Journal Club

We meet at 10.00 AM on Wednesdays in Room #4304 at 4515 McKinley.

Every couple of weeks, each lab member pitches an article that he or she has recently read. They have two minutes to sell the lab on the exciting findings and merits of the experiments. At the conclusion, we vote on the papers that will populate the coming weeks’ discussions.

Next paper :

05.02.2018 : Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6. pii: e29005.

Latest pitches (04.18.2018) :

Dana = Peccoud J, Lequime S, Moltini-Conclois I, Giraud I, Lambrechts L, Gilbert C. A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation. G3 (Bethesda). 2018 Mar 28;8(4):1129-1138.

Siqi = Ren G, Jin W, Cui K, Rodrigez J, Hu G, Zhang Z, Larson DR, Zhao K. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression. Mol Cell. 2017 Sep 21;67(6):1049-1058.e6.

Jeff = Mayran A, Khetchoumian K, Hariri F, Pastinen T, Gauthier Y, Balsalobre A, Drouin J. Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate. Nat Genet. 2018 Feb;50(2):259-269.

Max = Park J, Dies M, Lin Y, Hormoz S, Smith-Unna SE, Quinodoz S, Hernández-Jiménez MJ, Garcia-Ojalvo J, Locke JCW, Elowitz MB. Molecular Time Sharing through Dynamic Pulsing in Single Cells. Cell Syst. 2018 Feb 28;6(2):216-229.e15.

Clarice = Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6. pii: e29005.

Barak =

Previously discussed papers :

04.25.2018 : Ren G, Jin W, Cui K, Rodrigez J, Hu G, Zhang Z, Larson DR, Zhao K. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression. Mol Cell. 2017 Sep 21;67(6):1049-1058.e6.

01.31.2018 : Corrales M, Rosado A, Cortini R, van Arensbergen J, van Steensel B, Filion GJ. (2017). Clustering of Drosophila housekeeping promoters facilitates their expressionGenome Res. 27:1153-1161.

01.24.2018 : Jiang S, Liu Y, Xu C, et al. Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library. G3: Genes|Genomes|Genetics. 2017;7(12):3857-3866.

12.13.2017 : Ye Z, Chen Z, Sunkel B, et al. Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1Nucleic Acids Research. 2016;44(16):7540-7554. doi:10.1093/nar/gkw659.

02.10.2016 : Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, Gilad Y. (2016) Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCsPLoS Genet.12(1):e1005793

02.03.2016: Sorrells, T. R., Booth, L. N., Tuch, B. B., & Johnson, A. D. (2015) Intersecting transcription networks constrain gene regulatory evolution. Nature. 523(7560), 361–365.

01.27. 2016 : Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S (2015) Digital signaling decouples activation probability and population heterogeneity.Elife. 21(4):e08931

01.20.2016, , , , , Competition between binding sites determines gene expression at low transcription factor concentrations. Biorxiv.

12.16.2015 : Arttu Jolma, Yimeng Yin, Kazuhiro R. Nitta, Kashyap Dave, Alexander Popov, Minna Taipale, Martin Enge, Teemu Kivioja, Ekaterina Morgunova & Jussi Taipale (2015) DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature. 527,384–388

12.09.2015 : Gerald Stampfel, Tomáš Kazmar, Olga Frank, Sebastian Wienerroither, Franziska Reiter & Alexander Stark (2015) Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature. 528,147–151