New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/
www.biorxiv.org/content/10.6...
Our paper with @sokrypton.org using AlphaFold2 to predict small-molecule binding sites in proteins is now out in Nature Methods! 🧵
rdcu.be/e7SnX
www.nature.com/articles/s41...
this is awesome work!
Are you interested in how to predict functions of natural product biosynthetic gene clusters (BGCs) and their products? And/or do you love metallophores and would love to identify their producers in microbiomes? Check out @zachreitz.bsky.social 's new paper!
elifesciences.org/articles/109... 1/n
The most impt change at #NIH and to US science this year is bigger than grant cancellations— it’s how the agency is governed.
For 75 years NIH has been largely independent of presidential control. That’s changed this year. New piece from me and @nataliebaviles.bsky.social in @nature.com
🧪
Weird day for microbiology
President Trump on Saturday blamed Iran for an airstrike that hit an Iranian elementary school on February 28, killings scores of children. An analysis by The New York Times indicates that the school was most likely hit by an American airstrike. Follow live updates.
and the links:
region9a.uaw.org/news/driveact
www.mafamiliesforvaccines.org/actioncenter
www.aaup.org/event/nation...
Stand up For Science rally in Boston, March 7 2026
Great rally in Boston today! Here are some actions anyone can take:
-- support the DRIVE Initiative, which would invest $400M in MA research+higher education
-- support H.2554, which will close irresponsible loopholes in vaccine requirements for children in MA
-- Protest ICE and war on March 28
A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insects
Various phylogenetic secondary loss events are mapped to a tree of insects to explain the parsimony calculations necessary to explain the diversity of insect Drosomycin antimicrobial peptide genes
Antimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.
Pleased to finally share this fun collab that began at #Ento23
@cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun).
Horizontal transfer of an #AntimicrobialPeptide across insects
bit.ly/DrsHGT
1/🧵
The data also reinforce a message that should be clear: American leadership in science and medical research requires far more than getting across the line on top-line budget negotiations and will require continued vigilance to track how HHS treats applications and existing awards.
Happy to report that we submitted a new manuscript this week.
The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...
Don't panic, Organize! It was great to be able to represent @nihfellowsunited.bsky.social today at the Take Back Our Science Rally in DC to speak out against the attacks on our union and for scientist workers rights!
The problem with this poll is they polled the general public. But the general public is a well known echo chamber!
Should have polled X, which is well known for not being an echo chamber.
https://www.annenbergpublicpolicycenter.org/stark-divide-americans-more-confident-in-career-scientists-at-u-s-health-agencies-than-leaders/
A quick email before I head of to get ready for the @standupforscience.bsky.social rally.
1/3
Great news for the toxic PI that wants RNA seq data analysed in under a minute.
SUFS rallies this weekend will be so lit that Vinay has preemptively surrendered
Excited to share great work from @jingqian.bsky.social , now a second year graduate student in my lab, from research she conducted at her previous position at Shanghai Jiao Tong University!
Would have been cool to see comparisons to the SARS2-related spillovers in pangolins, and to the SARS-CoV-2 spillovers to white tailed deer!
In each case we know that there were spillovers, and testing each would show how sensitive these methods are to known spillovers of different sizes
MKado: a toolkit for McDonald-Kreitman tests of natural selection https://www.biorxiv.org/content/10.64898/2026.03.02.709122v1
made some tweaks to @iambic.bot recently so it never sends the same text twice; it's been on good form since
Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes
www.science.org/doi/10.1126/...
Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!
Linking below previous thread on our findings
STAND UP FOR SCIENCE ANNOUNCES DR. GARY RUVKUN - PROFESSOR OF GENETICS, HARVARD MEDICAL SCHOOL, NOBEL LAUREATE, AS A SPEAKER AT THE BOSTON, MA, NATIONAL DAY OF ACTION RALLY ON MARCH 7TH!
Stand Up For Science announces Dr. Gary Ruvkun, Professor of Genetics at Harvard Medical School, Nobel Laureate as a speaker at the Boston, MA National Day of Action rally on Saturday, March 7th!
Visit zurl.co/Sgt6r to find a rally near you!
#standupforscience
#March7Boston
Nice specialized model with some promise academic.oup.com/nar/article/...
But haven't seen much use of the ~foundation models~ , could be missing something though
Oh the best part of Evo by far is that it is a microbial model 😎
I think DNA language models are really nifty, but so far IME nobody has shown any use case in which are more useful than protein LMs. These must exist- use cases with noncoding promoters, oriVs- but I just haven't seen it yet!
Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social
www.nature.com/articles/s41...
this was also true for me the other day but seems to be fixed now
Blame all bugs on claude @arambaut.bsky.social 😇
➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔
🧵👇
