Check out this terrific thread by first author, @sungyalin.bsky.social, whose creativity, bravery, exactitude, and perseverance made this project a reality.

How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...

Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466

I feel irrationally annoyed at journals that ask for numerical scores and/or structured review responses. Assessing the reviews themselves is the job of the editors. I will refuse all review requests from journals who use such rubric devices for scientific papers as if they were term papers.

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...

Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted. liorpachter.wordpress.com/2018/05/18/j...

After almost 30 years, the Tree of Life Web Project has been retired as an actively growing site. It will be unavailable until we can build a static site that contains its final content. More details at subulatepalpomere.com/2025/11/02/t...

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

Our paper (Brieuc Lehmann is the first author) is now online in Genetics. academic.oup.com/genetics/adv...

To contribute to common knowledge :-) I too have been integrating AI tools closely into my research. This paper arxiv.org/abs/2507.09683 with @mkearnsphilly.bsky.social and Emily was my first experiment with this, and it was just accepted to SODA. I'll describe the process in thread.

Check out this new Levine-Lampson collaboration, led by the talented Hyuk-Joon Jeon. We explored the consequences of inheriting long telomeres from dad and short telomeres from mom. Or the reciprocal. Turns out, parent-of-origin matters (in mice, at least). authors.elsevier.com/c/1loW-3QW8S...

Excited to share a new method developed from my group thats published at Genome Biology. This was an amazing effort by my grad student Linh @linhngk.bsky.social. We developed Topsicle, a method that analyzes long read data for telomere analysis and length measuring. doi.org/10.1186/s130...

We've been busy in the lab, and I'm super proud of the team right now. These three papers are great examples of "Night Science", creative, curiosity driven work at its best! All are works in progress. www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

The #Drosophila Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that #fitness & #immunity are the likely primary evolutionary drivers of Dscam1 isoform diversity in #arthropods @plosbiology.org 🧪 plos.io/4gp8cWd

SINGER, our ARG inference method, is finally published and freely available online: doi.org/10.1038/s415... It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

Pretty amazing observation in nature rdcu.be/eEebw

Our latest: We developed a chemo-optogenetic system for precise spatiotemporal control of morphogen production. Using dual light + small molecule control of Sonic Hedgehog production, we recapitulated neural tube patterning in vitro & measured spread of Shh 🧵 www.sciencedirect.com/science/arti...

The 2025 Cold Spring Harbor Labs, Single Cell Analysis Meetings are here. This is the longest running single cell meeting, started in 2009. Please register and send an abstract! with streetslab.berkeley.edu ‪@saukaspengler.bsky.social‬ meetings.cshl.edu/meetings.asp...

Here’s some Gemini gaslighting: • giving a wrong answer to a puzzle • giving Python code that could test its claim • asserting it obtained results from the code supporting its claim • but when I ran the code myself, it showed the claim was false. g.co/gemini/share...

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

I have some BIG NEWS to share today! Today I begin my next adventure as Chief Editor of Nature Biomedical Engineering!! (a thread) @natmethods.nature.com @natbiomedeng.nature.com @natureportfolio.nature.com

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

My talk from this year's probgen is finally out. Where do linear mixed models and random effects come from? They emerge from *mutations* on Ancestral Recombination Graphs.

Discovery of a pH sensor that regulates inflammation. Zhou and Medzhitov provide a mechanistic tour-de-force in defining how BRD4 links changes in pH to inflammatory gene expression. Kudos to the authors on this exciting finding. www.sciencedirect.com/science/arti...

Wowee! Super-resolution stimulated X-ray Raman spectroscopy | Nature share.google/Mdn4Z0ddIy2t...

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful. It’s available on Amazon: tinyurl.com/mx2hewen

At #ICML 2025 to present our paper on single cell lineage tracing. Being one of "big 3, AI/ML", confs, I guess this is the ground zero of current AI. I'll have more to say about my obs, but one thing---it certainly is a lot more posh than your usual bio meetings. acrobat.adobe.com/id/urn:aaid:...

Happy to share my postdoc work—our new preprint is out! 🧬 It’s been a privilege to lead this project. I'm immensely grateful to Anton @golobor.bsky.social for being such an inspiring and supportive supervisor. Also truly thankful to @danielgerlich.bsky.social for his guidance and collaboration.

Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about biorxiv.org/content/earl... biorxiv.org/content/earl...

"Our observations should prompt an essential re-evaluation of the literature concerning astrocyte-neuron mitochondrial transfer" www.biorxiv.org/content/10.1...

There is more - at the end! Exciting finding about conservation in 3'UTRs.

I've started listening to vinyl again and enjoy going to used record stores. ~90% of them, I don't know the artists at all--but they were big enough to put out records. Then ~9%, I remember as huge but I doubt many people know them (Peter Frampton, anybody?). This is prob the fate of our papers.

Super excited to share my final postdoc paper from Rabinowitz lab- on how whole-body and tissue metabolism changes in viral infection! pubmed.ncbi.nlm.nih.gov/40581045/

If you asked me 5 years ago if it would be possible to use a de novo tool on DIA data, I would have thought it would only exist in science fiction. Love being proved wrong. Great work from Justin Sanders. #proteomics #massspectrometry www.nature.com/articles/s41...

The 500 additional GRFPs NSF awarded were not very evenly distributed across fields, it seems. www.science.org/content/arti...

The mechanism of hydrolysis of the peptidyl-tRNA at the stop codon published in Science by Polikanov and Gagnon labs. RFs induce structural change in tRNA utilising its unique intrinsic property - the 2'hydroxyl group that attacks the bond. This is a basic conserved step in translation termination.

Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...

Despite all that is going on, we are still all working on our science. Our 2nd collaboration with @jisaacmurray.bsky.social‬ and Bob Waterston (UW) is out: Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae | Science www.science.org/doi/10.1126/...

Xiao Wang is starting the last day of the Bioorganic GRC off strong telling us about their cool tricks to modify mRNA. www.nature.com/articles/s41... www.nature.com/articles/s41...

Also empirical estimates don't agree with the simulation.... pubmed.ncbi.nlm.nih.gov/24068246/

Harvard today, your institution tomorrow. It's all part of the Project 2025 plan to destroy high education in America. All leading US universities depend on federal funding and tuition dollars from international students. They severely curtailed the former. Now they're eliminating the latter.

Hmm...

A followup to my previous video, in which I now see how #Claude and #o4mini do at formalizing a slightly different proof of the same algebraic implication, after being given the initial informal and formal proofs as reference. www.youtube.com/watch?v=zZr5...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

Just finished the book. Setting aside the frightening scifi beliefs, the blind cosmic arguments of the Effective Altruism (EA) idiots reminded me of a football argument I overheard on a flight. 1/2

During these chaotic times, off to Seoul for RECOMB '25 to present our CellTreeQM (cell tree quartet metric) poster (Da Kuang and Guanwen Qui) to infer cell lineage trees from scRNA-seq using metric learning. An overview (warning long) 1/n A version of the paper is here: arxiv.org/abs/2503.13925

Check out our recent progress using 🧬 PAINT kinetics to decode molecular tension in super-resolution force imaging! 🔬 Great team effort from Seongho, Adam, Irving, and Kevin! 👏 #DNA-PAINT #tension #integrin #superresolution #adhesion doi.org/10.1002/advs...