Journal Club

Fall 2022 - Methods in Genetics and Genomics

September 28: Organizational Meeting
Introductions, GTP advising committee, Program expectations, How to critique a paper, Selection of Fall topic.

October 5: Chris Balak (Glass Lab)
Chen et al. (2015) RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090. [Journal] [PMC]

see also: Fang et al. (2022) Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science 377, 56–62. [Journal] [PMC]

October 12: Maya Gosztyla (Yeo Lab)
He et al. (2016) High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Mol. Cell 64, 416-430. [Journal] [PMC]

see also: Oksuz et al. (2022) Transcription factors interact with RNA to regulate genes. bioRxiv 2022.09.27.509776 [Preprint]

October 19: Alyssa Holman (Chi and Engler Labs)
Dixit et al. (2016) Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell 167, 1853-1866.e17 [Journal] [PMC]

October 26: Mike Cuoco 
Nishimura et al. (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nature Methods 6, 917-922. [Journal

see also: Rao et al. (2017) Cohesin Loss Eliminates All Loop Domains. Cell [Journal] [PMC]

November 2: Rebecca Melton (Gaulton Lab)
Lin et al. (2018) Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature Genetics 50, 754–763. [Journal]

see also: Lieberman-Aiden (2010) Comprehensive mapping of long range interactions reveals folding principles of the human genome. Science 326, 289-293. [Journal] [PMC]

November 9: Blair Jha (Ren Lab)
Kaya-Okur et al. (2019) CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature Communications 10, 1930. [Journal] Open Access.

November 16: Pratibha Jagannatha (Yeo Lab)
Shepard et al. (2022) Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 17, 761-772. [Journal] [PMC] Open Access.

November 23: No class scheduled Thanksgiving Holiday

November 30: Kween Agba (Zheng Lab)
Borm et al. (2022) Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH. Nature Biotechnology [Journal] [public via read cube]  

December 7: Faculty Panel. 
Responsible Conduct of Research Discussion: 

Select Winter topic.


Winter 2023 - Topic TBA

January 11: AJ Daniels (Signer and Bennett Labs)

January 18: Xiaomi Du (Majithia Lab)

January 25: Sam Hatch (Yeo Lab)

February 1: Mitchell Kong (Simonson Lab)

February 8: Brittany Leger (Palmer Lab)

February 15: Rachel McMillen (Carlin and Benner Labs)

February 22: Hannah Mummey (Gaulton Lab)

March 1: Mei Okino (Sander and Gaulton Labs)

March 8: 

March 15: Faculty Panel. 
Responsible Conduct of Research Discussion: 

Select Spring quarter topic.


Spring 2022 - Topic TBA

April 5: 

April 12: 

April 19: 

April 26: 

May 3: 

May 10: 

May 17: 

May 24: 

May 31: 

June 7: 

June 14: Faculty Panel. 
Responsible Conduct of Research Discussion: 

Summer Book Club selection