One of the most profound articles I've read. "Just try to be decent"

Anne Applebaum@anneapplebaum.wsocial.eu · 4w ago

Lindsey Graham was one of the main subjects of a @theatlantic.com cover story I wrote in 2020, on why people collaborate with regimes they know are immoral. Here's a gift link: www.theatlantic.com/magazine/arc...

New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵

Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...

mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity

Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.

cell.com

🚨first Bartman lab preprint! it's an LC-MS method to measure "total Coenzyme A" (sum of all acyl-CoAs). this will let us study coA synthesis flux using heavy-isotope tracing! huge congrats to first author Amelia Taylor and star coauthor @mzspectrum.bsky.social ! www.biorxiv.org/content/10.6...

If you know a graduating undergraduate looking for the chance to spend 1-2 years in a lab before graduate school, we're hiring! Our lab explores morphogenesis, defining how the cell adhesion & cytoskeletal machinery work together to allow cells to change shape & move tarheels.live/peiferlab/ 1/n RT

Insightful summary of an extraordinary person being extraordinarily fired: "you don't silence a woman of color who raised concerns about racism by silencing her...The fingerprints are distributed perfectly across the system." www.linkedin.com/pulse/uclas-...

UCLA's Most Decorated Ecologist Just Got Fired : Here's the sequence

In January of 2025, at the ICTP ICTS winter school at NCBS, Priyanga Amarasekare offered to take me and a few other students out for my birthday. She didn't have to do that.

linkedin.com

When the tech companies built their entire empire on algorithmically pushing what people want to hear to confirm their biases, why would they not do the same with LLMs

Jay Van Bavel, PhD@jayvanbavel.bsky.social · 4mo ago

A new paper in Science measured the prevalence of social sycophancy across 11 leading large language models. The model’s responses were nearly 50% more sycophantic than humans’, even when users engaged in unethical, illegal, or harmful behaviors. www.science.org/doi/10.1126/...

Well here's an answer to a question I hadn't thought of asking www.nature.com/articles/s41...

Limitations of serial cloning in mammals - Nature Communications

Here they show that extended serial somatic cell cloning imposes a threefold increase in de novo mutations compared to natural reproduction, progressively reducing birth rates and ultimately limiting ...

nature.com

@mukherja.bsky.social work on RNAPII clusters is in print today: www.nature.com/articles/s41... Congrats! TLDR: RNAPII clusters represent transcriptonally engaged molecules at single genes, not super-stochiometric assemblies. Please check it out and see the the thread below for a summary.

A single cluster of RNA Polymerase II molecules is stably associated with active genes - Nature Communications

Live molecular-scale imaging in fly embryos shows that a single RNA Polymerase II cluster stays bound to active genes during transcription. Cluster formation requires initiation, and intensity represe...

nature.com

Apratim (Appy) Mukherjee@mukherja.bsky.social · 11mo ago

(1/3) Excited to post our updated pre-print! We show RNAPII clusters are simply collections of polymerase molecules stably engaged at single genes & cluster intensity is strongly correlated with txn output during Drosophila embryogenesis. www.biorxiv.org/content/10.1...

There is accumulating evidence that sperm miRNAs function to regulate embryonic gene expression and transmit inherited phenotypes to offspring but how does this work since sperm cargo is massively diluted in the egg upon fertilization. Here we directly address this ? www.biorxiv.org/content/10.6...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.

Free markets are supposed to select for the good businesses and kill the bad. But, the hyper efficient capital markets allow transient feasting & abandoning the dying carcass. What we have now is a bunch of parasites on the economy evolving unbridled virulence. Now the viruses want to rule.

Dannagal Goldthwaite Young@dannagal.bsky.social · 5mo ago

What’s apparent to those of us who live in the actual world is that it’s not liberalism, but *unbridled capitalism* that has exhausted itself. It is responsible for: -Corruption of our elections -Untenable & growing income inequality -Gutting of institutions to extract capital, leaving them hollow

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

🚨New preprint! We built a cell-free genomics platform (GATO-seq) to probe transcriptional regulation and discovered a “super pause” sequence that triggers a new Pol II active-site conformation. Huge shout-out to @robertovn.bsky.social for pulling off this monster of a project. tinyurl.com/superpause

Now in print at ACS Synbio! Introducing Aviatar: a concept for inducible translocation to any cell compartment using only a 1-component probe pubs.acs.org/doi/10.1021/...

Optogenetic Translocation to Subcellular Compartments through Regulation of Protein Avidity

Inducible translocation to subcellular compartments is a common strategy for protein switches that control a variety of cell behaviors. However, existing switches achieve translocation through induced...

pubs.acs.org

Lukasz Bugaj@bugajlab.bsky.social · last yr.

Proteins often bind targets using avidity, the combined interaction strength of multiple weak binders. Now we’ve harnessed this principle for compact, *single*-component optogenetic tools for translocation. Lead by phenom PhD student @dennishuang.bsky.social #synbiosky🧵 📝 tinyurl.com/aviatar

Warren Center faculty affiliate Greg Ridgeway has developed and tested a statistical model using real-world data that could help police departments take steps to prevent future excessive force. penntoday.upenn.edu/...

Well that's cool Source: Nature search.app/FLn5P

Quantum spin resonance in engineered proteins for multimodal sensing - Nature

A recently developed class of magneto-sensitive fluorescent proteins are engineered to alter the properties of their response to magnetic fields and radio frequencies, enabling multimodal sensing of b...

search.app

This is how we first teach chirality to our undergrads !

David Shaywitz@dshaywitz.bsky.social · 7mo ago

Loved this from @simonmaechling.bsky.social - chemistry FTW… @dereklowe.bsky.social @carolynbertozzi.bskyverified.social

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

Since there are so much happenings that I can't breath, ill just have to take it out on this little irritant. What makes a workshop "prestigous" ? Does attending this give trainees prestige? Do organizers give themselves prestige for running it? Can we stop using language like this?

EvolDir@evoldir.bsky.social · 7mo ago

Join MBL's prestigious Workshop on Molecular Evolution, the longest-running in the field. Apply by Jan 26, 2026. More info: https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/workshop-molecular-evolution #workshop

Every week, Nature publishes yet another breathless puff piece about some AI startup, based only unpublished claims from the company and interviewing only those who work there. How can the leading scientific journal publish piece after piece that would make Kevin Roose blush? I think it's that...

and the winner of the "2025 best thing on Internet" has just arrived neal.fun/size-of-life/ @carlbergstrom.com

Size of Life

From an amoeba to a blue whale

neal.fun

I just finished my 28th yr of teaching grad compbio. Following the inevitable trend, a 3rd of the course is now Deep Learning (DL). One activity we did was a deep dive into the AlphaGenome pre-print (www.biorxiv.org/content/10.1...). Question is, how do we evaluate it as a science paper? 1/n

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence le...

biorxiv.org

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

nature.com

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

Sung-Ya Lin@sungyalin.bsky.social · 8mo ago

So excited to see my PhD work finally being published!!! It was such a pleasure working with a great team!!!

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/...

Rapid compensatory evolution within a multiprotein complex preserves telomere integrity

Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...

science.org

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...

Single-cell susceptibility to viral infection is driven by variable cell states

Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...

cell.com

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...

James Watson in his own words

“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…

liorpachter.wordpress.com