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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 (Gage Lab)
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. Professors Bambah-Mukku, Dickinson, Glass, and Winzeler
Responsible Conduct of Research Discussion: Experimental Design for Rigor and Reproducibility

Select Winter topic.


Winter 2023 - Viral Evolution

January 11: AJ Daniels (Signer and Bennett Labs)
Anderson et al. (2015) Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus. Cell 162, 738-750. [Journal] [PMC]

January 18: Xiaomi Du (Majithia Lab)
West et al. (2021) Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nat Commun 12, 4886.[OA Journal] [PMC

January 25: Sam Hatch (Yeo Lab)
Gandhi et al. (2022) De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Nature Communications 13, 1547 [OA Journal] [PMC]

See also: Szemiel (2021) In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. PLoS Pathogens 17, e1009929. [OA Journal] [PMC]

February 1: Mitchell Kong (Simonson Lab)
Laso-Pérez et al. (2023) Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome. Nature Microbiology [Journal] (Open Access)

February 8: Rachel McMillen (Carlin and Benner Labs)
Liu et al. (2017) Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes. Nature 545, 482-486. [Journal

February 15: Brittany Leger (Palmer Lab)
Feder et al. (2021) The clarifying role of time series data in the population genetics of HIV. PLoS Genet. 17, e1009050. [OA Journal]

February 22: Hannah Mummey (Gaulton Lab)
Pekar et al. (2022) The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science 377, 960-966. [Journal] [PMC]

March 1: Mei Okino (Sander and Gaulton Labs)
Bisio et al. (2023) Evolution of giant pandoravirus revealed by CRISPR/Cas9. Nature Communications 13, 222. [OA Journal]

March 8: Shams Al-Azam (Alexandrov Lab)
Gupta et al. (2022) Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2. Nature Communications 14, 428. [OA Journal]

March 15: Faculty Panel. Professors Dowdy, Kolodner, Mali, Winzeler
Responsible Conduct of Research Discussion: Managing Conflicts of Interest

Select Spring quarter topic.


Spring 2023 - Big Genomics Data

April 5: Liz Chamiec-Case (Bambah-Mukku Lab)
Woych et al. (2022) Cell-type profiling in salamanders identifies innovations in vertebrate forebrain evolution. Science 377, eabp9186 [Journal] [PMC]

April 12: Ethan Armand (Ren Lab)
Hu et al. (2023) Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. bioRxiv 2023.03.28.533945 [Preprint]

April 19: Weston Elison (Gaulton Lab)
Sakaue (2021) A cross-population atlas of genetic associations for 220 human phenotypes. Nature Genetics 53, 1415–1424. [Journal] [Preprint

April 26: David Ferranti (Rennison Lab)
Kingman et al. (2021) Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Science Advances 7, abg5285 [OA Journal]

May 3: Jon Freshman (Carlin Lab)
Sun et al. (2023) Phenotypic signatures of immune selection in HIV-1 reservoir cells.
Nature 614, 309–317. [Journal] [PMC]

May 10: Trent Gomberg (Yeo Lab)
Baxi et al. (2022) Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines. Nature Neuroscience 25, 226–237. [Journal] [PMC]

May 17: Anvita Komarla (Towers Lab)
Zhao et al. (2023) A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nature Genetics 55, 346–354. [Journal] [Preprint]

May 24: Gabrielle Meza (Dickinson Lab)
Yan et al. (2023): Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nature Genetics 55, 507–518. [Journal] [PMC]

May 31: Joseph Rainaldi (Mali Lab)
Bryant et al. (2021) Deep diversification of an AAV capsid protein by machine learning.
Nature Biotechnology 39, 691–696. [Journal]

June 7: Rachel Weinstein (Rifkin Lab)
Adams et al. (2023) Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms. Molecular Biology and Evolution 40, msad039 [OA Journal]

June 14: Professor Anthony Magit
Responsible Conduct of Research Discussion: Implicit bias.

Summer Book Club selection