Univ of Michigan

Dept of Ecol & Evol Biol

2014  
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
2013  
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
2012  
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
2011  
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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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