Dec 18, 2024
Presenter: Shuo Zhang
Paper:Xiaoqiang Zhu, Victor Emmanuel Cruz, He Zhang et al.
Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.
(2024) Science. doi: 10.1126/science.adq8587

May 24, 2023
Presenter: Bingke Jiao
Paper:Wlodzimierz, P., Rabanal, F.A., Burns, R. et al.
Cycles of satellite and transposon evolution in Arabidopsis centromeres.
(2023) Nature. doi:10.1038/s41586-023-06062-z

May 17, 2023
Presenter: Shuya Zhang
Paper:Dylus, D., Altenhoff, A., Majidian, S. et al.
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
(2023) Nat Biotechnol. doi:10.1038/s41587-023-01753-4

March 22, 2023
Presenter: Weiguang Wang
Paper:Verkuil Robert, Kabeli Ori et al.
Language models generalize beyond natural proteins.
(2022) bioRxiv. doi:10.1101/2022.12.21.521521

March 15, 2023
Presenter: Haotian Guo
Paper:Choi, J., Chen, W., Minkina, A et al.
A time-resolved, multi-symbol molecular recorder via sequential genome editing.
(2022) Nature 608, 98–107. doi:10.1038/s41586-022-04922-8

March 1, 2023
Presenter: Yu Wang
Paper:Joseph M. Replogle, Reuben A. Saunders, Angela N. Pogson, ..., Marco Jost, Thomas M. Norman, Jonathan S. Weissman et al.
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.
(2022) Cell 14, 2559-2575.e28. doi:10.1016/j.cell.2022.05.013

February 22, 2023
Presenter: Lu Gao
Paper:Yongjun Qian, Jiayun Li, Shengli Zhao et al.
Programmable RNA sensing for cell monitoring and manipulation.
(2022) Nature 610, 713–721. doi:10.1038/s41586-022-05280-1

February 15, 2023
Presenter: Shuo Zhang
Paper:Ferhat Alkan, Oscar G Wilkins, Santiago Hernández-Pérez et al.
Identifying ribosome heterogeneity using ribosome profiling.
(2022) Nucleic Acids Research 16, e95. doi:10.10.1093/nar/gkac484

July 6, 2022
Presenter: Jinhui Kong
Paper:Samuel A. Raven, Blake Payne, Mitchell Bruce et al.
In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold.
(2022) Nat Chem Biol 18, 403–411. doi:10.1038/s41589-022-00967-y

June 29, 2022
Presenter: WeiGuang Wang
Paper:Brian Hie, Ellen D. Zhong, Bonnie Berger et al.
Learning the language of viral evolution and escape.
(2021) Science 371, 284–288. doi:10.1126/science.abd7331

June 22, 2022
Presenter: HaoTian Guo
Paper:Calum Gabbutt, Ryan O. Schenck, Daniel J. Weisenberger et al.
Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues.
(2022) Nature Biotechnology 40, 720–730. doi:10.1038/s41587-021-01109-w

June 15, 2022
Presenter: Kejia Shan
Paper:Dian Yang, Matthew G. Jones, Santiago Naranjo et al.
Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.
(2022) Cell 185, 1905–1923. doi:10.1016/j.cell.2022.04.015

May 11, 2022
Presenter: Bingke Jiao
Paper:R. KellyDawe, Elizabeth G.Lowry, Jonathan I.Gent et al.
A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize.
(2018) Cell 4, 813-815. doi:10.1016/j.cell.2018.03.009

Apr 18, 2022
Presenter: Yu Wang
Paper:Xiaojie Qiu, Yan Zhang, Jorge D.Martin-Rufino, et al.
Mapping transcriptomic vector fields of single cells.
(2022) Cell 185, 690–711. doi:10.1016/j.cell.2021.12.045

Apr 6, 2022
Presenter: Lu Gao
Paper:Jeffrey A. Hussmann, Jia Ling, Purnima Ravisankar, et al.
Mapping the genetic landscape of DNA double-strand break repair.
(2021) Cell 184, 5653–5669. doi:10.1016/j.cell.2021.10.002

Mar 30, 2022
Presenter: ChangShuo Wei
Paper:Tyler N. Starr, Allison J. Greaney, Sarah K. Hilton, et al.
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.
(2020) Cell 182, 1295–1310. doi:10.1016/j.cell.2020.08.012

Mar 22, 2022
Presenter: Shuo Zhang
Paper:Eeshit Dhaval Vaishnav, Carl G. de Boer, Jennifer Molinet, et al.
The evolution, evolvability and engineering of gene regulatory DNA.
(2022) Nature 603, 455–463. doi:10.1038/s41586-022-04506-6

Mar 16, 2022
Presenter: Jinhui Kong
Paper:Luke W. Koblan, Mandana Arbab, Max W. Shen, et al.
Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning.
(2021) Nature Biotechnology 39, 1414–1425. doi:10.1038/s41587-021-00938-z

Mar 9, 2022
Presenter: Weiguang Wang
Paper:Julia M Flynn, Ammeret Rossouw, Pamela Cote-Hammarlof, et al.
Comprehensive fitness maps of Hsp90 show widespread environmental dependence.
(2020) elife 9, e53810. doi:10.7554/eLife.53810

Mar 2, 2022
Presenter: Haotian Guo
Paper:Theresa B. Loveless, Joseph H. Grotts, Mason W. Schechter, et al.
Lineage tracing and analog recording in mammalian cells by single-site DNA writing
(2021) Nature Chemical Biology. 17, 739–747. doi:10.1038/s41589-021-00769-8

Feb 23, 2022
Presenter: Kejia Shan
Paper:Martin A. M. Reijns David A. Parry, Thomas C. Williams, et al.
Signatures of TOP1 transcription-associated mutagenesis in cancer and germline
(2022) Nature. doi:10.1038/s41586-022-04403-y7

Feb 16, 2022
Presenter: Bingke Jiao
Paper:Tomohiro Kumon, Jun Ma, R. Brian Akins, et al.
Parallel pathways for recruiting effector proteins determine centromere drive and suppression.
(2021) Cell 184, 4904–4918. doi:10.1016/j.cell.2021.07.037

Jan 12, 2022
Presenter: Shuo Zhang
Paper:Amanda Koch, Luis Aguilera, Tatsuya Morisaki, et al.
Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells.
(2020) Nat Struct Mol Biol. 27, 1095–1104. doi:10.1038/s41594-020-0504-7

Jan 4, 2022
Presenter: Yu Wang
Paper:A. E. Richardson, J. Cheng, R. Johnston, et al.
Evolution of the grass leaf by primordium extension and petiole-lamina remodeling.
(2021) Science 6573, 1377-1381. doi:10.1126/science.abf9407

Dec 22, 2021
Presenter: Lu Gao
Paper:Margaux M Pinney, Daniel A Mokhtari, Eyal Akiva, et al.
Parallel molecular mechanisms for enzyme temperature adaptation.
(2021) Science 371(6533). doi:10.1126/science.aay2784

Dec 8, 2021
Presenter: Yanming Chen
Paper:Eyal Ben-David, Pinelopi Pliota, Sonya A.Widen, et al.
Ubiquitous Selfish Toxin-Antidote Elements in Caenorhabditis Species.
(2021) Current Biology 5, 990-1001. doi:10.1016/j.cub.2020.12.013

Dec 1, 2021
Presenter: Changshuo Wei
Paper:Jesper Svedberg, Aaron A. Vogan, Nicholas A. Rhoades, et al.
An introgressed gene causes meiotic drive in Neurospora sitophila.
(2021) PNAS 118 (17) e2026605118. doi:10.1073/pnas.2026605118

Nov 24, 2021
Presenter: Weiguang Wang
Paper:Surojit Biswas, Grigory Khimulya, and Ethan C. Alley, et al.
A Low-N protein engineering with data-efficient deep learning.
(2021) Nature Methods 18, 389–396. doi:10.1038/s41592-021-01100-y

Nov 10, 2021
Presenter: Haotian Guo
Paper:Ruoyan Li, Lin Di, and Jie Li, et al.
A body map of somatic mutagenesis in morphologically normal human tissues.
(2021) Nature 597, 398–403. doi:10.1038/s41586-021-03836-1

Nov 3, 2021
Presenter: Kejia Shan
Paper:Jessamyn I Perlmutter, Jane E Meyers, and Seth R Bordenstein
A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk.
(2021) eLife 67686. doi:10.7554/eLife.676860

Oct 20, 2021
Presenter: Yanming Chen
Paper:Georg Oberhofer, Tobin Ivy, and Bruce A. Hay
Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive.
(2019) Proc Natl Acad Sci USA 116, 6250–6259. doi:10.1073/pnas.1816928116

Oct 13, 2021
Presenter: Jinhui Kong
Paper:Nico Battich, Joep Beumer, and Buys de Barbanson, et al.
Sequencing metabolically labeled transcripts insingle cells reveals mRNA turnover strategies.
(2020) Science 367, 1151–1156. doi:10.1126/science.aax3072

Sep 22, 2021
Presenter: Jia Wang
Paper:Annina Denoth-Lippuner,Baptiste N.Jaeger,Tong Liang, et al.
Visualization of individual cell division history in complex tissues using iCOUNT.
(2021) Cell Stem Cell 28, 1–15. doi:10.1016/j.stem.2021.08.012

Sep 15, 2021
Presenter: Yu Wang
Paper:Thanh Hoang,Jie Wang, Patrick Boyd, et al.
Gene regulatory networks controlling vertebrateretinal regeneration.
(2020) Science 370, 934. doi:10.1126/science.abb8598

Sep 8, 2021
Presenter: Lu Gao
Paper:Furqan M.Fazal, Shuo Han, Kevin R.Parker, et al.
Atlas of Subcellular RNA Localization Revealed by APEX-Seq.
(2019) Cell, 178, 473-490. doi:10.1016/j.cell.2019.05.027

Sep 1, 2021
Presenter: Bingke Jiao
Paper:Eyal Ben-David, Alejandro Burga, and Leonid Kruglyak
A maternal-effect selfish genetic element in Caenorhabditis elegans.
(2017) Science, 356, 1051-1055 doi:10.1126/science.aan0621

Aug 11, 2021
Presenter: Ke Wang
Paper:Samuel G. Rodriques, Linlin M. Chen, Sophia Liu, et.al
RNA timestamps identify the age of single molecules in RNA sequencing.
(2021) Nature Biotechnology, 39, 320–325 doi:10.1038/s41587-020-0704-z

Aug 11, 2021
Presenter: Baqie Wusa
Paper:Kara L. Johnson, Zhijie Qi, Zhangming Yan, et.al
Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis.
(2016) Proc. Natl. Acad. Sci. USA. 113, 12226-12231 doi:10.1073/pnas.1609686113

Aug 11, 2021
Presenter: Kexin Pang
Paper:Quentin Helleu, Cécile Courret, David Ogereau, et.al
Revealing protein-protein interactions at the transcriptome scale by sequencing.
(2021) Molecular Cell 81, 1–13 doi:10.1016/j.molcel.2021.07.006

Aug 4, 2021
Presenter: Changshuo Wei
Paper:Quentin Helleu, Cécile Courret, David Ogereau, et.al
Sex-Ratio Meiotic Drive Shapes the Evolution of the Y Chromosome in Drosophila simulans.
(2019) Molecular Biology and Evolution, 36, 2668–2681 doi:10.1093/molbev/msz160

Jul 28, 2021
Presenter: Weiguang Wang
Paper:Paul Jannis Zurek, Philipp Knyphausen, Katharina Neufeld,, et.al
UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution.
(2020) Nature Communications volume 11, Article number: 6023 doi:10.1038/s41467-020-19687-9

Jul 21, 2021
Presenter: Haotian Guo
Paper:Reza Kalhor, Kian Kalhor, Leo Mejia, et.al
Developmental barcoding of whole mouse via homing CRISPR.
(2018) Science Vol. 361, Issue 6405, eaat9804 doi:10.1126/science.aat9804

Jul 14, 2021
Presenter: Yu Wang
Paper:Linde A. Miles, Robert L. Bowman, Tiffany R. Merlinsky, et.al
Single-cell mutation analysis of clonal evolution in myeloid malignancies.
(2020) Nature 587, 477–482 doi:10.1038/s41586-020-2864-x

Jul 07, 2021
Presenter: Kejia Shan
Paper:Martin Enge, H. Efsun Arda, Marco Mignardi et.al
Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.
(2017) Cell 171, Pages 321-330 doi:10.1016/j.cell.2017.09.004

Jun 30, 2021
Presenter: Changshuo Wei
Paper:RCécile Courret, Pierre R. Gérard, David Ogereau, et.al
X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression.
(2019) Heredity 122, 906–915 doi:10.1038/s41437-018-0163-1

Jun 23, 2021
Presenter: Yanming Chen
Paper:Hui Xu, Mingzhe Han, Shiyi Zhou, et.al
Chromosome drives via CRISPR-Cas9 in yeast.
(2020) Nature Communications volume 11, Article number: 4344 doi:10.1038/s41467-020-18222-0

Jun 16, 2021
Presenter: Jinhui Kong
Paper:RKristopher W. Brannan, Isaac A. Chaim, Ryan J. Marina, et.al
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
(2021) Nature Methods 18, 507–519 doi:10.1038/s41592-021-01128-0

Jun 9, 2021
Presenter: Shuo Zhang
Paper:Ramona Weber, Leon Kleemann, Insa Hirschberg, Min-Yi Chung, et.al
DAP5 enables translation re-initiation on structured messenger RNAs.
(2021) bioRxiv doi:10.1101/2021.01.21.427569

Jun 2, 2021
Presenter: Jia Wang
Paper:Wan-Jung C. Lai, Mohammad Kayedkhordeh, Erica V. Cornell, et.al
mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.
(2018) Nature Communications 9, Article number: 4328 doi:10.1038/s41467-018-06792-z

May 19, 2021
Presenter: Yu Wang
Paper:C. Clark, Cristina Gutiérrez-Vázquez, Michael A. Wheeler, et.al
Barcoded viral tracing of single-cell interactions in central nervous system inflammation.
(2021) Science Vol. 372, Issue 6540, eabf1230 doi:10.1126/science.abf1230

May 12, 2021
Presenter: Kejia Shan
Paper:Ke-Huan K. Chow, Mark W. Budde, Alejandro A. Granados, et.al
Imaging cell lineage with a synthetic digital recording system.
(2021) Science Vol. 372, Issue 6538, eabb3099. doi:10.1126/science.abb3099

Apr 28, 2021
Presenter: Changshuo Wei
Paper:Findley R. Finseth, Thomas C. Nelson, and Lila Fishman
Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers.
(2021) PLoS Genet 17(4) doi:10.1371/journal.pgen.1009418

Apr 21, 2021
Presenter: Yanming Chen
Paper:Marius Walter and Eric Verdin
Viral gene drive in herpesviruses.
(2020) Nature Communications. 11:4884. doi:10.1038/s41467-020-18678-0

Mar 31, 2021
Presenter: Jinhui Kong
Paper:Tim A.Hoek, Deepak Khuperkar, Rik G.H.Lindeboom, et.al
Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay.
(2019) Molecular Cell. 75, 324-339. doi:10.1016/j.molcel.2019.05.008

Mar 24, 2021
Presenter: Yuliang Zhang
Paper:Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando D. Camargo, et.al
Lineage tracing on transcriptional landscapes links state to fate during differentiation.
(2021) Science. Vol. 367, Issue 6479, eaaw3381. doi:10.1126/science.aaw3381

Mar 17, 2021
Presenter: Shuo Zhang
Paper: Kelsey L.Hickey, Kimberley Dickson, J. Zachery Cogan, et.al
GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control.
(2021) Molecular Cell. 79, 950-962. doi:10.1016/j.molcel.2020.07.007

Mar 10, 2021
Presenter: Jia Wang
Paper: Matilde Bertolini, Kai Fenzl, Ilia Kats, et.al
Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly.
(2021) Science. Vol.371, Issue 6524, pp. 57-64. doi:10.1126/science.abc7151

Mar 3, 2021
Presenter: Haotian Guo
Paper: Ryan Clarke, Alexander R. Terry, Hannah Pennington, et.al
Sequential Activation of Guide RNAs to Enable Successive CRISPR-Cas9 Activities.
(2021) Molecular Cell. 81, 226–238. doi: 10.1016/j.molcel.2020.12.003

Mar 3, 2021
Presenter: Weiguang Wang
Paper: Thuy-Lan V Lite, Robert A Grant, Isabel Nocedal, et.al
Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library.
(2020) eLife 2020;9:e60924 doi: 10.7554/eLife.60924

Jan 27, 2021
Presenter: Kejia Shan
Paper: Kunal Bhutani, Katherine Stansifer, Simina Ticau, et.al
Widespread haploid-biased gene expression enables sperm-level natural selection.
(2021) Science. eabb1723. doi: 10.1126/science.abb1723

Jan 20, 2021
Presenter: Changshuo Wei
Paper: Jackson Champer, Anna Buchman and Omar S. Akbari
Making a Murderer: The Evolutionary Framing of Hybrid Gamete-Killers.
(2016) Trends in Genetics. 35, 245-252. doi: 10.1016/j.tig.2019.01.004.

Jan 13, 2021
Presenter: Yanming Chen
Paper: Jackson Champer, Anna Buchman and Omar S. Akbari
Cheating evolution: engineering gene drives to manipulate the fate of wild populations.
(2016) Nature Reviews Genetics. 17, 146–159. doi: 10.1038/nrg.2015.34.

Dec 30, 2020
Presenter: Wenfeng Qian
Paper: Sarah E.Zanders and Robert L.Unckless
Fertility Costs of Meiotic Drivers.
(2019) Current Biology. 29, R512-R520. doi: 10.1016/j.cub.2019.03.046.

Dec 23, 2020
Presenter: Jia Wang
Paper: Qiushuang Wu, Matthew Wright, Madelaine M Gogol, et.al
Translation of small downstream ORFs enhances translation of canonical main open reading frames.
(2020) EMBO J. 39(17):e104763.doi: 10.15252/embj.2020104763.

Dec 09, 2020
Presenter: Yu Wang
Paper: Jeffrey J. Quinn, Matthew G. Jones, Ross A. Okimoto,et.al
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts.
(2020) bioRxiv.doi: https://doi.org/10.1101/2020.04.16.045245.

Dec 02, 2020
Presenter: Yuliang Zhang
Paper: Qian Gui, Shuyun Deng, Wenjun Shi,et.al
Transcriptome Analysis in Yeast Reveals the Externality of Position Effect.
(2020) bioRxiv.doi: 10.1101/2020.04.02.021162.

Nov 18, 2020
Presenter: Yanming Chen
Paper: Martin Mikl, Yitzhak Pilpel and Eran Segal
High-throughput interrogation of programmed ribosomal frameshifting in human cells.
(2020) Nature Communications 11, Article number: 3061doi: 10.1038/s41467-020-16961-8.

Nov 3, 2020
Presenter: Jinhui Kong
Paper: Jonathan Bohlen, Kai Fenz, Günter Kramer, et.al
Selective 40S Footprinting Reveals Cap-Tethered Ribosome Scanning in Human Cells.
(2020) Molecular Cell 79, 561–574.doi: 10.1016/j.molcel.2020.06.005.

Oct 21, 2020
Presenter: Kejia Shan
Paper: Jin Chen, Andreas-David Brunner, J. Zachery Cogan,et.al
Pervasive functional translation of noncanonical human open reading frames.
(2020) Science.doi: 10.1126/science.aay0262.

Oct 14, 2020
Presenter: Shuo Zhang
Paper: Pierre Murat, Guillaume Guilbaud and Julian E. Sale
DNA polymerase stalling at structured DNA constrains the expansion of short tandem repeats.
(2020) Genome Biology.doi: 10.1186/s13059-020-02124-x.

Sep 27, 2020
Presenter: Changshuo Wei
Paper: Yumeng Tan1,Yong Zhang, Yunbin Han,et.al
Directed evolution of an α1,3-fucosyltransferase using a single-cell ultrahigh-throughput screening method.
(2019) Science Advances.doi: 10.1126/sciadv.aaw8451.

Sep 09, 2020
Presenter: Weiguang Wang
Paper: Michael Heyne, Niv Papo and Julia M. Shifman
Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization.
(2020) Nature Communications.doi: 10.1038/s41467-019-13895-8.

Sep 02, 2020
Presenter: Haotian Guo
Paper: Ye Li, Logan A Walker, Yimeng Zhao, et.al
Bitbow: a digital format of Brainbow enables highly efficient neuronal lineage tracing and morphology reconstruction in single brains.
(2020) bioRxiv.doi: 10.1101/2020.04.07.030593.

Dec 25, 2019
Presenter: Yuliang Zhang
Paper:Claire N. Bedbrook, Kevin K. Yang, J. Elliott Robinson, et.al
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
(2019) Nature Methods.16, 1176–1184. doi: 10.1038/s41592-019-0583-8.

Nov 27, 2019
Presenter: Haotian Guo
Paper:Miriam Kaltenbach, Colin J Jackson, Eleanor C Campbell, et.al
Reverse evolution leads to genotypicincompatibility despite functional andactive site convergence.
(2015) eLife.2015;4:e06492. doi: 10.7554/eLife.06492.

Nov 20, 2019
Presenter: Yu Wang
Paper:Zhaoyang Li, Cen Wang, Ziying Wang, et.al
Allele-selective lowering of mutant HTT protein by HTT–LC3 linker compounds.
(2019) Nature. 575, 203–209. doi:10.1038/s41586-019-1722-1.

Nov 13, 2019
Presenter: Jinhui Kong
Paper:Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, et.al
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated qualitycontrol of poly(A) translation.
(2019) Genome Biology. 20, Article number: 216. doi:10.1186/s13059-019-1814-0.

Nov 6, 2019
Presenter: Ying Chen
Paper:Jia Zheng, Joshua L. Payne, and Andreas Wagner
Cryptic genetic variation acceleratesevolution by opening accessto diverse adaptive peaks.
(2019) Science. 365, 347-353. doi:10.1126/science.aax1837.

Oct 23, 2019
Presenter: Kejia Shan
Paper:Ben W. Dulken, Matthew T. Buckley, Paloma Navarro Negredo et.al
Single-cell analysis reveals T cell infiltration in old neurogenic niches.
(2019) Nature. 571, 205–210. doi: 10.1038/s41586-019-1362-5.

Oct 16, 2019
Presenter: Siyu Chen
Paper:Rachel S. Greenberg, Hannah K. Long, et.al
Single Amino Acid Change Underlies Distinct Rolesof H2A.Z Subtypes in Human Syndrome.
(2019) Cell. 178, 1421-1436. doi:110.1016/j.cell.2019.08.002.

Oct 9, 2019
Presenter: Yanming Chen
Paper:Marianthi Karageorgi, Simon C. Groen1,, Fidan Sumbul, et.al
Genome editing retraces the evolution of toxin resistance in the monarch butterfly.
(2019) Nature. 574, 409-412. doi:10.1038/s41586-019-1610-8.

Sep 25, 2019
Presenter: Jia Wang
Paper:Lea H. Gregersen, Richard Mitter, et.al
SCAF4 and SCAF8, mRNA Anti-Terminator Proteins.
(2019) Cell. 177, 1797-1813. doi:10.1016/j.cell.2019.04.038.

Sep 18, 2019
Presenter: Wenqing Cao
Paper:Nicolas Viphakone, Ian Sudbery, Llywelyn Griffith, et.al
ArticleCo-transcriptional Loading of RNA Export FactorsShapes the Human Transcriptome.
(2019) Molecular Cell. 75, 310-323. doi:10.1016/j.molcel.2019.04.034.

Sep 11, 2019
Presenter: Changshuo Wei
Paper:Arjun Ravikumar, Garri A. Arzumanyan, Muaeen K.A. Obadi, et.al
Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds.
(2018) Cell. 175, 1946-1957. doi:10.1016/j.cell.2018.10.021.

Sep 11, 2019
Presenter: Yafei Guo
Paper:Paper:Anna S. Nam, Kyu-Tae Kim, Ronan Chaligne,et.al
Somatic mutations and cell identity linked by Genotyping of Transcriptomes.
(2019) Nature. 571, 355–360. doi:10.1038/s41586-019-1367-0.

Jun 5, 2019
Presenter: Wenqing Cao
Paper:Suli Chen, Ruijia Wang,Dinghai Zheng,et.al
The mRNA Export Receptor NXF1 Coordinates Transcriptional Dynamics, Alternative Polyadenylation, and mRNA Export.
(2019) Molecular Cell. 74, 1–14. doi:10.1016/j.molcel.2019.01.026.

May 29, 2019
Presenter: Jinhui Kong
Paper:Mohamed A. El-Brolosy, Zacharias Kontarakis, et.al
Genetic compensation triggered by mutant mRNA degradation.
(2019) Nature. 568, 193–197. doi:10.1038/s41586-019-1064-z.

May 8, 2019
Presenter: Shuo Zhang
Paper:Julian Grünewald, Ronghao Zhou, et.al
Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors.
(2019) Nature. doi:10.1038/s41586-019-1161-z.

Apr 24, 2019
Presenter: Yuliang Zhang
Paper:Darren A. Cusanovich, Andrew J. Hill, et.al
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.
(2018) Cell. 174, 1309–1324. doi:10.1016/j.cell.2018.06.052.

Apr 17, 2019
Presenter: Ying Chen
Paper:Brad Nelms and Virginia Walbot
Defining the developmental program leading to meiosis in maize.
(2019) Science. 364, 52–56. doi:10.1126/science.aav6428.

Apr 3, 2019
Presenter: Kejia Shan
Paper:Ken Jean-Baptiste, José L McFaline-Figueroa, et.al
Dynamics of gene expression in single root cells of A. thaliana.
(2019) The Plant Cell. 31 ,Issue 2. doi:10.1105/tpc.18.00785.

Mar 27, 2019
Presenter: Siyu Chen
Paper:Anjali Gupta Hinch, Gang Zhang, et.al
Factors influencing meiotic recombination revealed by wholegenome sequencing of single sperm.
(2019) Science. 363 ,Issue 6433, eaau8861. doi:10.1126/science.aau8861.

Mar 20, 2019
Presenter: Yanming Chen
Paper:Leif S. Ludwig, Caleb A. Lareau, et.al
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.
(2019) Cell. 176 : 1325–1339. doi:10.1016/j.cell.2019.01.022.

Mar 13, 2019
Presenter: Jia Wang
Paper:Helmuth Gehart, Johan H. van Es, et.al
Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping.
(2019) Cell. 176 : 1158–1173. doi:10.1016/j.cell.2018.12.029.

Feb 27, 2019
Presenter: Xiao Chu
Paper:Anna Alemany1, Maria Florescu1, et.al
Whole-organism clone tracing using single-cell sequencing.
(2018) Nature. 556 : 108–112. doi:10.1038/nature25969.

Feb 20, 2019
Presenter: Chaorui Duan
Paper:Jeffrey t. Morgan1, Gerald r. Fink & David P. Bartel
Excised linear introns regulate growth in yeast.
(2019) Nature. 565 : 606–611. doi: 10.1038/s41586-018-0828-1.

Dec 26, 2018
Presenter: Shuo Zhang
Paper:Wolfgang H. Schmied, Zakir tnimov, Chayasith Uttamapinant et.al
Controlling orthogonal ribosome subunit interactions enables evolution of new function.
(2018) Nature. 71 : 229–243. doi: 10.1038/s41586-018-0773-z.

Dec 19, 2018
Presenter: Jinhui Kong
Paper:Alicia M. Darnell, Arvind R. Subramaniam* and Erin K. O’Shea
Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells.
(2018) Molecular Cell. 564 : 444–448. doi: 10.1016/j.molcel.2018.06.041.

Dec 12, 2018
Presenter: Yuqing Niu
Paper:Ayala Shiber, Kristina Döring, Ulrike Friedrich, et.al
Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling.
(2018) Nature. 561: 268–272. doi: 10.1038/s41586-018-0462-y.

Nov 28, 2018
Presenter: Yuling Zhang
Paper:Vitor Onuchic, Eugene Lurie, Ivenise Carrer, et.al
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.
(2018) Science. 361 eaar3146. doi: 10.1126/science.aar3146.

Nov 21, 2018
Presenter: Ying Chen
Paper:Daniel Arango, David Sturgill,Najwa Alhusaini, et.al
Acetylation of Cytidine in mRNA Promotes Translation Efficiency.
(2018) Cell. 175 : 1–15. doi: 10.1016/j.cell.2018.10.030.

Nov 14, 2018
Presenter: Kejia Shan
Paper:Zarmik Moqtaderi, Joseph V.Geisberg, KevinStruhl
Extensive Structural Differences of Closely Related 3′ mRNA Isoforms: Links to Pab1 Binding and mRNA Stability.
(2018) Molecular Cell. 72: 1–13. doi: 10.1016/j.molcel.2018.08.044.

Nov 7, 2018
Presenter: Siyu Chen
Paper:M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, et.al
The chromatin accessibility landscape of primary human cancers.
(2018) Science. 362 6413, eaav1898. doi: 10.1126/science.aav1898..

Oct 31, 2018
Presenter: Yanming Chen
Paper:Jacob M. Tome, Nathaniel D. Tippens and John T. Lis
Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers.
(2018) Nat Genet. 50 (11):1533-1541. doi: 10.1038/s41588-018-0234-5.

Oct 24, 2018
Presenter: Jia Wang
Paper:Junho Choe, Shuibin Lin, Wencai Zhang, et.al
mRNA circularization by METTL3–eIF3h enhances translation and promotes oncogenesis.
(2018) Nature. 561 (7724):556-560. doi: 10.1038/s41586-018-0538-8.

Oct 17, 2018
Presenter: Wenqing Cao
Paper:Chad M. Kurylo, Matthew M. Parks, Manuel F. Juette, et.al
Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype.
(2018) Cell Reports. 25 (1):236-248.e6. doi: 10.1016/j.celrep.2018.08.093.

Oct 10, 2018
Presenter: Xiao Chu
Paper:Eilon Sharon, Shi-An A. Chen, Neil M. Khosla, et.al
Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing.
(2018) Cell. 175 (2):544-557.e16. doi: 10.1016/j.cell.2018.08.057.

Sep 26, 2018
Presenter: Chaorui Duan
Paper:Lydia Robert, Jean Ollion, Jerome Robert, et.al
Mutation dynamics and fitness effects followed in single cells.
(2018) Science. 174 (359):1283–1286. doi: 10.1126/science.aan0797.

Sep 12, 2018
Presenter: Yuqing Niu
Paper:Janissen R, Arens MMA, Vtyurina NN, et.al
Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription.
(2018) Cell. 174 (5):1188-1199. doi: 10.1016/j.cell.2018.06.049.

Sep 05, 2018
Presenter: Yuliang Zhang
Paper:La Manno G, Soldatov R, Zeisel A, et.al
RNA velocity of single cells
(2018) Nature. 560 (7719):494-498. doi: 10.1038/s41586-018-0414-6.

Aug 22, 2018
Presenter: Yafei Guo
Paper:Young MD, Mitchell TJ, Vieira Braga FA, et.al
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.
(2018) Science. 361 (6402):594-599. doi: 10.1126/science.aat1699.

Aug 15, 2018
Presenter: Yu Wang
Paper:Wang L, Dou K, Moon S, et.al
Hijacking Oogenesis Enables Massive Propagation of LINE and Retroviral Transposons.
(2018) Cell. 174 (5):1082-1094.e12. doi: 10.1016/j.cell.2018.06.040.

Aug 08, 2018
Presenter: Kejia Shan
Paper:Lim J1, Kim D1, Lee YS, et.al
Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation.
(2018) Science. 361 (6403):701-704. doi: 10.1126/science.aam5794.

Aug 01, 2018
Presenter: Siyu Chen
Paper:Chen H, Li C, Zhou Z, et.al
Fast-Evolving Human-Specific Neural Enhancers Are Associated with Aging-Related Diseases.
(2018) Cell Syst. 6 (5):604-611.e4. doi: 10.1016/j.cels.2018.04.002.

July 25, 2018
Presenter: Yanming Chen
Paper:Riback JA, Katanski CD, Kear-Scott JL et.al
Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response.
(2017) Cell. 168 (6):1028-1040.e19 doi: 10.1016/j.cell.2017.02.027.

July 18, 2018
Presenter: Jia Wang
Paper:Rapino F, Delaunay S, Rambow F, et.al
Codon-specific translation reprogramming promotes resistance to targeted therapy.
(2018) Nature. 558 (7711):605-609 doi: 10.1038/s41586-018-0243-7.

July 11, 2018
Presenter: Taolan Zhao
Paper:Ivanov IP, Shin BS, Loughran G, et.al
Polyamine Control of Translation Elongation Regulates Start Site Selection on Antizyme Inhibitor mRNA via Ribosome Queuing.
(2018) Mol Cell. 70 (2):254-264.e6 doi: 10.1016/j.molcel.2018.03.015.

July 04, 2018
Presenter: Ke Li
Paper:Guenther UP, Weinberg DE, Zubradt MM, et.al
The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs.
(2018) Nature. 559 (7712):130-134. doi: 10.1038/s41586-018-0258-0.

June 27, 2018
Presenter: Wenqing Cao
Paper:Diss G1, Lehner B.
The genetic landscape of a physical interaction.
(2018) Elife. 7 pii: e32472. doi: 10.7554/eLife.32472.

June 20, 2018
Presenter: Xiao Chu
Paper:Giacomello S, Salmn F, Terebieniec BK, et al.
Spatially resolved transcriptome profiling in model plant species.
(2017) Nat Plant. 8 3:17061 doi: 10.1038/nplants.2017.61.

June 13, 2018
Presenter: Chaorui Duan
Paper:Domingo J1, Diss G1, Lehner B.
Pairwise and higher-order genetic interactions during the evolution of a tRNA.
(2018) Nature. 558 (7708):117-121 doi: 10.1038/s41586-018-0170-7

May 16, 2018
Presenter: Yuliang zhang
Paper:Cheung P, Vallania F, Warsinske HC, et al.
Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging.
(2018) Cell. 173 (6):1385-1397.e14 doi: 10.1016/j.cell.2018.03.079

May 09, 2018
Presenter: Ying Chen
Paper:Lalanne JB, Taggart JC, Guo MS, et al.
Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry.
(2017) Cell. 173 (3):749-761.e38 doi: 10.1016/j.cell.2018.03.007.

May 02, 2018
Presenter: Siyu Chen
Paper:Levo M, Avnit-Sagi T, Lotan-Pompan M, et al.
Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays.
(2017) Mol Cell. 65 (4)604-617.e6. doi: 10.1016/j.molcel.2017.01.007.

Apr 25, 2018
Presenter: Qing Huan
Paper:Chen CW, Tanaka M.
Genome-wide Translation Profiling by Ribosome-Bound tRNA Capture.
(2018) Cell Rep. 23 (2):608-621. doi: 10.1016/j.celrep.2018.03.035.

Apr 11, 2018
Presenter: Shaohuan Wu
Paper:Dao Duc K, Song YS.
The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.
(2018) PLoS Genet. 14 (1):e1007166 doi: 10.1371/journal.pgen.1007166.

Apr 04, 2018
Presenter: Yanming Chen
Paper:di Iulio J, Bartha I, Wong EHM, et al.
The human noncoding genome defined by genetic diversity
(2018) Nat Genet. 50. (3)333-337 doi: 10.1038/s41588-018-0062-7.

Mar 28, 2018
Presenter: Jia Wang
Paper:Zhou Z, Dang Y, Zhou M, et al.
Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation.
(2018) Elife. 7. pii: e33569. doi: 10.7554/eLife.33569.

Mar 21, 2018
Presenter: Yu Wang
Paper:Han X, Wang R, Zhou Y, et al.
Mapping the Mouse Cell Atlas by Microwell-Seq.
(2018) Cell. 172 (5):1091-107.e17. doi: 10.1016/j.cell.2018.02.001.

Mar 14, 2018
Presenter: Taolan Zhao
Paper:Diament A, Feldman A, Schochet E, et al.
The extent of ribosome queuing in budding yeast.
(2018) PLoS Comput Biol. 14 (1):e1005951 doi: 10.1371/journal.pcbi.1005951.

Mar 07, 2018
Presenter: Ke Li
Paper:Xu J1, Peng X1, Chen Y, et al.
Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity.
(2018) Elife. 27 (9):1461-1474. doi: 10.7554/eLife.28070.

Jan 24, 2018
Presenter: Kejia Shan
Paper:Guschanski K, Warnefors M, Kaessmann H.
The evolution of duplicate gene expression in mammalian organs.
(2017) Genome Res. 6 pii: e28070. doi: 10.1101/gr.215566.116.

Jan 10, 2018
Presenter: Wenqing Cao
Paper:Rabani M, Pieper L, Chew GL, et al.
A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation.
(2017) Mol Cell. 68 (6):1083-7094.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.

Dec 06, 2017
Presenter: Siyu Chen
Paper:Truong DM, Boeke JD.
Resetting the Yeast Epigenome with Human Nucleosomes
(2017) Cell. 171 (7):1508-1519.e13. doi: 10.1016/j.cell.2017.10.043.

Nov 29, 2017
Presenter: Shaohuan Wu
Paper:Rogers DW, B?ttcher MA, Traulsen A, et al.
Ribosome reinitiation can explain length-dependent translation of messenger RNA.
(2017) PLoS Comput Biol. 13 (6):e1005592. doi: 10.1371/journal.pcbi.1005592.

Nov 22, 2017
Presenter: Yuliang Zhang
Paper:Voichek Y, Bar-Ziv R, Barkai N.
Expression homeostasis during DNA replication
(2017) Science. 351 (6277):1087-1090. doi: 10.1126/science.aad1162

Nov 15, 2017
Presenter: Yanming Chen
Paper:Frigola J, Sabarinathan R, Mularoni L, et al.
Reduced mutation rate in exons due to differential mismatch repair
(2017) Nat Genet. 49 (12):1684-1692. doi: 10.1038/ng.3991.

Nov 08, 2017
Presenter: Jia Wang
Paper:Bazin J1, Baerenfaller K, Gosai SJ, et al.
Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation
(2017) PNAS. 114 (46):E10018-E10027. doi: 10.1073/pnas.1708433114.

Oct 25, 2017
Presenter: Taolan Zhao
Paper:Simsek D, Tiu GC, Flynn RA, et al.
The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity
(2017) Cell. 169 (6):1051-1065.e18. doi: 10.1016/j.cell.2017.05.022.

Oct 18, 2017
Presenter: Ke Li
Paper:Tukiainen T, Villani AC, Yen A, et al.
Landscape of X chromosome inactivation across human tissues
(2017) Nature 550 (7675):244-248. doi: 10.1038/nature24265.

Oct 11, 2017
Presenter: Ying Chen
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.