Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

Preprint - Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo. www.biorxiv.org/content/10.1...

After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE). 📄 www.medrxiv.org/content/10.1...

🔔Paper alert! Extremely excited to share a preprint from our lab! Spearheaded by @axel-schmidt.bsky.social, a super talented medical & computational geneticist, we studied latent Epstein-Barr virus (EBV) infection at population-scale. Interested in how this works & what we found? Read along! 👇

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1... Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

If you like transposons... If you you love genome editing... Or if you just like random bird animations, we have the paper for you! We (@kedmonds.bsky.social et al) are happy to share our work turning a songbird retrotransposon into a genome editing tool. 🐣 (1/n)

We have a 3-year funded postdoc position to work on structures of #amyloid filaments. If you are an expert in protein biochemistry, structural biology or #cryoEM / #cryoET, this could be for you! Feel free to email me with any questions. Come join us! 🤩 www.nature.com/naturecareer...

1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs. Full story here: www.biorxiv.org/content/10.1...

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

Thrilled to announce that I am joining DTU in Copenhagen in the fall, as an assistant professor of chemistry. My research group will focus on fundamental methodology in machine learning for molecules.

The amazing Sofia Lövestam initiated the below project, when she became interested in the vault particles that we sometimes observe in #cryoEM images of brain-derived #amyloid filaments. www.biorxiv.org/content/10.1...

We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social! www.biorxiv.org/content/10.1... #Chromatin #Asgard #Archaea #cryoEM

We were just notified that our contract to UCSD and Scripps Research to support wastewater surveillance in San Diego (searchcovid.info) was terminated immediately for the same reasons 👇. That means no more genomic wastewater surveillance, and our proposed extensions to measles, Hep A, others, gone.

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

Check out this amazing work by the superstar team of @guilhemfaure.bsky.social, Makoto Saito, and @maxewilkinson.bsky.social !!! Very curious what the natural function of TIGR-Tas is

we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓) We decided to call them TIGR-Tas systems 🐯

Attempting to read the language of B cell and T cell receptor sequences to diagnose immunological diseases: Our new paper, led by the outstanding Maxim Zaslavsky @maximzaslavsky.bsky.social sky.bsky.social with help from me and Anshul Kundaje @anshulkundaje.bsky.social. Link: buff.ly/3QvxSVf

BIG news: Jason Chin is leaving the Division of Protein & Nucleic Acid Chemistry of @mrclmb.bsky.social to spend yet another billionaire's ££ in Oxford. This will create a gap that will need filling! So, if you're thinking of making a move, now is the time to reach out! www.eit.org/news/profess...

One of the coolest and most novel findings I’ve seen in years. This is why I work in worms. To find things no one even really knew to look for. Like a conserved system that splices transposons out of mRNAs to prevent otherwise lethal insertions in essential genes! - www.biorxiv.org/content/10.1...

Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems Congrats Tana Wein! Thank you Kranzusch lab! www.nature.com/articles/s41...

After many years at @mrclmb.bsky.social, I've moved back home to start my own lab at @princetonmolbio.bsky.social. I'm so thankful to my mentors, especially Kelly Nguyen and Don Rio! We have some exciting results on LINE-1 in the works and are recruiting. Find out more: ghanim.lab.princeton.edu

Best way to start 2025! Thrilled to share our Nature paper about the structures of axonemal components from sperm flagella and from epithelial cilia of the oviduct and brain ventricles. Great collaboration with Tzviya Zeev-Ben-Mordehai and @alanbrownhms.bsky.social www.nature.com/articles/s41...

1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens TRACeR for MHC-I: go.nature.com/4gcLzn5 TRACeR for MHC-II: go.nature.com/4gj5OQk

www.biorxiv.org/content/10.1... Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.

We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered??? www.nature.com/articles/s41...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. 🌐 bfvd.foldseek.com 💾 bfvd.steineggerlab.workers.dev 📄 academic.oup.com/nar/advance-...

The preliminary sequence from the H5N1 human case in British Columbia has been posted and it is not good news. The virus potentially has a quasispecies at HA residue 226 (H3 numbering). This is bad news because we know that mutations at residue 226 can increase binding to human receptors. 1/