Journal Club

Fall 2024 - Genetics of Non-model Organisms

October 2: 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 9: Shams Al-Azam (Alexandrov Lab)
Preston et al. (2023) Elephant TP53-RETROGENE 9 induces transcription-independent apoptosis at the mitochondria. Cell Death Discov 9, 66. [Journal] [PMC]

October 16: Ethan Armand (Ren Lab)
Yin et al. (2021) Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. Nature Communications 12, 6858. [OA Journal]

October 30: Liz Chamiec-Case (Bambah-Mukku Lab)
Herbert et al. (2024) Ancient developmental genes underlie evolutionary novelties in walking fish. Current Biology S0960-9822(24)01157-6. [Journal] open access article, early online.

November 6: Jon Freshman (Carlin Lab)
Catchpole et al. (2023) A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea. Nature Microbiology 8, 1339-1347. [Journal] [PMC]

November 13: Weston Elison (Gaulton Lab)
Fortier and Pritchard (2024) Ancient Trans-Species Polymorphism at the Major Histocompatibility Complex in Primates. bioRxiv 2022.06.28.497781 [Preprint v2]

see also: Fortier and Pritchard (2024) The Primate Major Histocompatibility Complex: An Illustrative Example of Gene Family Evolution. bioRxiv 2024.09.16.613318 [Preprint]

November 20: Trent Gomberg (Yeo Lab)
Bao et al. (2019) The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology 17, 6. [OA Journal]

November 27: No class scheduled Thanksgiving Holiday

December 4: Rachel Weinstein (Rifkin Lab)
Tian et al. (2022) Severe inbreeding, increased mutation load and gene loss-of-function in the critically endangered Devils Hole pupfish. Proc. R. Soc. B 289: 20221561. [OA Journal] [PMC]

December 11: Tanmayi Vashist (Gaulton Lab)
Lotharukpong et al. (2024) A transcriptomic hourglass in brown algae. Nature 635, 129-135. [Journal] [PMC]

December 18: Joseph Rainaldi (Mali Lab)
Déjosez et al. (2023) Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Cell 186, 957-974. [Journal] [PMC]

Select Winter topic.

Winter 2025 - Genome Engineering / Gene Editing

January 8: Anvita Komarla (Towers Lab)
Pradella et al. (2024) Engineered extrachromosomal oncogene amplifications promote tumorigenesis. Nature. [Journal]

January 15: Grace Carter (Meharena Lab)
Sun et al. (2024) In vivo editing of lung stem cells for durable gene correction in mice. Science 384, 1196-1202. [Journal]

January 22: Tula Keal (Dixon Lab)
Policarpi et al. (2024) Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications. Nature Genetics 56, 1168–1180. [Journal] [PMC]

January 29: Challana Tea (Ferguson Lab)
Chen et al. (2024) Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR–Cas9 ribonucleoprotein. Nature Biotech. [Journal] [UC Free Full Text]

February 5: Camilo Londono (Zheng Lab)
Chung et al. (2024) Conditional knockout of Shank3 in the ventral CA1 by quantitative in vivo genome-editing impairs social memory in mice. Nature Communications 15, 4531. [OA Journal]

February 12: Jeffrey Chiu (Ren Lab)
Pinglay et al. (2025) Multiplex generation and single-cell analysis of structural variants in mammalian genomes. Science 387, eado5978. [Journal] [PMC]

February 19: Zach Krill (Komor Lab)
Pandey et al. (2025) Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing. Nature Biomedical Engineering 9, 22–39. [Journal] [PMC]

February 26: Jose Sandoval (Chi Lab)
Treblay et al. (2025) A potent epigenetic editor targeting human PCSK9 for durable reduction of low-density lipoprotein cholesterol levels. Nature Medicine. [Journal]

March 5: Isabella Ruud (Chavez Lab)
Durrant et al. (2024) Bridge RNAs direct programmable recombination of target and donor DNA.
Nature 630, 984–993. [OA at Journal]

March 12: Grace McAuley (Yeo Lab)
An, M., Davis, J.R., Levy, J.M. et al. In vivo base editing extends lifespan of a humanized mouse model of prion disease. Nature Medicine (2025). [OA at Journal]

March 19: Responsible Conduct of Research Discussion: Germline engineering?
Professors Cherqui, Komor, Biering, and Heinz

Visscher, P.M., Gyngell, C., Yengo, L. et al. (2025) Heritable polygenic editing: the next frontier in genomic medicine? Nature 637, 637–645. [Journal] [PMC]

Select Spring quarter topic.

Spring 2025 - Genetics of Disease

April 2: Gianna Elias (Chavez Lab)
Hung et al. (2024) Coordinated inheritance of extrachromosomal DNAs in cancer cells. Nature 635, 201–209. [Journal] [PMC]

April 9: Shazreh Hassan (Bambah-Mukku Lab)
Machlovi et al. (2024) APOE4 confers transcriptomic and functional alterations to primary mouse microglia. Neurobiology of Disease 164, 105615. [Journal] [PMC]

April 16: Rebecca Kirby (Biering Lab)
Klunk et al. (2022) Evolution of immune genes is associated with the Black Death. Nature 611, 312–319 (2022) [Journal]
and
Barton et al. (2025) Insufficient evidence for natural selection associated with the Black Death. Nature 638, E19–E22 (2025) [Journal] [bioRxiv]

April 23: Molly Huang (Fisch Lab)
Umeda, M. et al. (2024) A new genomic framework to categorize pediatric acute myeloid leukemia. Nature Genetics 56, 281–293. [Journal] [PMC]

April 30: Megan Huang (Gaulton Lab)
Liu et al. (2025) Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants. Science 387, eadp4753 [Journal]

May 7: Krysten Jones (Lewis Lab)
Seddighi et al. (2024) Mis-spliced transcripts generate de novo proteins in TDP-43–related ALS/FTD. Science Translational Medicine 16, eadg7162. [Journal] [PMC]

May 14: Shivani Lakkaraju (Ren and Gaulton Labs)
Kong et al., (2024) Engineered FSHD mutations results in D4Z4 heterochromatin disruption and feedforward DUX4 network activation. iScience 27, 109357 [OA Journal]

May 21: Terry Noblin (Yeo Lab)
TBA

May 28: Mari Williams (Telese Lab)
TBA

June 4: Siri Yendluri (Nizet Lab)
TBA

June 11: Responsible Conduct of Research Discussion
Topic TBA

Summer Book Club selection