Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics www.nature.com/articles/s41...

Announcing such a major change to NSF GRFP this late in the cycle is incredibly cruel. 2nd yr students (mine included) have been working so hard on their proposals despite ongoing uncertainty. They are driven and passionate about being outstanding scientists and helping those coming up behind them.

Are you bravely deciding to do a postdoc in the US? And also interested in some combination of genomics, immunology, and transposons? If so, consider applying to my lab at the BioFrontiers Institute in Boulder, Colorado! jobs.colorado.edu/jobs/JobDeta... 🧪🧬 #TESky #interferosky

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit! tinyurl.com/ydn6e3ac

Today, NSF added another 500 GRFP awardees, bringing this year’s total to 1500 www.research.gov/grfp/Awardee...

💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development www.pnas.org/doi/10.1073/... Led heroically by Sylvia Chang & @jonowells.bsky.social A study which has changed the way I think of #transposons! No less! 🧵 1/n

🚨 Preprint alert 🚨 Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇 doi.org/10.1101/2025...

Congratulations to Abby McGee and Val Browning on being awarded NSF Fellowships, and to Matt Chaw, Marazzano Colon, Bria Metzger, Rachel Powell, and Catherine Sniezek on receiving honorable mention!

🧪 NSF GRFP update! New graduate NSF fellowships will likely be announced this week for the GRFP (see bottom of 🧵 for why). First off, I'm *very* glad to hear of those going forward, given the otherwise bleak year so far for graduate training. Some observations... 1/12

We're so thrilled to finally share with you the published version of our CUT&Tag optimization and benchmarking paper "CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks" - out in @naturecomms.bsky.social today: www.nature.com/articles/s41...

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development. Loss of a single CTCF motif is sufficient to cause embryonic lethality. www.sciencedirect.com/science/arti...

😡 F'ing ridiculous. After updating its FAQ yesterday, NSF refused to directly answer a simple question: "Will the NSF Graduate Research Fellowship Program (GRFP) continue to award fellowships in 2025?" GRFPs are a lifeline that support 2,000+ graduate students/year. www.nsf.gov/executive-or...

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨ We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation. 📥 Free-download link: authors.elsevier.com/a/1keGn,LqAr...

@science.org RNA polymerase II at histone genes predicts outcome in human cancer 🧬💊 @fredhutch.bsky.social @hhmi.bsky.social www.science.org/doi/10.1126/...

Hello Bluesky from UW Genome Sciences! We're happy to join other members of our department over here bsky.app/starter-pack... .

Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex... A short thread to highlight some of our findings 🧵

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

How proximal is proximity labeling❓ Using DNA nanorulers we found that TurboID/BioID are largely contact labeling, while APEX2 also bears a major contact labeling pathway in parallel with diffusive labeling. www.biorxiv.org/content/10.1... Special thanks to @aliceyting.bsky.social for discussions

This work just out in Science Advances by Tom Sexton’s lab (to which Mariano Barbieri from our lab contributed modeling data) is a thorough demonstration of how extrusion- and transcription-centric interactions are predominantly antagonistic. Must read! www.science.org/doi/10.1126/...

I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪

Imagine a mouse in which all 10 billion cells keep a diary from fertilization. Imagine sentinel cells recording your experiences and sending out dispatches in the form of DNA. Here's a story I wrote about cell recorders 🧪 Gift link: nyti.ms/3Z3Mqza

It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture. If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)

I made a starter pack of folks affiliated with UW Genome Sciences (past and present) go.bsky.app/L8RAbiJ It's fairly sparse for now, so please let me know if you'd like to be added!

"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements. www.biorxiv.org/content/10.1...

The pSABER paper is now online! pSABER is a new method for amplifying in situ hybridization signals This work was driven by Sahar Attar and co-led by Ram Akliesh ([at] podocytes on the other app) with help from @shechnerlab.bsky.social @dschweppe.bsky.social doi.org/10.1038/s415... 🧵 1/12