Journal Club

Fall 2020 - Revisiting old ideas with new methods

October 7: Organizational Meeting
Introductions, GTP advising committee, Program expectations, How to critique a paper, Selection of Fall topic.

October 14: Noorsher Ahmed (Yeo Lab)
Fürth et al. (2019) In situ transcriptome accessibility sequencing (INSTA-seq). bioRxiv 2019/08/06/722819 [bioRxiv]

October 21: Melinda Beccari (Cleveland Lab)
Wu et al. (2012) Clonal selection drives genetic divergence of metastatic medulloblastoma. Nature. 482, 529-533. [Nature] [PMC]

October 28: Jessica Bloom (Rifkin Lab)
Farley et al. (2016) Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. PNAS 113, 6508-6513. [PNAS] [PMC]

November 4: Corrina Elder (Pasquinelli Lab)
Zhang et al. (2015) The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans. Development 142, 4374-4384. [Development] [PMC]

THURSDAY November 12: Emily Ho (Mellon Lab)
Anzalone et al. (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157. [Nature] [PMC]

November 18: James Hocker (Ren Lab)
Schmidt et al. (2018) Transcriptional recording by CRISPR spacer acquisition from RNA.
Nature 562, 380–385. [Nature]

November 25: Thanksgiving Holiday

December 2: Erin Ritchie (Jin Lab)
Jin et al. (2020) In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science 370, eaaz6063 [Science] [bioRxiv]

December 9: Faculty Panel. Professors K. Frazer, A. Komor, B. Ren, K. Zhang
Responsible Conduct of Research Discussion: Validating new technologies for rigor and reproducibility

Select Winter topic.

Winter 2020 - The Right Stuff: Unique organism attributes and opportunities that allow new findings

January 6: Patrick Bruck (Muotri Lab)
Poltorak et al. (1998) Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science 282, 2085-2088. [Science]

January 13: Krypton Carolino (Winzeler Lab)
Gantz and Bier (2015) The mutagenic chain reaction: A method for converting heterozygous to homozygous mutations. Science 348, 442-444. [Science] [PMC]

January 20: Carmine Chavez-Martinez (Zheng Lab)
Kucharski et al. (2008) Nutritional Control of Reproductive Status in Honeybees via DNA Methylation. Science 319, 1827-1830. [Science]

January 27: Tiffany Chu (Muotri Lab)
Johnson et al. (2018) Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size. Nature 556, 370-375. [Nature] [PMC]

February 3: Natalie DeForest (Majithia Lab)
Surendran et al. (2020) Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals. Nature Genetics 52, 1314–1332. [Nature Genetics]

February 10: Jenna Kovsky (Sander Lab)
Sanor et al. (2020) Multiplex CRISPR/Cas screen in regenerating haploid limbs of chimeric Axolotls. eLife 9, e48511. [eLife]

February 17: Sara Elmasaouri (Yeo Lab)
Chen et al. (2020) Live-imaging of astrocyte morphogenesis and function in zebrafish neural circuits. Nature Neuroscience 23, 1297-1306. [Nature Neuroscience] [PMC7530038 available on ]

February 24: Danielle Schafer (Yeo Lab)
Vazquez et al. (2018) A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage. Cell Reports 24, 1765-1776. [Cell Reports] [bioRxiv]

March 3: Eleanora Rachtman (Bafna Lab)
Valenzano et al. (2015) The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell 163, 1539-1554. [Cell] [PMC]

March 10: Faculty Panel. Professors Hamilton, Jin, Majithia, Sander, and Winzeler
Responsible Conduct of Research Discussion: Authorship
Counicl of Science Editors White Paper on Publication Ethics. (2018) [website]
Sauermann and Haeussler (2017) Authorship and contribution disclosures. [Science Advances]

Select Spring quarter topic.

Spring 2021 - 3D Genome

March 31: James Yu (Simonson Lab)
Klann et al. (2017) CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nature Biotechnology 35, 561-568. [Nature Biotech] [PMC]

April 7: Chris Balak (Glass Lab)
Grubert et al. (2020) Landscape of cohesin-mediated chromatin loops in the human genome. Nature 583, 737-743. [Nature] [PMC]

April 14: Lizmarie Garcia-Rivera (Wechler-Reya and Furnari Labs)
Wu et al. (2019) Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699-703. [Nature] [PMC]

April 21: Maya Gosztyla (Yeo Lab)
Luo et al. (2021) 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Cell 184, 723-740.e21. [Cell] [no open copies found]

April 28: Alyssa Holman (Chi and Engler Labs)
Shah et al. (2021) Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell, in press. [Cell Press] [no open copies found]

May 5: Pratibha Jagannatha (Yeo Lab)
Beagan et al. (2020) Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. Nature Neuroscience 23, 707-717. [Nature Neuro] [PMC]

May 12: Blair Jha (Ren Lab)
Arnould et al. (2021) Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 590, 660–665. [Nature] [bioRxiv]

May 19: Eric Kofman (Glass Lab)
Lee et al. (2019) Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nature Methods 16, 999-1006. [Nature Methods] [PMC]

May 26: Rebecca Melton (Gaulton Lab)
Liu et al. (2020) 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk. bioRxiv 2020.09.04.279554 [bioRxiv]

June 2: Faculty Panel. Professors Farley, Gaulton, Gymrek, and Ren
Responsible Conduct of Research Discussion: Data transparency in publication–what, where, and when?

Summer Book Club selection.