Thomson Hallmark, PhD

@artemnemudryi @SantiagoFrangos @NatureMicrobiol Nice story, congratulations!

Our work on bacterial Schlafens in phage defense is out today @NatureMicrobiol ! Check out the final version here: rdcu.be/e7Bmz We are looking for postdocs and students to expand our team! Official postings are coming soon. Please reach out if you're interested!

@SternbergLab @LeifuChangLab Nice! Very cool!

Out now! In collaboration with @LeifuChangLab, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems! Links to the articles in the following tweet:

@1992shaikhyahya @palermo_lab Probably not a good idea to put your personal contact info on a public internet post 😬

@palermo_lab Hi good afternoon. Ma'am will you please tell me which software you used to create these graphics it's really amazing. I am really grateful to you. Anticipated thanks Thanks & Regards Dr. Shaikh Yahya Jamia Hamdard New Delhi shaikhyahya07@gmail.com +919028029671

Check out our review on Graph #NeuralNetworks #GNNs in #MolecularDynamics! We show how #AI is used for #ForceFields, free-energy and analysis - including our recent attention-based GNN workflow - and how you can integrate your favorite AI in #compchem! sciencedirect.com/science/articl…

@ScienceNews This post sound like the opening line of a scifi horror flick

At a remote field camp in West Antarctica, scientists drilled through 1,100 meters of ice to reach the perpetually dark waters of the subglacial Lake Mercer. sciencenews.org/article/antarc…

@NikoMcCarty This sounds like such a useful book!

I'm (slowly) writing the book I've been thinking about for the last 3+ years. Nothing official yet, but I'm hoping to write a deeply mechanistic and interactive, Bartosz Ciechanowski-style book about how a single E. coli cell works. It will cover DNA, transcription, signaling, diffusion, metabolism, and so on. It will present everything through a quantitative lens, such that readers get a real "sense" of these things; how they look, how big they are, how fast they move. There will be boxes in each chapter that actually explain where those numbers came from, and the experiments through which they were collected. It's sort of an intellectual continuation of my prior @AsimovPress essays on this subject: Biology is a Burrito, Fast Biology, Recipe for a Cell, What Limits a Cell's Size? and The Weight of a Cell. I'd like to publish every chapter for free, online, and then do a print book later. Heavily inspired by Stewart Brand's "Book in Progress" for @WorksInProgMag and Michael Nielsen's Quantum Country textbook. If you are a biophysicist, or just someone who might enjoy reading this book, or an illustrator/animator, I'd really love to talk with you and get ideas. (I'm also looking for a publisher!) My dream would be for this book to supplant some of the textbooks currently used in high school biology classes. Let me know what you think. What should I cover? (Painting by David Goodsell.)

@artemnemudryi @rafapinilla92 Congratulations Artem! Cool story!

First preprint from the Nemudryi Lab! In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages⬇️ biorxiv.org/content/10.110…

@KathyYWei1 You'll probably need to do experimental phasing (metal soaks, etc.). AF is no good with small peptides, especially if there is any conformation switching.

Hey smart people out there, what structure does this protein fold into? Hint: AlphaFold, ESMFold, Boltz, Chai, etc are wrong 🤭. Good luck! >whatami MKIAVIGATGQVGREIAKLLAEKGHEVTAIASRSKNPEEVAKLGIEAVYVDGEVLDFKSVEEAVKNADVVISVAGG

@NikoMcCarty $10k gets you a lamaner flow cabinet and 1 month postdoc salary

What is a specific problem in biology that would be useful to solve, and could be solved for ~$10,000?

@ItaiYanai Not while on the Beagle, he didn't.

If you don’t have time to take a walk, then you don’t have time to do science. Charles Darwin would take two walks every day on his "thinking path", not as a break from science, but as a crucial part of it.

@ATinyGreenCell Definitely read this as "kids" first and was a tad concerned by tone and the response in comments...

I may have to start making kits for at home biology exploration soon. There is lots of thought-terminating edutainment kits out there and no one seems to want to make open ended biotech sandboxes. The state of material guidence for amateur biologists is profoundly disappointing.

@0xluffy You need to relax. Usually short sleep is because of stress (I'd usually only get 4is for the last year of my PhD studies)

body just wakes up at 4-5th hour now how do i stay asleep for 8 please help. already doing magnesium, thealine and melatonin

@tunguz Only in the USA lol

Every day for the next ten days is going tho be the same backwards: 5/20/25 5/21/25 5/22/25 5/23/25 5/24/25 5/25/25 5/26/25 5/27/25 5/28/25 5/29/25

Awesome story!

Today in @ScienceMagazine we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells, a collaboration with @SternbergLab. 1/13 drive.google.com/file/d/1I-UbCR…

@davidasinclair I don't want to see 10x increase in lifespan. Old people gotta go. Let them rest

Can’t see 10x happening but I am keen to see if the epigenetic reprogramming experiments translate to humans next year🤞

Cool postdoc opportunity in the Ke lab!

@cblatts This is a cool aspect of ChatGPT. I find that giving it a persona greatly impacts the kind of answer/feedback I get. Tailoring the initial persona is almost as important as all the training data imo

Then I tried something new. I asked it to pretend it was Esther Duflo and to give an unflinching critique. It gave good suggestions, like "Your targeting tools sound clever, but what’s your causal evidence that they actually improve outcomes?"

Finally, on the one day my field team had before they went on holiday (pretty sure there are more holidays in Colombia than work days), I asked them to hurriedly make some bullets in the full proposal about what they thought was especially relevant as a direction. Uploaded that.

@SergioCruzLeon1 @jpkreysing @MarinaLusic @Beck_Laboratory @MPIbp Woah... this is so cool!

Excited to share our pre-print on the molecular architecture of heterochromatin in human cells🧬🔬 w/ @jpkreysing, Johannes Betz,Turoňová lab, @MarinaLusic, Hummer lab, @Beck_Laboratory, @MPIbp 🔗 Preprint here: doi.org/10.1101/2025.0…

@crypticprophage Makes sense because dying cells leave small DNA fragments in the environment for other cells to pick up that could be integrated into CRISPR arrays.

biorxiv.org/content/10.110… Persisters probably do allow for CRISPR adaptation, but this work has nothing to do with persisters since Fig. 1 shows cells are simply dying and never reach anything like a plateau. So another intepretation is that dying cells increase CRISPR adaptation.

@wc_ratcliff @hankgreen I think made a post a while ago about the algorithm deprioritizing posts containing external links. Could be part of the problem if you included links to your papers

Scientists, is it even worth the effort to post here anymore? For comparison, my twitter post about two recent big papers got a whopping 5 likes. My post at the other place got a lot of community engagement. Either the community here is dead, or algo attention is pay to play.