Xun Chen

Super excited to share our latest #preprint on the TE classification/annotation and regulatory evolution from our lab @guilbourque at @Ashbi_KyotoU. Check it out here! 🧵 Cryptic endogenous retrovirus subfamilies in the primate lineage doi.org/10.1101/2023.1…

New preprint from our lab! Why is not everyone working on Transposons? Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons biorxiv.org/content/10.110…

Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq dlvr.it/TJW2bx

Why don't humans have tails? A genetics study finds that a mobile genetic sequence inserted into a gene for tail development contributed to tail loss as early apes evolved. go.nature.com/3Te8t4C

Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites dlvr.it/T2DH8X

Our paper on the ancestral genome-assisted TE annotation method/resource is out in @CellGenomics! Enhanced annotation is now available for multiple species, including human and mouse, with ~70% increase in ancient TEs. cell.com/cell-genomics/…

#Pangenome graphs improve the analysis of SVs for rare genetic diseases. Our new study is out! Great collaboration with the lab of Tomi Pastinen and congrats to @groza_cristian for the amazing work! nature.com/articles/s4146…

I've gotten several requests recently for permission to use the notes from my computational biology class: github.com/pachterlab/BI-… A reminder that they're licensed under CC BY 4.0: you're free to share and adapt, just give appropriate credit and indicate if changes were made.

[News release] ASHBi researchers identify and selectively manipulate the neural circuits underlying the balance of risk vs. reward decision-making using optogenetics in primates. ➡️Article science.org/doi/10.1126/sc… ➡️Press Release ashbi.kyoto-u.ac.jp/news/20240105_… @ScienceMagazine

Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits dlvr.it/T0htWb

🔥🔥How does the LINE-1 retrotransposon jump around in the human genome? Super excited to present my postdoctoral work answering this published today @Nature together with twitterless Kathy Collins's lab and @NogalesLab @UCBerkeley nature.com/articles/s4158… A 🧵

Check out our latest review | LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities by @CarlosMendezPhD. Our thanks to @GenesDev. genesdev.cshlp.org/content/early/…

“Transposable elements contribute to nearly 80% of human-specific candidate cis-regulatory elements in cortical cells” 🧠 …🤯 literally! Amazing dataset 🔥 Congrats to all involved! nature.com/articles/s4158…

Very happy to share our new paper on how SOX2 instructs pluripotency program transition in vivo in mouse E3.5-E7.5 embryos. Spearheaded by our super team: Lijia Li, Fangnong Lai, Xiaoyu Hu and Bofeng Liu. Wonderful collaboration with Amy Ralston. (1/n) science.org/doi/10.1126/sc…

Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci dlvr.it/T0D5Tk

💥 New preprint! Really excited about this work brilliantly led by Manu @manvendr7 & Sabrina Leddy in collab with @TheNixonLab - check it out and let us know what you think!