QianLab
Institute of Genetics and Developmental Biology
Chinese Academy of Sciences
 
 
 
 
Alumni
Teaching

~~Journal Club ~~

   
 

 

Jan 10, 2018
Presenter: WenQin Cao
Paper:
Rabani M, Pieper L, Chew GL, et al.
A Massively Parallel Reporter Assay of 30 UTR Sequences Identifies In Vivo Rules for mRNA Degradation
(2017) Mol Cell. 68 (6):1083-1094.e5 doi:10.1016/j.molcel.2017.11.014.

Jan 03, 2018
Presenter: Xiao Chu
Paper:
Enge M, Arda HE, Mignardi M, et al.
Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns
(2017) Cell. 171 (2):321-330. doi: 10.1016/j.cell.2017.09.004

Dec 27, 2017
Presenter: Chaorui Duan
Paper:
Muniz L, Deb MK, Aguirrebengoa M, et al.
Control of Gene Expression in Senescence through Transcriptional Read-Through of Convergent Protein-Coding Genes
(2017) Cell Rep. 21 (9):2433-2446. doi: 10.1016/j.celrep.2017.11.006.

Dec 20, 2017
Presenter: Yu Wang
Paper:
Barbieri I, Tzelepis K, Pandolfini L, et al.
Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control
(2017) Nature 552: (7683):126-131. doi: 10.1038/nature24678.

Oct 11, 2017
Presenter:
Paper:
Hubstenberger A, Courel M, Benard M, et al.
P-Body Purification Reveals the Condensation of Repressed mRNA Regulons
(2017) Mol Cell. 68 (1):1-14. doi: 10.1016/j.molcel.2017.09.003

Sep 27, 2017
Presenter: Qing Huan
Paper:
Teschendorff AE, Enver T
Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome
(2017) Nat. Commun. 8 15599. doi : 10.1038/ncomms15599.

Sep 20, 2017
Presenter: Wenqing Cao
Paper:
Kustatscher G, Grabowski P, Rappsilber J.
Pervasive coexpression of spatially proximal genes is buffered at the protein level.
(2017) Mol Syst Biol. 13 (8):937. doi: 10.15252/msb.20177548.

Sep 13, 2017
Presenter: Xiao Chu
Paper:
Nagano T, Lubling Y, Varinai C, Dudley C, Leung W, Baran Y, Mendelson Cohen N, Wingett S, Fraser P, Tanay A.
Cell-cycle dynamics of chromosomal organization at single-cell resolution.
(2017) Nature. 547 (7661):61-67. doi: 10.1038/nature23001.

Sep 6, 2017
Presenter: Chaorui Duan
Paper:
Lin L, Jiang P, Park JW, Wang J, Lu ZX, Lam MP, Ping P, Xing Y.
The contribution of Alu exons to the human proteome.
(2016) Genome Biol. 17 :15. doi: 10.1186/s13059-016-0876-5.

Aug 30, 2017
Presenter: Siyu Chen
Paper:
Peng G, Suo S, Chen J, Chen W, Liu C, Yu F, Wang R, Chen S, Sun N, Cui G, Song L, Tam PP, Han JD, Jing N.
Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo.
(2016) Dev Cell. 36 (6):681-97. doi: 10.1016/j.devcel.2016.02.020.

Aug 23, 2017
Presenter: Linghui Tang
Paper:
Jin Y, Eser U, Struhl K, Churchman LS.
The Ground State and Evolution of Promoter Region Directionality.
(2017) Cell. pii: S0092-8674 (17)30813-9. doi: 10.1016/j.cell.2017.07.006

Aug 9, 2017
Presenter: Shaohuan Wu
Paper:
Shah P, Gilchrist MA.
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.
(2010) PLoS Genet. 6 (9):e1001128. doi: 10.1371/journal.pgen.1001128

Aug 2, 2017
Presenter: Kejia Shan
Paper:
Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ.
The evolutionary landscape of alternative splicing in vertebrate species.
(2012) Science. 338 (6114):1587-93

Jul 26, 2017
Presenter: Yuliang Zhang
Paper:
Shi Z, Fujii K, Kovary KM, Genuth NR, Rost HL, Teruel MN, Barna M.
Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.
(2017) Mol Cell. 67 (1):71-83.e7

Jul 19, 2017
Presenter: Yanming Chen
Paper:
Wang X, Hou J, Quedenau C, Chen W.
Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals.
(2016) Mol Syst Biol. 12 (7):875

Jun 28, 2017
Presenter: Taolan Zhao
Paper:
Pelechano V, Alepuz P.
eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences.
(2017) Nucleic Acids Res. 26 doi: 10.1093/nar/gkx479

Jun 21, 2017
Presenter: Ke Li
Paper:
Slobodin B, Han R, Calderone V, Vrielink JA, Loayza-Puch F, Elkon R, Agami R.
Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation.
(2017) Cell. 169 (2):326-337.e12

Jun 14, 2017
Presenter: Ying Chen
Paper:
Nocedal I, Mancera E, Johnson AD.
Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator.
(2017) Elife. pii: e23250

Jun 7, 2017
Presenter: Qing Huan
Paper:
Swings T, Van den Bergh B, Wuyts S, Oeyen E, Voordeckers K, Verstrepen KJ, Fauvart M, Verstraeten N, Michiels J.
Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli.
(2017) Elife. pii: e22939

May 31, 2017
Presenter: Wenqing Cao
Paper:
Wu X, Bartel DP.
Widespread Influence of 3'-End Structures on Mammalian mRNA Processing and Stability.
(2017) Cell. 169 (5):905-917.e11

May 24, 2017
Presenter: Xiao Chu
Paper:
Schor IE, Degner JF, Harnett D, Cannav, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE.
Promoter shape varies across populations and affects promoter evolution and expression noise.
(2017) Nat Genet. 49 (4):550-558

May 17, 2017
Presenter: Chaorui Duan
Paper:
Long H, Miller SF, Strauss C, Zhao C, Cheng L, Ye Z, Griffin K, Te R, Lee H, Chen CC, Lynch M.
Antibiotic treatment enhances the genome-wide mutation rate of target cells.
(2016) PNAS. 113 (18):E2498-505

May 10, 2017
Presenter: Siyu Chen
Paper:
Burkhardt DH, Rouskin S, Zhang Y, Li GW, Weissman JS, Gross CA.
Operon mRNAs are organized into ORF-centric structures that predict translation efficiency.
(2017) Elife. 6 pii: e22037

Apr 26, 2017
Presenter: Shaohuan Wu
Paper:
Franks A, Airoldi E, Slavov N.
Post-transcriptional regulation across human tissues.
(2015) bioRxiv. doi: http://dx.doi.org/10.1101/020206

Apr 19, 2017
Presenter: Kejia Shan
Paper:
Marquez Y, Hopfler M, Ayatollahi Z, Barta A, Kalyna M.
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
(2015) Genome Res. 25 (7):995-1007

Apr 12, 2017
Presenter: Jia Wang
Paper:
He BZ, Zhou X, O'Shea EK.
Evolution of reduced co-Activator dependence led to target expansion of a starvation response pathway.
(2017) bioRxiv. doi: https://doi.org/10.1101/101154

Apr 5, 2017
Presenter: Xiaoqing Zhang
Paper:
Lall S, Friedman CC, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Davis RE.
Contribution of trans-splicing, 5' -leader length, cap-poly(A) synergism, and initiation factors to nematode translation in an Ascaris suum embryo cell-free system.
(2004) J Biol Chem. 279 (44):45573-85

Mar 29, 2017
Presenter: Taolan Zhao
Paper:
Sendoel A, Dunn JG, Rodriguez EH, Naik S, Gomez NC, Hurwitz B, Levorse J, Dill BD, Schramek D, Molina H, Weissman JS, Fuchs E.
Translation from unconventional 5' start sites drives tumour initiation.
(2017) Nature. 541 (7638):494-499

Mar 22, 2017
Presenter: Wenfeng Qian
Paper:
Reinius B, Mold JE, Ramskold D, Deng Q, Johnsson P, Michaelsson J, Frisen J, Sandberg R.
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.
(2016) Nat Genet. 48 (11):1430-1435

Mar 15, 2017
Presenter: Ke Li
Paper:
Adamson B, Norman TM, Jost M, Cho MY, Nunez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS.
A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response.
(2016) Cell. 167 (7):1867-1882

Mar 8, 2017
Presenter: Ying Chen
Paper:
Ma L, Zhao B, Chen K, Thomas A, Tuteja JH, He X, He C, White KP.
Evolution of transcript modification by N6-methyladenosine in primates.
(2017) Genome Res. 27 (3):385-392

Mar 1, 2017
Presenter: Qing Huan
Paper:
Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, Maldotti M, Anselmi F, Oliviero S.
Intragenic DNA methylation prevents spurious transcription initiation.
(2017) Nature doi:10.1038/nature21373.

Feb 22, 2017
Presenter: Wenqing Cao
Paper:
Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Bruning L, Raineri E, Navarro P, Bohnsack MT, Leidel SA, Diez J.
A novel translational control mechanism involving RNA structures within coding sequences.
(2017) Genome Res. 27 (1):95-106

Feb 15, 2017
Presenter: Xiao Chu
Paper:
Swart EC, Serra V, Petroni G, Nowacki M.
Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination
(2016) Cell 166 (3):691-702

Feb 8, 2017
Presenter: Chaorui Duan
Paper:
Chen X, Yang JR, Zhang J.
Nascent RNA folding mitigates transcription-associated mutagenesis
(2016) Genome Res 26 (1):50-9

Jan 11, 2017
Presenter: Siyu Chen
Paper:
Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y.
Gene Architectures that Minimize Cost of Gene Expression
(2017) Mol Cell 65 (1):142-153

Jan 4, 2017
Presenter: Shaohuan Wu
Paper:
Battle A; Khan Z; Wang SH; Mitrano A; Ford MJ; Pritchard JK; Gilad Y.
Impact of regulatory variation from RNA to protein
(2015) Science 347 (6222):664-7

Dec 28, 2016
Presenter: Kejia Shan
Paper:
Xiao MS; Zhang B; Li YS; Gao Q; Sun W; Chen W.
Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation
(2016) Mol Syst Biol. 12 (12):890

Dec 21, 2016
Presenter: Wenqing Cao
Paper:
Sigova AA; Abraham BJ; Ji X; Molinie B; Hannett NM; Guo YE; Jangi M; Giallourakis CC; Sharp PA; Young RA.
Transcription factor trapping by RNA in gene regulatory elements
(2015) Science 350 (6263):978-81

Dec 14, 2016
Presenter: Xiao Chu
Paper:
Lange, J.; Yamada, S.; Tischfield, S. E.; Pan, J.; Kim, S.; Zhu, X.; Socci, N. D.; Jasin, M.; Keeney, S.
The landscape of mouse meiotic double-strand break formation, processing, and repair
(2016) Cell 167 (3):695-708

Nov 30, 2016
Presenter: Jia Wang
Paper:
Heyer, E. E.; Moore, M. J.
Redefining the translational status of 80S monosomes
(2016) Cell 164 (4):757-69

Nov 23, 2016
Presenter: Xiaoqing Zhang
Paper:
Mohammad, F.; Woolstenhulme, C. J.; Green, R.; Buskirk, A. R.
Clarifying the translational pausing landscape in bacteria by ribosome profiling
(2016) Cell Rep 14 (4):686-94

Nov 16, 2016
Presenter: Taolan Zhao
Paper:
Chotewutmontri, P.; Barkan, A.
Dynamics of chloroplast translation during chloroplast differentiation in maize
(2016) PLoS Genet 12 (7):e1006106

Nov 9, 2016
Presenter: Yanan Han
Paper:
Engreitz, J. M.; Haines, J. E.; Perez, E. M.; Munson, G.; Chen, J.; Kane, M.; McDonel, P. E.; Guttman, M.; Lander, E. S.
Local regulation of gene expression by lncRNA promoters, transcription and splicing
(2016) Nature

Nov 2, 2016
Presenter: Ke Li
Paper:
Yan, X.; Hoek, T. A.; Vale, R. D.; Tanenbaum, M. E.
Dynamics of Translation of Single mRNA Molecules In Vivo
(2016) Cell 165 (4):976-89

Oct 26, 2016
Presenter: Ying Chen
Paper:
Healey, D.; Axelrod, K.; Gore, J.
Negative frequency-dependent interactions can underlie phenotypic heterogeneity in a clonal microbial population
(2016) Mol Syst Biol 12 (8):877

Oct 19, 2016
Presenter: Qing Huan
Paper:
Archer, S. K.; Shirokikh, N. E.; Beilharz, T. H.; Preiss, T.
Dynamics of ribosome scanning and recycling revealed by translation complex profiling
(2016) Nature 535 (7613):570-4

Oct 12, 2016
Presenter: Chaorui Duan
Paper:
Johnstone, T. G.; Bazzini, A. A.; Giraldez, A. J.
Upstream ORFs are prevalent translational repressors in vertebrates
(2016) EMBO J 35 (7):706-23

Sep 21, 2016
Presenter: Siyu Chen
Paper:
Radhakrishnan, A.; Chen, Y. H.; Martin, S.; Alhusaini, N.; Green, R.; Coller, J.
The DEAD-box protein Dhh1p couples mRNA decay and translation by monitoring codon optimality
(2016) Cell DOI: http://dx.doi.org/10.1016/j.cell.2016.08.053

Sep 14, 2016
Presenter: Yufei Yang
Paper:
Bazzini, A. A.; Del Viso, F.; Moreno-Mateos, M. A.; Johnstone, T. G.; Vejnar, C. E.; Qin, Y.; Yao, J.; Khokha, M. K.; Giraldez, A. J.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
(2016) EMBO J e201694699

Sep 7, 2016
Presenter: Shaohuan Wu
Paper:
Keren, L.; Hausser, J.; Lotan-Pompan, M.; Vainberg Slutskin, I.; Alisar, H.; Kaminski, S.; Weinberger, A.; Alon, U.; Milo, R.; Segal, E.
Massively parallel interrogation of the effects of gene expression levels on fitness
(2016) Cell 166 (5):1282-94

Aug 23, 2016
Presenter: Yanming Chen
Paper:
Frokjaer-Jensen, C.; Jain, N.; Hansen, L.; Davis, M. W.; Li, Y.; Zhao, D.; Rebora, K.; Millet, J. R.; Liu, X.; Kim, S. K.; Dupuy, D.; Jorgensen, E. M.; Fire, A. Z.
An abundant class of non-coding DNA can prevent stochastic gene silencing in the C. elegans germline
(2016) Cell 166 (2):343-57

Aug 17, 2016
Presenter: Xiaoqing Zhang
Paper:
Guydosh, N. R.; Green, R.
Dom34 Rescues Ribosomes in 3' untranslated Regions
(2014) Cell 156 (5):950-62

Aug 10, 2016
Presenter: Yuliang Zhang
Paper:
Kachroo, A. H.; Laurent, J. M.; Yellman, C. M.; Meyer, A. G.; Wilke, C. O.; Marcotte, E. M.
Systematic humanization of yeast genes reveals conserved functions and genetic modularity
(2015) Science 348 (6237):921-5

Aug 3, 2016
Presenter: Qing Huan
Paper:
Gamble, C. E.; Brule, C. E.; Dean, K. M.; Fields, S.; Grayhack, E. J.
Adjacent codons act in concert to modulate translation efficiency in yeast
(2016) Cell 166 (3):679-90

Jul 27, 2016
Presenter: Taolan Zhao
Paper:
McKenna, A.; Findlay, G. M.; Gagnon, J. A.; Horwitz, M. S.; Schier, A. F.; Shendure, J.
Whole organism lineage tracing by combinatorial and cumulative genome editing
(2016) Science

Jul 20, 2016
Presenter: Yanan Han
Paper:
Chen, X.; Zhang, J.
The genomic landscape of position effects on protein expression level and noise in yeast
(2016) Cell Syst 2 (5):347-54

Jun 29, 2016
Presenter: Ke Li
Paper:
Couvillion, M. T.; Soto, I. C.; Shipkovenska, G.; Churchman, L. S.
Synchronized mitochondrial and cytosolic translation programs
(2016) Nature 533 (7604):499-503

Jun 22, 2016
Presenter: Ying Chen
Paper:
Huber, F.; Bunina, D.; Gupta, I.; Khmelinskii, A.; Meurer, M.; Theer, P.; Steinmetz, L. M.; Knop, M.
Protein abundance control by non-coding antisense transcription
(2016) Cell Rep

Jun 15, 2016
Presenter: Qing Huan
Paper:
Arribere, J. A.; Cenik, E. S.; Jain, N.; Hess, G. T.; Lee, C. H.; Bassik, M. C.; Fire, A. Z.
Translation readthrough mitigation
(2016) Nature

Jun 1, 2016
Presenter: Xiao Chu
Paper:
Lu, Z.; Zhang, Q. C.; Lee, B.; Flynn, R. A.; Smith, M. A.; Robinson, J. T.; Davidovich, C.; Gooding, A. R.; Goodrich, K. J.; Mattick, J. S.; Mesirov, J. P.; Cech, T. R.; Chang, H. Y.
RNA duplex map in living cells reveals higher-order transcriptome structure
(2016) Cell 165 (5):1267-79

May 18, 2016
Presenter: Siyu Chen
Paper:
Sarkisyan, K. S.; Bolotin, D. A.; Meer, M. V.; Usmanova, D. R.; Mishin, A. S.; Sharonov, G. V.; Ivankov, D. N.; Bozhanova, N. G.; Baranov, M. S.; Soylemez, O.; Bogatyreva, N. S.; Vlasov, P. K.; Egorov, E. S.; Logacheva, M. D.; Kondrashov, A. S.; Chudakov, D. M.; Putintseva, E. V.; Mamedov, I. Z.; Tawfik, D. S.; Lukyanov, K. A.; Kondrashov, F. A.
Local fitness landscape of the green fluorescent protein
(2016) Nature 533 (7603):397-401

May 11, 2016
Presenter: Yufei Yang
Paper:
Zhang, D.; Bai, L.
Interallelic interaction and gene regulation in budding yeast
(2016) PNAS 113 (16):4428-33

May 4, 2016
Presenter: Shaohuan Wu
Paper:
Gu, W.; Zhou, T.; Wilke, C. O.
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
(2010) PLoS Comput Biol 6 (2):e1000664

Apr 27, 2016
Presenter: Jia Wang
Paper:
Young, D. J.; Guydosh, N. R.; Zhang, F.; Hinnebusch, A. G.; Green, R.
Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3'UTRs In Vivo
(2015) Cell 162 (4):872-84

Mar 23, 2016
Presenter: Ke Li
Paper:
Velten, L.; Anders, S.; Pekowska, A.; Jarvelin, A. I.; Huber, W.; Pelechano, V.; Steinmetz, L. M.
Single-cell polyadenylation site mapping reveals 3' isoform choice variability
(2015) Mol Syst Biol 11 (6):812

Mar 16, 2016
Presenter: Yuliang Zhang
Paper:
Chong, Y. T.; Koh, J. L.; Friesen, H.; Duffy, S. K.; Cox, M. J.; Moses, A.; Moffat, J.; Boone, C.; Andrews, B. J.
Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis
(2015) Cell 161 (6):1413-24

Mar 9, 2016
Presenter: Yanming Chen
Paper:
Uphoff, S.; Lord, N. D.; Okumus, B.; Potvin-Trottier, L.; Sherratt, D. J.; Paulsson, J.
Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation
(2016) Science 351 (6277):1094-1097

Feb 24, 2016
Presenter: Ying Chen
Paper:
Kafri, M.; Metzl-Raz, E.; Jona, G.; Barkai, N.
The Cost of Protein Production
(2016) Cell Rep 14 (1):22-31

Feb 17, 2016
Presenter: Qing Huan
Paper:
Dominissini, D.; Nachtergaele, S.; Moshitch-Moshkovitz, S.; Peer, E.; Kol, N.; Ben-Haim, M. S.; Dai, Q.; Di Segni, A.; Salmon-Divon, M.; Clark, W. C.; Zheng, G.; Pan, T.; Solomon, O.; Eyal, E.; Hershkovitz, V.; Han, D.; Dore, L. C.; Amariglio, N.; Rechavi, G.; He, C.
The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
(2016) Nature

Jan 27, 2016
Presenter: Wenqing Cao
Paper:
Liu, G.; Yong, M. Y.; Yurieva, M.; Srinivasan, K. G.; Liu, J.; Lim, J. S.; Poidinger, M.; Wright, G. D.; Zolezzi, F.; Choi, H.; Pavelka, N.; Rancati, G.
Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability
(2015) Cell 163 (6):1388-99.

Jan 13, 2016
Presenter: Chaorui Duan
Paper:
Holmes, R. K.; Tuck, A. C.; Zhu, C.; Dunn-Davies, H. R.; Kudla, G.; Clauder-Munster, S.; Granneman, S.; Steinmetz, L. M.; Guthrie, C.; Tollervey, D.
Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough
(2015) PLoS Genet 11 (12):e1005735.

Dec 30, 2015
Presenter: Siyu Chen
Paper:
Larson, M. H.; Mooney, R. A.; Peters, J. M.; Windgassen, T.; Nayak, D.; Gross, C. A.; Block, S. M.; Greenleaf, W. J.; Landick, R.; Weissman, J. S.
A pause sequence enriched at translation start sites drives transcription dynamics in vivo
(2014) Science 344 (6187):1042-1047.

Dec 23, 2015
Presenter: Xiaoqing Zhang
Paper:
Thoreen, C. C.; Chantranupong, L.; Keys, H. R.; Wang, T.; Gray, N. S.; Sabatini, D. M.
A unifying model for mTORC1-mediated regulation of mRNA translation
(2012) Nature 485 (7396):109-13.

Dec 16, 2015
Presenter: Yufei Yang
Paper:
Rosenberg, A. B.; Patwardhan, R. P.; Shendure, J.; Seelig, G.
Learning the sequence determinants of alternative splicing from millions of random sequences
(2015) Cell 163 (3):698-711.

Dec 9, 2015
Presenter: Shaohuan Wu
Paper:
Michel, A. M.; Choudhury, K. R.; Firth, A. E.; Ingolia, N. T.; Atkins, J. F.; Baranov, P. V.
Observation of dually decoded regions of the human genome using ribosome profiling data
(2015) Genome Res 22 (11):2219-29.

Dec 2, 2015
Presenter: Jia Wang
Paper:
Costello, J.; Castelli, L. M.; Rowe, W.; Kershaw, C. J.; Talavera, D.; Mohammad-Qureshi, S. S.; Sims, P. F.; Grant, C. M.; Pavitt, G. D.; Hubbard, S. J.; Ashe, M. P.
Global mRNA selection mechanisms for translation initiation
(2015) Genome Biol 16 :10.

Nov 18, 2015
Presenter: Yuliang Zhang
Paper:
Kong, Y.; Zhou, H.; Yu, Y.; Chen, L.; Hao, P.; Li, X.
The evolutionary landscape of intergenic trans-splicing events in insects
(2015) Nat Commun 6 :8734.

Nov 4, 2015
Presenter: Ying Chen
Paper:
Hansen, A. S.O'Shea, E. K.
cis Determinants of promoter threshold and activation timescale
(2015) Cell Rep 12 (8):1226-33.

Oct 28, 2015
Presenter: Qing Huan
Paper:
Zhou, J.; Wan, J.; Gao, X.; Zhang, X.; Jaffrey, S. R.; Qian, S. B.
Dynamic m(6)A mRNA methylation directs translational control of heat shock response
(2015) Nature 526 (7574):591-4.

Oct 21, 2015
Presenter: Wenqing Cao
Paper:
Zhang, Z. G.; Zhou, L.; Hu, L. D.; Zhu, Y. F.; Xu, H.; Liu, Y.; Chen, X. F.; Yi, X. F.; Kong, X. Y.; Hurst, L. D.
Nonsense-mediated decay targets have multiple sequence-related features that can inhibit translation
(2010) Mol Syst Biol 6 :442.

Oct 14, 2015
Presenter: Xiao Chu
Paper:
van Dijk, D.; Dhar, R.; Missarova, A. M.; Espinar, L.; Blevins, W. R.; Lehner, B.; Carey, L. B.
Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage
(2015) Nat Commun 6.

Sep 30, 2015
Presenter: Chaorui Duan
Paper:
Shor, E.; Fox, C. A.; Broach, J. R.
The yeast environmental stress response regulates mutagenesis induced by proteotoxic stress
(2013) PLoS Genet 9 (8):e1003680.

Sep 23, 2015
Presenter: Ke Li
Paper:
Presnyak, V.; Alhusaini, N.; Chen, Y. H.; Martin, S.; Morris, N.; Kline, N.; Olson, S.; Weinberg, D.; Baker, K. E.; Graveley, B. R.; Coller, J.
Codon optimality is a major determinant of mRNA stability
(2015) Cell 160 (6):1111-24.

Sep 16, 2015
Presenter: Siyu Chen
Paper:
Weinberg, David E.; Shah, Premal; Eichhorm, Stephen W.; Hussmann, Jeffrey A.; Plotkin, Joshua B.; Bartel, David P.
Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation
(2015) bioRxiv June 26.

Sep 9, 2015
Presenter: Xiaoqing Zhang
Paper:
Sen, N. D.; Zhou, F.; Ingolia, N. T.; Hinnebusch, A. G.
Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
(2015) Genome Res 25 (8):1196-205.

Sep 2, 2015
Presenter: Yufei Yang
Paper:
Guo, Y. Xu, Q.; Canzio, D.; Shou, J.; Li, J.; Gorkin, D. U.; Jung, I.; Wu, H.; Zhai, Y.; Tang, Y.; Lu, Y.; Wu, Y.; Jia, Z.; Li, W.; Zhang, M. Q.; Ren, B.; Krainer, A. R.; Maniatis, T.; Wu, Q.
CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function
(2015) Cell 162 (4):900-10.

Aug 26, 2015
Presenter: Shaohuan Wu
Paper:
Stadler, M.; Fire, A.
Conserved translatome remodeling in nematode species executing a shared developmental transition
(2013) PLoS Genet 9 (10):e1003739.

Aug 5, 2015
Presenter: Xiao Chu
Paper:
Yang, S.; Wang, L.; Huang, J.; Zhang, X.; Yuan, Y.; Chen, J. Q.; Hurst, L. D.; Tian, D.
Parent-progeny sequencing indicates higher mutation rates in heterozygotes
(2015) Nature 523 (7561):463-7.

Jul 8, 2015
Presenter: Chaorui Duan
Paper:
Schmid, M.; Olszewski, P.; Pelechano, V.; Gupta, I.; Steinmetz, L. M.; Jensen, T. H.
The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production
(2015) Cell Rep 12 (1):1-12.

Jul 1, 2015
Presenter: Ke Li
Paper:
Pelechano, V.; Wei, W.; Steinmetz, L. M.
Widespread co-translational RNA decay reveals ribosome dynamics
(2015) Cell 161 (6):1400-12.

Jun 24, 2015
Presenter: Siyu Chen
Paper:
Parenteau, J.; Durand, M.; Morin, G.; Gagnon, J.; Lucier, J. F.; Wellinger, R. J.; Chabot, B.; Elela, S. A.
Introns within ribosomal protein genes regulate the production and function of yeast ribosomes
(2011) Cell 147 (2):320-31.

Jun 17, 2015
Presenter: Xiaoqing Zhang
Paper:
Schafer, S.; Adami, E.; Heinig, M.; Rodrigues, K. E.; Kreuchwig, F.; Silhavy, J.; van Heesch, S.; Simaite, D.; Rajewsky, N.; Cuppen, E.; Pravenec, M.; Vingron, M.; Cook, S. A.; Hubner, N.
Translational regulation shapes the molecular landscape of complex disease phenotypes
(2015) Nat Commun 6 :7200.

Jun 10, 2015
Presenter: Yufei Yang
Paper:
Metzger, B. P.; Yuan, D. C.; Gruber, J. D.; Duveau, F.; Wittkopp, P. J.
Selection on noise constrains variation in a eukaryotic promoter
(2015) Nature 521 (7552):344-7.

Jun 3, 2015
Presenter: Shaohuan Wu
Paper:
Burga, A.; Casanueva, M. O.; Lehner, B.
Predicting mutation outcome from early stochastic variation in genetic interaction partners
(2011) Nature 480 (7376):250-3.

May 27, 2015
Presenter: Wenqing Cao
Paper:
Kennedy, S. R.; Schultz, E. M.; Chappell, T. M.; Kohrn, B.; Knowels, G. M.; Herr, A. J.
Volatility of mutator phenotypes at single cell resolution
(2015) PLoS Genet 11 (4):e1005151.

Apr 22, 2015
Presenter: Ke Li
Paper:
Gruber, J. D.; Vogel, K.; Kalay, G.; Wittkopp, P. J.
Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance
(2012) PLoS Genet 8 (2):e1002497.

Apr 8, 2015
Presenter: Yanan Han
Paper:
Yang, J. R.; Chen, X.; Zhang, J.
Codon-by-codon modulation of translational speed and accuracy via mRNA folding
(2014) PLoS Biol 12 (7):e1001910.

Apr 1, 2015
Presenter: Xiao Chu
Paper:
Weinberger, L.; Voichek, Y.; Tirosh, I.; Hornung, G.; Amit, I.; Barkai, N.
Expression noise and acetylation profiles distinguish HDAC functions.
(2012) Mol Cell 47 (2):193-202.

Mar 25, 2015
Presenter: Yufei Yang
Paper:
Povolotskaya, I. S.; Kondrashov, F. A.
Sequence space and the ongoing expansion of the protein universe.
(2010) Nature 465 (7300):922-6.

Mar 18, 2015
Presenter: Shaohuan Wu
Paper:
Podgornaia, A. I.; Laub, M. T.
Pervasive degeneracy and epistasis in a protein-protein interface.
(2015) Science 347 (6222):673-7.

Mar 11th, 2015
Presenter: Wenqing Cao
Paper:
Stiffler, M. A.; Hekstra, D. R.; Ranganathan, R.
Evolvability as a function of purifying selection in TEM-1 beta-Lactamase
(2015) Cell 160 (5):882-92.

Jan 21th, 2015
Presenter: Wenqing Cao
Paper:
DeLuna, A.; Springer, M.; Kirschner, M. W.; Kishony, R.
Need-based up-regulation of protein levels in response to deletion of their duplicate genes
(2010) PLoS Biol 8 (3):e1000347.

Jan 14th, 2015
Presenter: Ke Li
Paper:
Zeevi, D.; Lubliner, S.; Lotan-Pompan, M.; Hodis, E.; Vesterman, R.; Weinberger, A.; Segal, E.
Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
(2014) Genome Res 24 (12):1991-9.

Jan 7th, 2015
Presenter: Qing Huan
Paper:
Dori-Bachash, M.; Shema, E.; Tirosh, I.
Coupled evolution of transcription and mRNA degradation
(2011) PLoS Biol 9 (7):e1001106.

Dec 31th, 2014
Presenter: Siyu Chen
Paper:
Verzijlbergen, K. F.; van Welsem, T.; Sie, D.; Lenstra, T. L.; Turner, D. J.; Holstege, F. C.; Kerkhoven, R. M.; van Leeuwen, F.
A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover
(2011) PLoS Genet 7 (10):e1002284.

Dec 17th, 2014
Presenter: Xiaoqing Zhang
Paper:
Li, G. W.; Burkhardt, D.; Gross, C.; Weissman, J. S.
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources
(2014) Cell 157 (3):624-35.

Dec 3th, 2014
Presenter: Yufei Yang
Paper:
Sharon, E.; van Dijk, D.; Kalma, Y.; Keren, L.; Manor, O.; Yakhini, Z.; Segal, E.
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
(2014) Genome Res 24 (10):1698-706.

Nov 26th, 2014
Presenter: Yanan Han
Paper:
Bank, C.; Hietpas, R. T.; Jensen, J. D.; Bolon, D. N.
A systematic survey of an intragenic epistatic landscape
(2014) Mol Biol Evol

Nov 19th, 2014
Presenter: Wenfeng Qian
Paper:
Albert, F. W.; Treusch, S.; Shockley, A. H.; Bloom, J. S.; Kruglyak, L.
Genetics of single-cell protein abundance variation in large yeast populations
(2014) Nature 506 (7489):494-7.

Nov 5th, 2014
Presenter: Xiao Chu
Paper:
Xu, G.; Zhang, J.
Human coding RNA editing is generally nonadaptive
(2014) Proc Natl Acad Sci U S A 111 (10):3769-74.

Oct 29th, 2014
Presenter: Wenqing Cao
Paper:
Hemani, G.; Shakhbazov, K.; Westra, H. J.; Esko, T.; Henders, A. K.; McRae, A. F.; Yang, J.; Gibson, G.; Martin, N. G.; Metspalu, A.; Franke, L.; Montgomery, G. W.; Visscher, P. M.; Powell, J. E.
Detection and replication of epistasis influencing transcription in humans
(2014) Nature 508 (7495):249-53.

Oct 22th, 2014
Presenter: Chaorui Duan
Paper:
Zhang, X. O.; Wang, H. B.; Zhang, Y.; Lu, X.; Chen, L. L.; Yang, L.
Complementary sequence-mediated exon circularization
(2014) Cell 159 (1):134-47.

Sep 24th, 2014
Presenter: Shaohuan Wu
Paper:
Lehner, B.
Conflict between noise and plasticity in yeast
(2010) PLoS Genet 6 (11):e1001185.

Sep 17th, 2014
Presenter: Qiushi Sun
Paper:
Li, G. W.; Oh, E.; Weissman, J. S.
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
(2012) Nature 484 (7395):538-41.

Sep 10th, 2014
Presenter: Siyu Chen
Paper:
Stergachis, A. B.;Haugen, E.; Shafer, A.;Fu, W.; Vernot, B.;Reynolds, A.; Raubitschek, A.;Ziegler, S.;LeProust, E. M.;Akey, J. M.; Stamatoyannopoulos, J. A.
Exonic transcription factor binding directs codon choice and affects protein evolution
(2013) Science 342 (6164):1367-72.

Aug 27th, 2014
Presenter: Qing Huan
Paper:
Zid, B. M.; O'Shea, E. K.
Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast
(2014) Nature Published online 03 August 2014.

Aug 20th, 2014
Presenter: Xiaoyu Li
Paper:
Guo, H.; Zhu, P.; Yan, L.; Li, R.; Hu, B.; Lian, Y.; Yan, J.; Ren, X.; Lin, S.; Li, J.; Jin, X.; Shi, X.; Liu, P.; Wang, X.; Wang, W.; Wei, Y.; Li, X.; Guo, F.; Wu, X.; Fan, X.; Yong, J.; Wen, L.; Xie, S. X.; Tang, F.; Qiao, J.
The DNA methylation landscape of human early embryos
(2014) Nature 511 (7511):606-10.

Jul 23th, 2014
Presenter: Xiao Chu
Paper:
Subtelny, A. O.; Eichhorn, S. W.; Chen, G. R.; Sive, H.; Bartel, D. P.
Poly(A)-tail profiling reveals an embryonic switch in translational control
(2014) Nature 508 (7494):66-71.

Jul 16th, 2014
Presenter: Yingshu Li
Paper:
Chen, M.; Licon, K.; Otsuka, R.; Pillus, L.; Ideker, T.
Decoupling epigenetic and genetic effects through systematic analysis of gene position
(2013) Cell Rep 3 (1):128-37.

Jul 9th, 2014
Presenter: Qiushi Sun
Paper:
Sharon, E.; Kalma, Y.; Sharp, A.; Raveh-Sadka, T.; Levo, M.; Zeevi, D.; Keren, L.; Yakhini, Z.; Weinberger, A.; Segal, E.
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
(2012) Nat Biotechnol 30 (6):521-30.

Jul 2th, 2014
Presenter: Wenfeng Qian
Paper:
Lang, G. I.; Botstein, D.
A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast
(2011) PLoS One 6 (9):e25290.

Jun 25th, 2014
Presenter: Shaohuan Wu
Paper:
Marinov, G. K.; Williams, B. A.; McCue, K.; Schroth, G. P.; Gertz, J.; Myers, R. M.; Wold, B. J.
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing
(2014) Genome Res 24 (3):496-510.

Jun 4th, 2014
Presenter: Yufei Yang
Paper:
Kilpinen, H.; Waszak, S. M.; Gschwind, A. R.; Raghav, S. K.; Witwicki, R. M.; Orioli, A.; Migliavacca, E.; Wiederkehr, M.; Gutierrez-Arcelus, M.; Panousis, N. I.; Yurovsky, A.; Lappalainen, T.; Romano-Palumbo, L.; Planchon, A.; Bielser, D.; Bryois, J.; Padioleau, I.; Udin, G.; Thurnheer, S.; Hacker, D.; Core, L. J.; Lis, J. T.; Hernandez, N.; Reymond, A.; Deplancke, B.; Dermitzakis, E. T.
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription
(2013) Science 342 (6159):744-7.

May 28th, 2014
Presenter: Siyu Chen
Paper:
Khan, Z.; Ford, M. J.; Cusanovich, D. A.; Mitrano, A.; Pritchard, J. K.; Gilad, Y.
Primate transcript and protein expression levels evolve under compensatory selection pressures
(2013) Science 342 (6162):1100-4.

May 21th, 2014
Presenter: Xiaoqing Zhang
Paper:
McManus, C. J.; May, G. E.; Spealman, P.; Shteyman, A.
Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
(2014) Genome Res 24 (3):422-30.

May 14th, 2014
Presenter: Jin Xu
Paper:
Raj, A.; Rifkin, S. A.; Andersen, E.; van Oudenaarden, A.
Variability in gene expression underlies incomplete penetrance
(2010) Nature 463 (7283):913-8.

May 7th, 2014
Presenter: Qing Huan
Paper:
Chu, D.; Kazana, E.; Bellanger, N.; Singh, T.; Tuite, M. F.; von der Haar, T.
Translation elongation can control translation initiation on eukaryotic mRNAs
(2014) EMBO J. 33 (1):21-34.

Apr 30th, 2014
Presenter: Xiao Chu
Paper:
Dadiani, M.; van Dijk, D.; Segal, B.; Field, Y.; Ben-Artzi, G.; Raveh-Sadka, T.; Levo, M.; Kaplow, I.; Weinberger, A.; Segal, E.
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
(2013) Genome Res 23 (6):966-76.

Apr 16th, 2014
Presenter: Meixiang Li
Paper:
Cortijo, S.; Wardenaar, R.; Colome-Tatche, M.; Gilly, A.; Etcheverry, M.; Labadie, K.; Caillieux, E.; Hospital, F.; Aury, J. M.; Wincker, P.; Roudier, F.; Jansen, R. C.; Colot, V.; Johannes, F.
Mapping the epigenetic basis of complex traits
(2014) Science 343 (6175):1145-8.

Apr 9th, 2014
Presenter: Qiushi Sun
Paper:
Allen, M. A.; Hillier, L. W.; Waterston, R. H.; Blumenthal, T.
A global analysis of C. elegans trans-splicing
(2011) Genome Res 21 (2):255-64.

Apr 2th, 2014
Presenter: Wenfeng Qian
Paper:
Dai, Z.; Xiong, Y.; Dai, X.
Neighboring genes show interchromosomal colocalization after their separation
(2014) Mol Biol Evol doi:10.1093/molbev/msu065.

Mar 26th, 2014
Presenter: Shaohuan Wu
Paper:
Deng, Q.; Ramskold, D.; Reinius, B.; Sandberg, R.
Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
(2014) Science 343 (6167):193-6.

Mar 19th, 2014
Presenter: Yufei Yang
Paper:
Landry, C. R.; Lemos, B.; Rifkin, S. A.; Dickinson, W. J.; Hartl, D. L.
Genetic properties influencing the evolvability of gene expression
(2007) Science 317 (5834):118-21.

Mar 12th, 2014
Presenter: Hui Li
Paper:
Wang, G.; Yang, E.; Brinkmeyer-Langford, C. L.; Cai, J. J.
Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort
(2014) Genetics 196 (2):413-25.

Mar 5th, 2014
Presenter: Xiaoqing Zhang
Paper:
Kudla, G.; Murray, A. W.; Tollervey, D.; Plotkin, J. B.
Coding-sequence determinants of gene expression in Escherichia coli.
(2009) Science 324 (5924):255-8.

Feb 26th, 2014
Presenter: Siyu Chen
Paper:
Kristensen, A. R.; Gsponer, J.; Foster, L. J.
Protein synthesis rate is the predominant regulator of protein expression during differentiation.
(2013) Mol Syst Biol 9 : 689.

Feb 19th, 2014
Presenter: Qing Huan
Paper:
Capaldi, A. P.; Kaplan, T.; Liu, Y.; Habib, N.; Regev, A.; Friedman, N.; O'Shea, E. K.
Structure and function of a transcriptional network activated by the MAPK Hog1.
(2008) Nat Genet 40 (11):1300-6.

Jan 15th, 2014
Presenter: Wenfeng Qian
Paper:
Khan, Z.; Bloom, J. S.; Amini, S.; Singh, M.; Perlman, D. H.; Caudy, A. A.; Kruglyak, L.
Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.
(2012) Mol Syst Biol 8 : 602.

Dec 25th, 2013
Presenter: Wenqing Cao
Paper:
Wilson, M. D.; Barbosa-Morais, N. L.; Schmidt, D.; Conboy, C. M.; Vanes, L.; Tybulewicz, V. L.; Fisher, E. M.; Tavare, S.; Odom, D. T.
Species-specific transcription in mice carrying human chromosome 21.
(2008) Science 322 (5900):434-8.

Dec 4th, 2013
Presenter: Hui Li
Paper:
Hulse, A. M.; Cai, J. J.
Genetic variants contribute to gene expression variability in humans.
(2013) Genetics 193 (1):95-108.

Nov 27th, 2013
Presenter: Siyu Chen
Paper:
Hittinger, C. T.; Carroll, S. B.
Gene duplication and the adaptive evolution of a classic genetic switch.
(2007) Nature 449 (7163):677-81.

Nov 20th, 2013
Presenter: Xiao Chu
Paper:
Gout, J. F.; Thomas, W. K.; Smith, Z.; Okamoto, K.; Lynch, M.
Large-scale detection of in vivo transcription errors.
(2013) Proc Natl Acad Sci U S A 110 (46):18584-9.

Oct 30th, 2013
Presenter: Wenqing Cao
Paper:
Loh, E.; Salk, J. J.; Loeb, L. A.
Optimization of DNA polymerase mutation rates during bacterial evolution.
(2010) Proc Natl Acad Sci U S A 107 (3):1154-9.

Oct 23th, 2013
Presenter: Qing Huan
Paper:
Nagano, A. J.; Sato, Y.; Mihara, M.; Antonio, B. A.; Motoyama, R.; Itoh, H.; Nagamura, Y.; Izawa, T.
Deciphering and prediction of transcriptome dynamics under fluctuating field conditions.
(2012) Cell 151 (6):1358-69.

Oct 16th, 2013
Presenter: Yufei Yang
Paper:
Lappalainen, T.; Sammeth, M.; Friedlander, M. R.; t Hoen, P. A.; Monlong, J.; Rivas, M. A.; Gonzalez-Porta, M.; Kurbatova, N.; Griebel, T.; Ferreira, P. G.; Barann, M.; Wieland, T.; Greger, L.; van Iterson, M.; Almlof, J.; Ribeca, P.; Pulyakhina, I.; Esser, D.; Giger, T.; Tikhonov, A.; Sultan, M.; Bertier, G.; MacArthur, D. G.; Lek, M.; Lizano, E.; Buermans, H. P.; Padioleau, I.; Schwarzmayr, T.; Karlberg, O.; Ongen, H.; Kilpinen, H.; Beltran, S.; Gut, M.; Kahlem, K.; Amstislavskiy, V.; Stegle, O.; Pirinen, M.; Montgomery, S. B.; Donnelly, P.; McCarthy, M. I.; Flicek, P.; Strom, T. M.; Lehrach, H.; Schreiber, S.; Sudbrak, R.; Carracedo, A.; Antonarakis, S. E.; Hasler, R.; Syvanen, A. C.; van Ommen, G. J.; Brazma, A.; Meitinger, T.; Rosenstiel, P.; Guigo, R.; Gut, I. G.; Estivill, X.; Dermitzakis, E. T.; Palotie, A.; Deleuze, J. F.; Gyllensten, U.; Brunner, H.; Veltman, J.; Cambon-Thomsen, A.; Mangion, J.; Bentley, D.; Hamosh, A.
Transcriptome and genome sequencing uncovers functional variation in humans.
(2013) Nature 501 (7468):506-11.

Oct 9th, 2013
Presenter :Wenqing Cao
Paper:
Tirosh, I.; Reikhav, S.; Levy, A. A.; Barkai, N.
A yeast hybrid provides insight into the evolution of gene expression regulation.
(2009) Science 324 (5927):659-62.

Sep 25th, 2013
Presenter :Shaohuan Wu
Paper:
Newman, J. R.; Ghaemmaghami, S.; Ihmels, J.; Breslow, D. K.; Noble, M.; DeRisi, J. L.; Weissman, J. S.
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.
(2006) Nature 441 (7095):840-6.

Sep 18th, 2013
Presenter :Wenfeng Qian
Paper:
Akhtar, W.; de Jong, J.; Pindyurin, A. V.; Pagie, L.; Meuleman, W.; de Ridder, J.; Berns, A.; Wessels, L. F.; van Lohuizen, M.; van Steensel, B.
Chromatin position effects assayed by thousands of reporters integrated in parallel.
(2013) Cell 154 (4):914-27.

Sep 11th, 2013
Presenter :Hui Li
Paper:
Kalinka, A. T.; Varga, K. M.; Gerrard, D. T.; Preibisch, S.; Corcoran, D. L.; Jarrells, J.; Ohler, U.; Bergman, C. M.; Tomancak, P.
Gene expression divergence recapitulates the developmental hourglass model.
(2010) Nature 468 (7325):811-4 .

Sep 4th, 2013
Presenter :Yufei Yang
Paper:
Xue, Z.; Huang, K.; Cai, C.; Cai, L.; Jiang, C. Y.; Feng, Y.; Liu, Z.; Zeng, Q.; Cheng, L.; Sun, Y. E.; Liu, J. Y.; Horvath, S.; Fan, G.
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.
(2013) Nature 500 (7464):593-7 .

Aug 28th, 2013
Presenter :Qing Huan
Paper:
Jonathan M. Raser, Erin K. O'Shea
Control of stochasticity in eukaryotic gene expression.
(2004) Science 304 (5678):1811-4 .

Aug 21th, 2013
Presenter :Xiaoqing Zhang
Paper:
Gloria A. Brar, Moran Yassour, Nir Friedman, Aviv Regev, Nicholas T. Ingolia, Jonathan S. Weissman
High-resolution view of the yeast meiotic program revealed by ribosome profiling.
(2012) Science 335 (6068):552-7 .

Aug 14th, 2013
Presenter :Siyu Chen
Paper: Murat Acar, Jerome T Mettetal & Alexander van Oudenaarden
Stochastic switching as a survival strategy in fluctuating environments.
(2008) Nat Genet 40 (4):471-5 .

Aug 7th, 2013
Presenter :Xiao Chu
Paper: Stephen A Ramsey, Jennifer J Smith, David Orrell, Marcello Marelli, Timothy W Petersen, Pedro de Atauri, Hamid Bolouri & John D Aitchison
Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.
(2006) Nat Genet 38 (9):1082-7 .

Jul 17th, 2013
Presenter :Bingke Jiao
Paper: Bjorn Schwanhausser, Dorothea Busse, Na Li, Gunnar Dittmar, Johannes Schuchhardt, Jana Wolf, Wei Chen & Matthias Selbach
Global quantification of mammalian gene expression control.
(2011) Nature 473 (7347):337-42 .

Jul 17th, 2013
Presenter :Fang Wang
Paper: Eran Eden, Naama Geva-Zatorsky, Irina Issaeva, Ariel Cohen, Erez Dekel, Tamar Danon, Lydia Cohen, Avi Mayo, Uri Alon
Proteome half-life dynamics in living human cells.
(2011) Science 331 (6018):764-8 .

Apr 10th, 2013
Presenter :Yakun Song
Paper: Eric J. Hayden, Evandro Ferrada & Andreas Wagner.
Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme.
(2011) Nature 474 (7349):92-5 .

Apr 4th, 2013
Presenter :Xiao Chu
Paper: Pitt JN, Ferre-D'Amare, A. R.
Rapid construction of empirical RNA fitness landscapes.
(2010) Science 330(6002):376-9.

Mar 27th, 2013

Presenter :Ling Zhu
Paper: Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al.
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
(2012) Nature 485

Presenter:Siyu Chen
Paper:Kertesz M, Wan Y, Mazor E, et al.
Genome-wide measurement of RNA secondary structure in yeast.
(2010) Nature 467

Mar 20th, 2013
Presenter: Yufei Yang
Paper: Moyle LC, Nakazato T
Hybrid Incompatibility ''Snowballs'' Between Solanum Species.
(2010) Science 329, 1521-23

Mar 13th, 2013
Presenter: Hui Li
Paper: Fraser HB, Moses AM, Schadt EE
Evidence for widespread adaptive evolution of gene expression in budding yeast.

(2010) Proc Natl Acad Sci U S A. 107(7):2977-82

Mar 6th, 2013
Presenter: Qing Huan
Paper: Coolon JD, Stevenson KR, McManus CJ, et al.
Genomic imprinting absent in Drosophila melanogaster adult females.
(2012) Cell Rep.2(1):69-75

Feb 27th, 2013
Presenter: Yakun Song
Paper: Wittkopp PJ, Haerum BK, Clark AG.
Regulatory changes underlying expression differences within and between Drosophila species.
(2008) Nat Genet.40(3):346-50

Jan 30th, 2013
Presenter: Ling Zhu
Paper: Smith NG, Eyre-Walker A.
Adaptive protein evolution in Drosophila.
(2002) Nature 415(6875):1022-4

Jan 23th, 2013
Presenter: Siyu Chen
Paper: Dekel E, Alon U.
Optimality and evolutionary tuning of the expression level of a protein.
(2005) Nature 436(7050):588-92.

Jan 16th, 2013
Presenter: Xiao Chu
Paper: Brandman O, Ferrell JE Jr, Li R, Meyer T.
Interlinked fast and slow positive feedback loops drive reliable cell decisions.
(2005) Science 310(5747):496-8

Jan 9th, 2013
Presenter: Wenfeng Qian
Paper: Sorek R, Zhu Y, Creevey CJ, et al.
Genome-wide experimental determination of barriers to horizontal gene transfer.
(2007) Science 318(5855):1449-52.

   
     
     
     
     
     
     
     
       
             
 

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