Journal Club
Fall 2025 - Epistasis
October 1: Organization and Responsible Conduct of Research Discussion
Introductions, GTP advising committee, Program expectations, Selection of Fall topic.
Disucssion: What belongs in a paper? How should we evaluate published work?
October 8: Grace Carter (Meharena Lab)
Zebell et al. (2025) Cryptic variation fuels plant phenotypic change through hierarchical epistasis. Nature 644, 984-992. [Journal] [PMC]
October 15: Jeffrey Chiu (Ren and Glass Labs)
Lin et al. (2022) Nested epistasis enhancer networs for robust genome regulation. Science 377, 1077-1085. [Journal] [PMC]
October 22: Tula Keal (Dixon Lab)
Xin et al. (2025) Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation. Cell 188, 4517-4529.e15 [Journal]
October 29: Challana Tea (Ferguson Lab)
Hebert et al. (2025) Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis. Molecular Biology and Evolution 42, msaf02 [Journal] [PMC]
November 5: Krysten Jones (Heinz Lab)
Liang (2025) Epistasis in the receptor-binding domain of contemporary H3N2 viruses that reverted to bind sialylated di-LacNAc repeats. Cell Reports 44, 116007. [OA Journal]
November 12: Isabella Ruud (Chavez Lab)
Zhang et al. (2024) Epistasis between genetic variations on mdmyb109 and mdhxk1 exerts a large effect on sugar content in Apple Fruit. The Plant Journal 121, e17187 [Journal]
November 19: Jose Sandoval (Chi Lab)
Snyder et al. (2025) Divergence in a eukaryotic transcription factor’s co-TF dependence involves multiple intrinsically disordered regions. Nature Communications 16, 5340 [OA Journal]
November 26: No class scheduled Thanksgiving Holiday
December 3: Camilo Londono (Zheng Lab)
Libé-Philippot et al. (2024) Synaptic neoteny of human cortical neurons requires species-specific balancing of SRGAP2-SYNGAP1 cross-inhibition. Neuron 112, 3602-3617.e9. [Journal][PMC]
December 10: Responsible Conduct of Research Discussion:
Experimental Design for Rigor and Reproducibility
Professors Carter, Chavez, Ecker, Heinz
Select Winter topic.
Winter 2026 - New Tools for Genetics and Genomics
January 7: Gianna Elias (Chavez Lab)
Witte et al. (2025) Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase. Science 388, eadt5199. [Journal] [PMC]
January 14: Shazreh Hassan (Bambah-Mukku Lab)
Ramani et al. (2025) CRISPR screening by AAV episome-sequencing (CrAAVe-seq): a scalable cell-type-specific in vivo platform uncovers neuronal essential genes. Nature Neuroscience 28, 2129–2140. [Journal] [PMC]
January 21: Megan Huang (Gaulton Lab)
Stein et al. (2025) Expanding the utility of variant effect predictions with phenotype-specific models. Nature Communications 16, 11113 [OA Journal] [PMC]
January 28: Molly Huang (Fisch Lab)
Luebbert et al. (2025) Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes. Nature Biotechnol. [Journal] [ReadCube]
February 4: Rebecca Kirby (Biering Lab)
Carlson et al. (2025) Single-cell image-based screens identify host regulators of Ebola virus infection dynamics. Nature Microbiology 10, 1989-2002. [Journal] [preprint]
February 11: Zach Krill (Komor Lab)
Pierce et al. (2025) Prime editing-installed suppressor tRNAs for disease-agnostic genome editing. Nature 648, 191-202. [Journal] [PMC]
February 18: Shivani Lakkaraju (Ren and Gaulton Labs)
Musunuru et al. (2025) Patient-Specific In Vivo Gene Editing to Treat a Rare Genetic Disease. N Engl J Med 392, 2235-2243 [Journal] [PMC]
February 25: Grace McAuley (Yeo Lab)
CANCELLED
March 4: Tanmayi Vashist (Gaulton Lab)
Song et al. (2025) Spatially resolved mapping of cells associated with human complex traits. Nature 641, 932–941. [Journal] [PMC]
March 11: Mari Williams (Telese Lab)
Arnould et al. (2025) Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity. bioRxiv 2025.06.11.658967 [bioRxiv] PRE-PRINT
March 18: Responsible Conduct of Research Discussion:
Ethical use of AI in research
Professors Benner, Fisch, Goren, Majithia.
Select Spring quarter topic.
Spring 2026 - Enhancers and other CREs
April 1: Siri Yendluri (Nizet Lab)
Chavez et al. (2025) IRF1 cooperates with ISGF3 or GAF to form innate immune de novo enhancers in macrophages. Science Signaling 18, eado8860. [Journal] [PMC]
April 8: Morgan Black (Dixon lab)
Eder, Moene, et al. (2025) Functional maps of a genomic locus reveal confinement of an enhancer by its target gene. Science 389, eads6552. [Journal] [PMC]
April 15: Nichelle Camden (Simonson lab)
Ren et al. (2026) CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription. Nature Communications, in press. [OA Journal]
April 22: Natalie Castillo (Rose lab)
Yu et al. (2025) Recent evolution of the developing human intestine affects metabolic and barrier functions. Science. 389, eadr8628 [Journal] [PMC]
April 29: Eduardo Modelo (Goren lab)
Goel et al. (2025) Dynamics of microcompartment formation at the mitosis-to-G1 transition. Nat Struct Mol Biol 32, 2614–2627. [Journal] [PMC]
May 6: Madeleine Pittigher (Gaulton lab)
Yang et al. (2025) A cis-regulatory element of the PHYTOCHROME A gene confers the submergence escape capacity for amphibious plants. Nature Communications 16, 11167. [Journal] [PMC]
May 13: Noa Popko (Carter lab)
Kraft et al. (2025) Enhancer activation from transposable elements in extrachromosomal DNA. Nat Cell Biol 27, 1914–1924. [Journal] [PMC]
May 20: Dylan Walmsley (Tuszynski lab)
TBA [Journal] [PMC]
May 27: Ellen Wang (Zheng lab)
Hansen et al. (2025) Synergy between regulatory elements can render cohesin dispensable for distal enhancer function. Science 391, eadt4221. [Journal] [bioRxiv]
June 3: Rosan Wang (Ecker lab)
Hu et al. (2025) Multiscale footprints reveal the organization of cis-regulatory elements. Nature 638, 779–786. [Journal] [PMC]
June 10: Responsible Conduct of Research Discussion:
Conflicts of Interest
Professors Komor, Rao, Yeo
Summer Book Club selection: