🎉 LEE LAB PAPER ANNOUNCEMENT for this month's issue of #GENETICS! We're celebrating from both coasts, bc after defending her MS in 2024, Deepshi's now a biotech researcher in the Bay Area. tl;dr: nucleosome remodeling is necessary to repair germline DNA damage 🧬 academic.oup.com/genetics/art...

I would like to think @wyomingwormboy.bsky.social for describing the Sledgehammer Approach (to research) in WormBook. It is invaluable advice that I share with every trainee.

I was feeling somewhat guilty about saying No to many recent requests but then I re-read the “children’s book”, The Giving Tree. Felt better. Apparently some people interpret the tree’s hyper accommodating behavior as a positive example! I’m pretty sure that was not the author’s intention!

Please stop saying the bill allows "no more multi-year funding" - or at least be clear the 'more' is in reference to disastrous FY25 levels. The bill allows 39% MYF, same as in FY25, which contributed substantially to a 24% drop in new research. The bill has some wins. MYF is not one of them.

For the same reason that Indiana, which is virtually the same size as Massachusetts received nearly $349 million last year in farm subsidies, while Massachusetts got only about $9 million, 1/39th of Indiana’s boon.

Excited to see this out in the world. The CGC is launching a curated strains collection, the first being protein degradation systems and this is a pilot primer to pair with it authored by myself, Dave Reiner, Ann Rougvie, and Aric Daul. We review the state of the field and provide use guidance (1)

I have an answer. He’s just another self promoting D-bag who traded in legit credentials for cash.

One reason to have kids is that they sometimes do clever things. (Note the signs on the side of the trail)

Absolutely essential

DeGette Introduces Bill to Protect NIH From Political Interference bit.ly/4qBQEuz @degette.house.gov

snow on branches ❄️

Going through boxes of old tee shirts today…

Cool paper from Ron Ellis and colleagues.

Job alert! Assistant professor position in the Department of Molecular Genetics (University of Toronto). Amazing department and city. jobs.utoronto.ca/job/Toronto-... Please share.

Somewhat humorously, when you google "SciENcv opinions", this is the top hit. I've also been told that it will be far less informative for reviewers because you can't easily figure out what the applicant has accomplished publication-wise.

When I was the DGS of an umbrella-type PhD program, I worked to put in a rule that PhD students needed a minimum of one 1st-author research paper to graduate. The main intent was to protect students from advisors that were slackers about publishing. No 1st-author pubs really hurts students. 1/3

Qiuyuan Yin, Chonglin Yang et al. reveal a plasma membrane-to-lysosome signaling pathway mediated by the non-receptor tyrosine kinase FGR and the serine/threonine kinase AKT2, which regulates TFEB/TFE3 activation for #lysosome biogenesis in #endocytosis. rupress.org/jcb/article/... #Organelles

New preprint alert: we use sign errors as a test of how well TWAS works. Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇

Another YouTube Tutorial – This one on Proximity Labeling and connected to our recent EMBO J. paper (PMID: 41381733). This is a recording of a talk at the IDeA National Resource for Quantitative Proteomics in Little Rock AR. One of the top facilities in the country! www.youtube.com/watch?v=0T9P...

This was a cool race for a bunch reasons. It was not just a test of ski prowess but also social skills. To do well you had to reach out to racers from other countries and agree to work together. That two Americans were the ones to figure this out is a point of pride and gives me some needed hope.

Nice description of ipTM problems & how actifPTM, LIS, & ipSAE fix those for scoring protein-protein interactions. New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.

Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2 www.youtube.com/watch?v=u63o...

Review @cp-cancercell.bsky.social @mdanderson.bsky.social Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications www.cell.com/cancer-cell/...

Happy new year! Sharing a 🧬🚨REVISED PREPRINT🚨 with major updates to our placental long-read transcriptome paper! Thanks to thorough reviewer feedback, we've strengthened the manuscript with new analyses & clarifications. Key figures in this thread 🧵 www.biorxiv.org/content/10.1...

My Christmas present this year was a partially detached retina! But here was my real present. Immediate access to health care, competent caring medical professionals, health insurance, and financial security to make up the difference. How many Americans lack this and why is that acceptable???

A legitimately cogent essay arguing against an unnecessary medical procedure from The Onion.

I'm on the Board of @biologists.bsky.social. Many know them as publishers of @dev-journal.bsky.social, @jcellsci.bsky.social, @jexpbiol.bsky.social , DMM, and @biologyopen.bsky.social --but they also are a major funder of small grants that empower young biologists and enable scientific meetings 🧪

Happy to announce the publication of our foray into studying what happens to the transcriptomes of nuclei when cells fuse to form a syncytium. More to follow in the coming few years. One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!

Chaos is beautiful.

Happy place. Dark Angel.

Sunset

Never gets old.

Sunrise over driveway

🎉 Excited to share our latest preprint📰 ! www.biorxiv.org/cgi/content/... Many thanks to everyone involved in this project ! Using a zebrafish model 🐟 and iPSC-derived motor neurons 🔬 we show that restoring the calpastatin/calpain pathway preserves motoneuron survival and function in C9orf72 ALS!

Deadline for this post-doc position in my lab extended to Jan 11th!

Hot off the press at EMBO Journal. The culmination of several years of work and hopefully useful to people in the field! BIG Shout-out to Review Commons, who handled the submission. It's a sensible and efficient model and all the journals I like (Society and NFP) are already participating. 🙏

If plants could grow on Mars…

The amazing silversword plant

Crater at sunset

Crater from the south.

Haleakala crater from the north side.

There is no lower life form than a bagel swindler! Bagels are sacred. cowboystatedaily.com/2025/12/01/f...

Coffee shop

Oh man, what a race! Last year of racing for the best cross country skier in the history of North America.