificity through promiscuous intermediates. Cell, 163: 1-13 (2015). [PDF] |
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Date: 10/15/2015 Presenter: Andrea Reference: Leducq JB, Nielly-Thibault L, Charron G, Eberlein C, Verta JP, Samani P, et al. Speciation driven by hybridization and chromosomal plasticity in a wild yeast. bioRxiv, 027383 (2015). [PDF] |
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Date: 10/08/2015 Presenter: Brian Reference: Wolf L, Silander OK, van Nimwegen EJ. Expression noise facilitates the evolution of gene regulation. eLife, 4: e05856 (2015). [PDF] |
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Date: 10/01/2015 Presenter: Jian-Rong Reference: Ghalambor CK, Hoke KL, Ruell EW, Fischer EK, Reznick DN, Hughes KA. Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature. Nature, 525: 372-375 (2015). [PDF] |
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Date: 09/24/2015 Presenter: Wei-Chin Reference: Marcet-Houben M, Gabaldón T. Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage. PLoS Biol, 13:e1002220 (2015). [PDF] |
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Date: 09/17/2015 Presenter: Soochin Reference: Wang J, Atolia E, Hua B, Savir Y, Escalante-Chong R, Springer M. Natural variation in preparation for nutrient depletion reveals a cost-benefit tradeoff. PLoS Biol, 13: e1002041 (2015). [PDF] |
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Date: 09/10/2015 Presenter: Xinzhu Reference: González C, Ray JCJ, Manhart M, Adams RM, Nevozhay D, Morozov AV, Balázsi G. Stress-response balance drives the evolution of a network module and its host genome. Molecular Systems Biology, 11:827 (2015). [PDF] |
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Date: 08/27/2015 Presenter: Chuan Reference: Young DJ, Guydosh NR, Zhang F, Hinnebusch AG, Green R. Rli1/ABCE1 recycles terminating ribosomes and controls translation reinitiation in 3' UTRs in vivo. Cell, 162: 872-884 (2015). [PDF] |
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Date: 08/20/2015 Presenter: Daniel Reference: Kim J, Kim I, Han SK, Bowie JU, Kim S. Network rewiring is an important mechanism of gene essentiality change. Scientific reports, 2 (2015). [PDF] |
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Date: 08/13/2015 Presenter: Xiaoshu Reference: Hsieh THS, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping nucleosome resolution chromosome folding in yeast by Micro-C Cell, 162: 108-119 (2015). [PDF] |
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Date: 08/07/2015 Presenter: Fabien Reference: Sorrells TR, Booth LN, Tuch BB, Johnson AD. Intersecting transcription networks constrain gene regulatory evolution. Nature, 523: 361-365 (2015). [PDF] |
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Date: 07/23/2015 Presenter: Jian-Rong Reference: Yang S, Wang L, Huang J, Zhang X, Yuan Y, et al. Parent-progeny sequencing indicates higher mutation rates in heterozygotes. Nature (2015). [PDF] |
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Date: 07/09/2015 Presenter: Calum Reference: Rogers DW, Denton JA, McConnell E, Greig D. Experimental evolution of species recognition. Curr Bio, 25: 1753-1758 (2015). [PDF] |
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Date: 07/02/2015 Presenter: Soochin Reference: Hose J, Yong CM, Sardi M, Wang Z, Newton MA, Gasch AP. Dosage compensation can buffer copy-number variation in wild yeast. eLife, 4: e05462 (2015). [PDF] |
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Date: 06/18/2015 Presenter: Brian Reference: Assaf ZJ, Petrov DA, Blundell JR. Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. Proc Natl Acad Sci U S A, 112: E2658-2666 (2015). [PDF] |
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Date: 06/11/2015 Presenter: Zhengting Reference: Berthelot C, Muffato M, Abecassis J, Crollius HR. The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions. Cell Rep, 10: 1913-1924 (2015). [PDF] |
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Date: 06/04/2015 Presenter: Bryan Reference: Lan X, Pritchard JK. Long-term survival of duplicate genes despite absence of subfunctionalized expression. bioRxiv, (2015). [PDF] |
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Date: 05/28/2015 Presenter: Andrea Reference: Bloom JS, Kotenko I, Sadhu M, Treusch S, Albert FW, Kruglyak L. The role of genetic interactions in yeast quantitative traits. bioRxiv, (2015). [PDF] |
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Date: 05/21/2015 Presenter: Xinzhu Reference: Katajisto P, Dohla J, Chaffer CL, Pentinmikko N, Marjanovic N, et al. Asymmetric apportioning of aged mitochondria between daughter cells is required for stemness. Science, 348: 340-343 (2015). [PDF] |
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Date: 05/07/2015 Presenter: Wei-Chin Reference: Corbett-Detig RB, Hartl DL, Sackton TB. Natural selection constrains neutral diversity across a wide range of species. PLoS Biol, 13: e1002112 (2015). [PDF] |
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Date: 04/28/2015 Presenter: Jonathan Reference: Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Bluthgen N, et al. MicroRNA control of protein expression noise. Science, 348: 128-132 (2015). [PDF] |
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Date: 04/07/2015 Presenter: Calum Reference: Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, et al. Polyploidy can drive rapid adaptation in yeast. Nature, 519: 349-352 (2015). [PDF] |
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Date: 03/31/2015 Presenter: Fabien Reference: Levy SF, Blundell JR, Venkataram S, Petrov DA, Fisher DS, et al. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature, 519: 181-186 (2015). [PDF] |
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Date: 03/24/2015 Presenter: Sujal Reference: Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, et al. Codon optimality is a major determinant of mRNA stability. Cell, 160: 1111-1124 (2015). [PDF] |
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Date: 03/17/2015 Presenter: Andrea Reference: Bauer CR, Li S, Siegal ML. Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness. Mol Syst Biol, 11: 773 (2015). [PDF] |
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Date: 03/10/2015 Presenter: Chuan Reference: Stiffler MA, Hekstra DR, Ranganathan R. Evolvability as a function of purifying selection in TEM-1 beta-lactamase. Cell, 160: 882-892 (2015). [PDF] |
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Date: 02/24/2015 Presenter: Bryan Reference: Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, et al. Gene age predicts the strength of purifying selection acting on gene expression variation in humans. Am J Hum Genet, 95: 660-674 (2014). [PDF] |
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Date: 02/17/2015 Presenter: Zhengting Reference: Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, et al. Enhancer Evolution across 20 Mammalian Species. Cell 160: 554-566 (2015). [PDF] |
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Date: 02/10/2015 Presenter: Brian Reference: Podgornaia AI, Laub MT. Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface. Science, 347: 673-677 (2015). [PDF] |
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Date: 02/03/2015 Presenter: Jinrui Reference: Reijns MA, Kemp H, Ding J, de Proce SM, Jackson AP, et al. Lagging-strand replication shapes the mutational landscape of the genome.. Nature (2015). [PDF] |
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Date: 01/27/2015 Presenter: Jian-Rong Reference: Campos M, Surovtsev IV, Kato S, Paintdakhi A, Beltran B, et al. A constant size extension drives bacterial cell size homeostasis. Cell, 159: 1433-1446 (2014). [PDF] |
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Date: 01/20/2015 Presenter: Wei-Chin Reference: Zaborske JM, DuMont VL, Wallace EW, Pan T, Aquadro CF, et al. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. PLoS Biol. 12: e1002015 (2014). [PDF] |
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Date: 01/13/2015 Presenter: Xinzhu Reference: Koren A, Handsaker RE, Kamitaki N, Karli R, Ghosh S, et al. Genetic variation in human DNA replication timing. Cell, 159: 1015-1026 (2014). [PDF] |
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| 2014 | |
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Date: 12/12/2014 Presenter: Bryan Reference: Ruiz-Orera J, Messeguer X, Subirana JA, Alba MM. Long non-coding RNAs as a source of new peptides. Elife. 3: e03523 (2014). [PDF] |
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Date: 12/05/2014 Presenter: Fabien Reference: Wildenberg GA, Murray AW. Evolving a 24-hr oscillator in budding yeast. Elife, 3 (2014). [PDF] |
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Date: 11/21/2014 Presenter: Calum Reference: Zid BM, O'Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature. 514: 117-121. [PDF] |
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Date: 11/07/2014 Presenter: Chuan Reference: Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife, 2: e01179 (2013). [PDF] |
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Date: 10/31/2014 Presenter: Zhengting Reference: Le Dily F, Bau D, Pohl A, Vicent GP, Serra F, et al. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev. 28: 2151-2162 (2014). [PDF] |
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Date: 10/24/2014 Presenter: Wei-Chin Reference: Szamecz B, Boross G, Kalapis D, Kovacs K, et al. The genomic landscape of compensatory evolution. PLoS Biol., 12: e1001935 (2014). [PDF] |
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Date: 10/17/2014 Presenter: Jinrui Reference: Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, et al. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature (2014). [PDF] |
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Date: 09/26/2014 Presenter: Brian Reference: Pougach K, Voet A, Kondrashov FA, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nat Commun., 5: 4868 (2014). [PDF] |
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Date: 09/19/2014 Presenter: Jian-Rong Reference: Farkash-Amar S, Zimmer A, Eden E, et al. Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells. PLoS Genet. 10: e1004176 (2014). [PDF] |
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Date: 08/28/2014 Presenter: Andrea Reference: Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, et al. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res., (2014). [PDF] |
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Date: 08/21/2014 Presenter: George Reference: Wiser MJ, Ribeck N, Lenski RE. Long-term dynamics of adaptation in asexual populations. Science. 342: 1364-1367 (2013). [PDF] |
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Date: 08/07/2014 Presenter: Isaac Reference: Washietl S, Kellis M, Garber M. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res., 24: 616-628 (2014). [PDF] |
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Date: 07/31/2014 Presenter: Zhengting Reference: Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos CJ, et al. Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1. PLoS Genet. 10: e1004439 (2014). [PDF] |
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Date: 07/24/2014 Presenter: Sujal Reference: Yofe I, Zafrir Z, Blau R, Schuldiner M, Tuller T, et al. Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae. PLoS Genet., 10: e1004407 (2014). [PDF] |
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Date: 07/17/2014 Presenter: Calum Reference: Hom EF, Murray AW. Niche engineering demonstrates a latent capacity for fungal-algal mutualism. Nature345: 94-98 (2014). [PDF] |
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Date: 07/10/2014 Presenter: Brian Reference: Kryazhimskiy S, Rice DP, Jerison ER, Desai MM. Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science, 344: 1519-1522 (2014). [PDF] |
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Date: 06/26/2014 Presenter: Xiaoshu Reference: Shalek AK, Satija R, Shuga J, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature509: 363-369 (2014). [PDF] |
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Date: 06/19/2014 Presenter: Bryan Reference: O'Maille PE, Malone A, et al. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat Chem Biol, 4: 617-623 (2008). [PDF] |
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Date: 06/05/2014 Presenter: Fabien Reference: Larson MH, Mooney RA, et al. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science344: 1042-1047 (2014). [PDF] |
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Date: 05/29/2014 Presenter: Wei-Chin Reference: Leiby N, Marx CJ. Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biology, 12: e1001789 (2014). [PDF] |
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Date: 05/22/2014 Presenter: Xinzhu Reference: Gong LI, Bloom JD. Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution. PLoS genetics, 10: e1004328 (2014). [PDF] |
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Date: 05/15/2014 Presenter: Jinrui Reference: Li GW, Burkhardt D, Gross C, Weissman JS. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell, 157: 624-635 (2014). [PDF] |
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Date: 05/08/2014 Presenter: Chuan Reference: van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJ, et al. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science, 343: 1245114 (2014). [PDF] |
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Date: 05/01/2014 Presenter: Jianrong Reference: Muzzey D, Sherlock G, Weissman JS. Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. Genome Res., (2014). [PDF] |
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Date: 04/24/2014 Presenter: Calum Reference: Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, et al. Total synthesis of a functional designer eukaryotic chromosome. Science, 344: 55-58 (2014). [PDF] |
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Date: 04/03/2014 Presenter: Brian Reference: Albert FW, Treusch S, Shockley AH, Bloom JS, Kruglyak L. Genetics of single-cell protein abundance variation in large yeast populations. Nature, 506: 494-497 (2014). [PDF] |
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Date: 03/06/2014 Presenter: Xiaoshu Reference: Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, et al. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell, 154: 914-927 (2013). [PDF] |
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Date: 02/27/2014 Presenter: Bryan Reference: Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, et al. The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species. Cell reports, 6: 285-292 (2014). [PDF] |
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Date: 02/20/2014 Presenter: Wei-Chin Reference: New AM, Cerulus B, Govers SK, Perez-Samper G, Zhu B, et al. Different levels of catabolite repression optimize growth in stable and variable environments. Plos biology, 12: e1001764 (2014). [PDF] |
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Date: 02/13/2014 Presenter: Xinzhu Reference: Corbett-Detig RB, Zhou J, Clark AG, Hartl DL, Ayroles JF. Genetic incompatibilities are widespread within species. Nature, 504: 135-137 (2013). [PDF] |
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Date: 02/06/2014 Presenter: Fabien Reference: Acevedo A, Brodsky L, Andino R Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature, 505: 686-690 (2014). [PDF] |
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Date: 01/30/2014 Presenter: Chuan Reference: Stergachis AB, Haugen E, Shafer A, et al. Exonic transcription factor binding directs codon choice and affects protein evolution. Science, 342: 1367-1372 (2013). [PDF] |
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Date: 01/23/2014 Presenter: Jinrui Reference: Deng Q, Ramskold D, Reinius B, Sandberg R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science, 343: 193-196 (2014). [PDF] |
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Date: 01/17/2014 Presenter: Jian-Rong Reference: Artieri CG, Fraser HB. Evolution at two levels of gene expression in yeast. Genome research. (2013). [PDF] |
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Date: 01/09/2014 Presenter: George Reference: Bachmann H, Fischlechner M, Rabbers I, et al. Availability of public goods shapes the evolution of competing metabolic strategies. Proc. Natl. Acad. Sci. USA, 110: 14302-14307 (2013). [PDF] |
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| 2013 | |
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Date: 12/12/2013 Presenter: Bryan Reference: Abrusan G. Integration of new genes into cellular networks, and their structural maturation. Genetics, 195: 1407-1417 (2013). [PDF] |
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Date: 12/05/2013 Presenter: Jianrong Reference: Keren L, Zackay O, Lotan-Pompan M, Barenholz U, et al. Promoters maintain their relative activity levels under different growth conditions. Molecular systems biology, 9: 701 (2013). [PDF] |
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Date: 11/14/2013 Presenter: Xiaoshu Reference: Le TB, Imakaev MV, Mirny LA, Laub MT. High-resolution mapping of the spatial organization of a bacterial chromosome. Science, 342: 731-734 (2013). [PDF] |
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Date: 10/31/2013 Presenter: Wei-Chin Reference: Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, et al. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature, 500: 571-574 (2013). [PDF] |
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Date: 10/24/2013 Presenter: Xinzhu Reference: Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, et al. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature, 498: 241-245 (2013). [PDF] |
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Date: 10/17/2013 Presenter: Fabien Reference: Baker CR, Hanson-Smith V, Johnson AD. Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science, 342: 104-108 (2013). [PDF] |
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Date: 10/10/2013 Presenter: Zhengting Reference: Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, et al. Genome-wide signatures of convergent evolution in echolocating mammals. Nature, 502: 228-231 (2013). [PDF] |
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Date: 10/03/2013 Presenter: Guixia Reference: Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, et al. Drift and conservation of differential exon usage across tissues in primate species. Proc. Natl. Acad. Sci. USA, 110: 15377-15382 (2013). [PDF] |
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Date: 09/26/2013 Presenter: Jinrui Reference: Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW. Evolution of increased complexity in a molecular machine. Nature, 481: 360-364 (2012). [PDF] |
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Date: 09/19/2013 Presenter: Chuan Reference: Jimenez JI, Xulvi-Brunet R, Campbell GW, Turk-Macleod R, Chen IA. Comprehensive experimental fitness landscape and evolutionary network for small RNA. Proc. Natl. Acad. Sci. USA, 110: 14984-14989 (2013). [PDF] |
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Date: 09/12/2013 Presenter: Diyan Reference: Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science, 339: 950-953 (2013). [PDF] |
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Date: 09/06/2013 Presenter: Calum Reference: McGary KL, Slot JC, Rokas A. Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proc. Natl. Acad. Sci. USA, 110: 11481-11486 (2013). [PDF] |
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Date: 08/30/2013 Presenter: Bryan Reference: Neme R, Tautz D. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC genomics, 14: 117. (2013). [PDF] |
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Date: 08/23/2013 Presenter: Jianrong Reference: Lawrie DS, Messer PW, Hershberg R, Petrov DA. Strong purifying selection at synonymous sites in D. melanogaster. PLoS genetics, 9: e1003527 (2013). [PDF] |
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Date: 08/16/2013 Presenter: Brian Reference: Brown CR, Mao C, Falkovskaia E, Jurica MS, Boeger H. Linking stochastic fluctuations in chromatin structure and gene expression. PLoS biology, 11: e1001621 (2013). [PDF] |
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Date: 08/09/2013 Presenter: Xiaoshu Reference: Mano Y, Kobayashi TJ, Nakayama J, Uchida H, Oki M. Single Cell Visualization of Yeast Gene Expression Shows Correlation of Epigenetic Switching between Multiple Heterochromatic Regions through Multiple Generations. PLoS Biology, 11: e1001601 (2013). [PDF] |
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Date: 07/19/2013 Presenter: Fabien Reference: Moqtaderi Z, Geisberg JV, Jin Y, Fan X, Struhl K. Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts. Proc. Natl. Acad. Sci. USA, 110: 11073-11078 (2013). [PDF] |
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Date: 06/21/2013 Presenter: Wei-chin Reference: Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, et al. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res., (2013). [PDF] |
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Date: 06/14/2013 Presenter: Calum Reference: Pelechano V, Wei W, Steinmetz LM. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature, 497: 127-131 (2013). [PDF] |
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Date: 06/07/2013 Presenter: Jinrui Reference: Marsh JA, Hernandez H, Hall Z, Ahnert SE, Perica T, et al. Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell, 153: 461-470 (2013). [PDF] |
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Date: 05/24/2013 Presenter: Chuan Reference: Woods S, Coghlan A, Rivers D, Warnecke T, Jeffries SJ, et al. Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses. PLoS genetics, 9: e1003330 (2013). [PDF] |
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Date: 05/17/2013 Presenter: Guixia Reference: Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495: 333-338 (2013). [PDF] |
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Date: 05/10/2013 Presenter: Diyan Reference: Fares MA, Keane OM, Toft C, Carretero-Paulet L, Jones GW. The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PLoS genetics, 9: e1003176 (2013). [PDF] |
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Date: 05/03/2013 Presenter: Bryan Reference: Cole HA, Howard BH, Clark DJ. Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes. Nucleic acids research, 39: 9521-9535 (2011). [PDF] |
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Date: 04/26/2013 Presenter: Jianrong Reference: Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, et al. Birth and expression evolution of mammalian microRNA genes. Genome research, 23: 34-45 (2013). [PDF] |
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Date: 04/19/2013 Presenter: Brian Reference: Feng Y, Chen HL, Chiu CH. Differential genomic variation between short- and long-term bacterial evolution revealed by ultradeep sequencing. Genome biology and evolution, 5: 572-577 (2013). [PDF] |
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Date: 04/12/2013 Presenter: Xiaoshu Reference: Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E. Promoter Sequence Determines the Relationship between Expression Level and Noise. PLoS biology, 11: e1001528 (2013). [PDF] |
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Date: 04/05/2013 Presenter: Fabien Reference: Holmes DL, Lancaster AK, Lindquist S, Halfmann R. Heritable remodeling of yeast multicellularity by an environmentally responsive prion. Cell, 153: 153-165 (2013). [PDF] |
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Date: 03/29/2013 Presenter: Wei-chin Reference: Habib N, Wapinski I, Friedman N et al A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Molecular systems biology, 8: 619 (2012). [PDF] |
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Date: 03/22/2013 Presenter: Calum Reference: Charneski CA, Hurst LD. Positively Charged Residues Are the Major Determinants of Ribosomal Velocity. PLoS Biol., 11(3): e1001508 (2013). [PDF] |
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Date: 03/15/2013 Presenter: Jinrui Reference: Elde NC, Child SJ, Eickbush MT, et al. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell, 150: 831-841 (2012). [PDF] |
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Date: 03/08/2013 Presenter: Chuan Reference: Robins WP, Faruque SM, Mekalanos JJ Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene. Proc. Natl. Acad. Sci. USA, 110: E848-857 (2013). [PDF] |
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Date: 03/01/2013 Presenter: Guixia Reference: Subramaniam AR, Pan T, Cluzel P Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria. Proc. Natl. Acad. Sci. USA, 110: 2419-2424 (2013). [PDF] |
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Date: 02/22/2013 Presenter: Diyan Reference: Lindsey HA, Gallie J, Taylor S, Kerr B Evolutionary rescue from extinction is contingent on a lower rate of environmental change Nature, (2013). [PDF] |
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Date: 02/08/2013 Presenter: Bryan Reference: Makanae K, Kintaka R, Makino T, Kitano H, Moriya H Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method. Genome research, 23: 300-311 (2013). [PDF] |
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Date: 02/01/2013 Presenter: Jianrong Reference: Dori-Bachash M, Shalem O, Manor YS, et al. Widespread promoter-mediated coordination of transcription and mRNA degradation. Genome biology, 13: R114 (2012). [PDF] |
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Date: 01/25/2013 Presenter: Xiaoshu Reference: Chen M, Licon K, Otsuka R, Pillus L, et al. Decoupling Epigenetic and Genetic Effects through Systematic Analysis of Gene Position. Cell reports, (2013). [PDF] |
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Date: 01/18/2013 Presenter: Brian Reference: Barbosa-Morais NL, Irimia M, Xiong HY, Gueroussov S, et al. The evolutionary landscape of alternative splicing in vertebrate species. Science, 338: 1587-1593 (2012). [PDF] |
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| 2012 | |
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Date: 12/14/2012 Presenter: Diyan Reference: Yona AH, Manor YS, Herbst RH, Romano GH, Mitchell A, et al. Chromosomal duplication is a transient evolutionary solution to stress. Proc. Natl. Acad. Sci. USA, epub 12/01 (2012). [PDF] |
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Date: 12/07/2012 Presenter: Guixia Reference: Capra EJ, Perchuk BS, Skerker JM, Laub MT. Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families. Cell, 150: 222-232 (2012). [PDF] |
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Date: 11/30/2012 Presenter: Chuan Reference: Waite AJ, Shou W. Feature Article: Adaptation to a new environment allows cooperators to purge cheaters stochastically. Proc. Natl. Acad. Sci. USA, 109: 19079-19086 (2012). [PDF] |
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Date: 11/16/2012 Presenter: Shiya Reference: Makino T, McLysaght A. Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant. Genome research, (2012). [PDF] |
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Date: 11/09/2012 Presenter: Jinrui Reference: Breen MS, Kemena C, Vlasov PK, Notredame C, et al. Epistasis as the primary factor in molecular evolution. Nature, 490: 535-538 (2012). [PDF] |
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Date: 11/02/2012 Presenter: Calum Reference: Nasvall J, Sun L, Roth JR, Andersson DI. Real-time evolution of new genes by innovation, amplification, and divergence. Science, 338: 384-387 (2012). [PDF] |
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Date: 10/26/2012 Presenter: Wei-Chin Reference: Blount ZD, Barrick JE, Davidson CJ, Lenski RE. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature, 489: 513-518 (2012). [PDF] |
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Date: 10/12/2012 Presenter: Bryan Reference: Hornung G, Bar-Ziv R, Rosin D, Tokuriki N, Tawfik DS, et al. Noise-mean relationship in mutated promoters. Genome Rearch, (2012). [PDF] |
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Date: 10/05/2012 Presenter: Jianrong Reference: Maurano MT, Wang H, Kutyavin T, Stamatoyannopoulos JA. Widespread site-dependent buffering of human regulatory polymorphism. PLoS Genetics, 8: e1002599 (2012). [PDF] |
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Date: 09/28/2012 Presenter: Xiaoshu Reference: Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature, 489: 109-113 (2012). [PDF] |
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Date: 09/21/2012 Presenter: Brian Reference: Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature, 484: 251-255 (2012). [PDF] |
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Date: 09/14/2012 Presenter: Chungoo Reference: Xiao S, Xie D, Cao X, Yu P, Xing X, et al. Comparative epigenomic annotation of regulatory DNA. Cell, 149: 1381-1392 (2012). [PDF] |
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Date: 08/10/2012 Presenter: Guixia Reference: Dennis MY, Nuttle X, Sudmant PH, et al. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell, 149: 912-922 (2012). [PDF] |
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Date: 08/03/2012 Presenter: Chuan Reference: Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, et al. A whole-cell computational model predicts phenotype from genotype. Cell, 150: 389-401 (2012). [PDF] |
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Date: 07/27/2012 Presenter: Calum Reference: Levy SF, Ziv N, Siegal ML. Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant. PLoS Biology, 10: e1001325 (2012). [PDF] |
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Date: 07/04/2012 Presenter: Jinrui Reference: Carvunis AR, Rolland T, Wapinski I, Yildirim MA, et al. Proto-genes and de novo gene birth. Nature, 487: 370-374 (2012). [PDF] |
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Date: 06/15/2012 Presenter: Wei-Chin Reference: Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U. Multidimensional optimality of microbial metabolism. Science, 336: 601-604 (2012). [PDF] |
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Date: 06/08/2012 Presenter: Wenfeng Reference: Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, et al. Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science, 336: 1157-1160 (2012). [PDF] |
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Date: 06/01/2012 Presenter: Jianzhi Reference: Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, et al. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nature Genetics, 44: 743-750 (2012). [PDF] |
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Date: 05/25/2012 Presenter: Xiaoshu Reference: Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485: 376-380 (2012). [PDF] |
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Date: 05/18/2012 Presenter: Brian Reference: Rockman MV. The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution; International Journal Of Organic Evolution, 66: 1-17 (2012). [PDF] |
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Date: 05/11/2012 Presenter: Jianrong Reference: Zur H, Tuller T. Strong association between mRNA folding strength and protein abundance in S. EMBO Reports, 13: 272-277 (2012). [PDF] |
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Date: 05/04/2012 Presenter: Chungoo Reference: Martincorena I, Seshasayee AS, Luscombe NM. Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature, 485: 95-98 (2012). [PDF] |
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Date: 04/06/2012 Presenter: Jinrui Reference: Wang M, Caetano-Anolles G. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure, 17: 66-78 (2009). [PDF] |
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Date: 03/30/2012 Presenter: Amy Reference: Sellis D, Callahan BJ, Petrov DA, Messer PW. Heterozygote advantage as a natural consequence of adaptation in diploids. Proc. Natl. Acad. Sci. USA, 108: 20666-20671 (2011). [PDF] |
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Date: 03/23/2012 Presenter: Wei-Chin Reference: Ramani AK, Chuluunbaatar T, Verster AJ, Na H, Vu V, et al. The majority of animal genes are required for wild-type fitness. Cell, 148: 792-802 (2012). [PDF] |
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Date: 03/16/2012 Presenter: Chuan Reference: Toprak E, Veres A, Michel JB, Chait R, Hartl DL, et al. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nature Genetics, 44: 101-105 (2012). [PDF] |
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Date: 03/09/2012 Presenter: Bryan Reference: Woo YH, Li WH. Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes. Proc. Natl. Acad. Sci. USA, 108: 3306-3311 (2011). [PDF] |
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Date: 02/24/2012 Presenter: Chungoo Reference: Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology, 30: 253-260 (2012). [PDF] |
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Date: 02/17/2012 Presenter: Wenfeng Reference: Ackermann M, Beyer A. Systematic detection of epistatic interactions based on allele pair frequencies. PLoS Genetics, 8: e1002463 (2012). [PDF] |
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Date: 02/10/2012 Presenter: Calum Reference: Ratcliff WC, Denison RF, Borrello M, Travisano M. Experimental evolution of multicellularity. Proc. Natl. Acad. Sci. USA, 109: 1595-1600 (2012). [PDF] |
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Date: 02/03/2012 Presenter: Xiaoshu Reference: Silander OK, Nikolic N, Zaslaver A, Bren A, Kikoin I, et al. A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genetics, 8: e1002443 (2012). [PDF] |
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Date: 01/27/2012 Presenter: Brian Reference: Lynch VJ, May G, Wagner GP. Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB. Nature, 480: 383-386 (2011). [PDF] |
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Date: 01/20/2012 Presenter: Jianrong Reference: Kuchina A, Espinar L, Cagatay T, Balbin AO, Zhang F, et al. Temporal competition between differentiation programs determines cell fate choice. Molecular Systems Biology, 7: 557 (2011). [PDF] |
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Date: 01/13/2012 Presenter: Jianzhi Reference: Burga A, Casanueva MO, Lehner B. Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature, 480: 250-253 (2011). [PDF] |
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Date: 12/08/2011 Presenter: Huabin Reference: Hines HM, Counterman BA, Papa R, Cardoso MZ, et al. Wing patterning gene redefines the mimetic history of Heliconius butterflies. Proc. Natl. Acad. Sci. USA, 108: 19666-19671 (2011). [PDF] |
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Date: 11/17/2011 Presenter: Wei-Chin Reference: Cusack BP, Arndt PF, Duret L, Roest Crollius H. Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genetics, 7: e1002276 (2011). [PDF] |
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Date: 11/10/2011 Presenter: Chuan Reference: Manhes P, Velicer GJ. Experimental evolution of selfish policing in social bacteria. Proc. Natl. Acad. Sci. USA, 108: 8357-8362 (2011). [PDF] |
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Date: 11/03/2011 Presenter: Ying Reference: Parenteau J, Durand M, Morin G, Gagnon J, Lucier JF, et al. Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell, 147: 320-331 (2011). [PDF] |
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Date: 10/27/2011 Presenter: Calum Reference: Locke JC, Young JW, Fontes M, Elowitz MB. Stochastic pulse regulation in bacterial stress response. Science, 334: 366-369 (2011). [PDF] |
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Date: 09/22/2011 Presenter: Jianzhi Reference: Rebeiz M, Jikomes N, Kassner VA, Carroll SB. Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences. Proc. Natl. Acad. Sci. USA, 108: 10036-10043 (2011). [PDF] |
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Date: 10/20/2011 Presenter: Amy Reference: Jimenez-Gomez JM, Corwin JA, Kliebenstein DJ. Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genetics, 7: e1002295 (2011). [PDF] |
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Date: 10/13/2011 Presenter: Jinrui Reference: Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, et al. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325: 1544-1549 (2009). [PDF] |
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Date: 09/29/2011 Presenter: Chungoo Reference: Li M, Wang IX, Li Y, Bruzel A, Richards AL, et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science, 333: 53-58 (2011). [PDF] |
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Date: 09/15/2011 Presenter: Brian Reference: Foss EJ, Radulovic D, Shaffer SA, Kruglyak L, et al. Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biology, 9: e1001144 (2011). [PDF] |
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Date: 09/08/2011 Presenter: Zengguang Reference: Poelwijk FJ, de Vos MG, Tans SJ. Tradeoffs and optimality in the evolution of gene regulation. Cell, 146: 462-470 (2011). [PDF] |
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Date: 08/24/2011 Presenter: Huabin Reference: Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, et al. Three periods of regulatory innovation during vertebrate evolution. Science, 333: 1019-1024 (2011). [PDF] |
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Date: 08/19/2011 Presenter: Wenfeng Reference: Koschwanez JH, Foster KR, Murray AW. Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. PLoS Biology, 9: e1001122 (2011). [PDF] |
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Date: 08/12/2011 Presenter: Ying Reference: Muegge BD, Kuczynski J, Knights D, Gonzalez A, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, 332: 970-974 (2011). [PDF] |
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Date: 07/05/2011 Presenter: Jinrui Reference: Fernandez A, Lynch M. Non-adaptive origins of interactome complexity. Nature, 474: 502-505 (2011). [PDF] |
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