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Journal Club

Fall 2023 - Sex Differences

September 27: Organizational Meeting
Introductions, GTP advising committee, Program expectations, How to critique a paper, Selection of Fall topic.

October 4: Kween Agba (Zheng Lab)
Ge et al. (2018) The histone demethylase KDM6B regulates temperature-dependent sex determination in a turtle species. Science 360, 645-648. [Journal]

October 11: AJ Daniels (Signer and Bennett Labs)
Lee et al. (2023) Sex-biased T-cell exhaustion drives differential immune responses in glioblastoma. Cancer Discovery 13, 2091-2105. [Journal] [PMC]

October 18: Xiaomi Du (Majithia Lab)
Wingo et al. (2023) Sex differences in brain protein expression and disease. Nature Medicine 29, 2224-2232. [Journal] [PMC]

October 25: Sam Hatch (Yeo Lab)
Gegenhuber et al. (2022) Gene regulation by gonadal hormone receptors underlies brain sex differences. Nature 606, 153-159. [Journal] [PMC]

November 1: CANCELLED

November 8: Brittany Leger (Palmer Lab)
Wang et al. (2022) Sex disparities in influenza: A multiscale network
analysis. iScience 25, 104192. [Journal] [PMC]

November 15: Rachel McMillen (Carlin and Benner Labs)
Sierra et al. (2023) Unusual X chromosome inactivation maintenance in female alveolar type 2 cells is correlated with increased numbers of X-linked escape genes and sex-biased gene expression. Stem Cell Reports 14;18(2):489-502. [Journal] [PMC]

November 22: No class scheduled Thanksgiving Holiday

November 29: Hannah Mummey (Gaulton Lab)
Todd et al. (2019) Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change. Science Advances 5, eaaw7006. [Journal] [PMC]

December 6: Mei Okino (Sander and Gaulton Labs)
Cheng et al. (2023) The X-linked epigenetic regulator UTX controls NK cell-intrinsic sex differences. Nature Immunology 24, 780–791. [Journal] [Preprint]

December 13: Faculty Panel. Professors Chavez, Hamilton, and Zheng
Responsible Conduct of Research Discussion: Credit Where Due – Authorship and Citation
COPE Authorship and Contributorship Guidelines [link]

Select Winter topic.


Winter 2024 - Non-coding variants

January 10: CANCELLED

January 17: Shams Al-Azam (Alexandrov Lab)
Baxter et al. (2023) Properties of non-coding mutation hotspots as urinary biomarkers for bladder cancer detection. Scientific Reports 13, 1060. [Journal] [PMC]

January 24: Ethan Armand (Ren Lab)
Mostafavi et al. (2023) Systematic differences in discovery of genetic effects on gene expression and complex traits. Nature Genetics 55, 1866–1875. [Journal]

January 31: Liz Chamiec-Case (Bambah-Mukku Lab)
Parey et al. (2023) Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits. Genome Research 33, 1513-1526. [Journal] [PMC]

February 7: Weston Elison (Gaulton Lab)
Kang et al. (2023) Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nature Genetics 55, 2255–2268. [Journal] [MedRxiv]

February 14: Jon Freshman (Carlin Lab)
Slonchak et al. (2022) Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution. Nature Communications 13, 1279 [Journal] OA

February 21: Trent Gomberg (Yeo Lab)
Jaganathan et al. (2019) Predicting Splicing from Primary Sequence with Deep Learning. Cell 176, 535-548.e24. [Journal] OA

February 28: Anvita Komarla (Towers Lab)
Rheinbay et al. (2020) Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578, 102-111. [Journal] [PMC]

March 6: Gabrielle Meza (Dickinson Lab)
Liu & Zhing (2024) Epiallelic variation of non-coding RNA genes and their phenotypic consequences. Nature Communications 15, 1375. OA [Journal]

March 13: Joseph Rainaldi (Mali Lab)
Allou et al. (2021) Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 592, 93-98. [Journal]

March 20: Faculty Panel. Professors Bamabah-Mukku, Chi, Dixon, Ferguson, and Yeo.
Responsible Conduct of Research Discussion: NIH Public Access Policy (

Select Spring quarter topic.


Spring 2024 - Transposable Elements

April 3: Rachel Weinstein (Rifkin Lab)
Hannon-Hatfield, et al. (2024) Evolution of a Restriction Factor by Domestication of a Yeast Retrotransposon. Molecular Biology and Evolution 41, msae050. OA [Journal]

April 10: Grace Carter (Meharena Lab)
Choudhary, et al. (2023) Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes. Nature Communications 14, 634. OA [Journal]

April 17: Tula Keal (Dixon Lab)
Toda et al. (2024) Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation. Cell Reports 43, 113774. OA [Journal] [PMC]

April 24: Challana Tea (Ferguson Lab)
Garza et al. (2023) LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. Science Advances 9, eadh9543. OA [Journal] [PMC]

May 1: Camilo Londono (Zheng Lab)
Scopa et al. (2023) JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer’s disease. Nature Communications 14, 8021. OA [Journal]

May 8: Jeffrey Chiu (Ren Lab)
Ochoa et al. (2023) Pathogenic tau–induced transposable element–derived dsRNA drives neuroinflammation. Science Advances 9, eabq5423. OA [Journal] [PMC]

May 15: Krysten Jones (Lewis Lab)
Mita et al. (2020) BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nature Structural & Molecular Biology 27, pages179–191. [Journal] [PMC]

May 22: Jose Sandoval (Chi Lab)
Sala et al. (2023) AGO2 silences mobile transposons in the nucleus of quiescent cells. Nature Structural & Molecular Biology 30, 1985–1995. [Journal]  2022 bioRxiv [preprint]

June 5: Isabella Ruud (Chavez Lab)
Klompe et al. (2019) Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature 571, 219-225. [Journal]

see alsoLampe (2024) Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Nature Biotechnology 42, 87–98. [Journal]

June 12: ProfessorFaculty Panel. Professors TBA
Responsible Conduct of Research Discussion: Topic TBA

Summer Book Club selection