Excited that the final version of our experimental assessment of AI protein interaction predictions is out: www.nature.com/articles/s41... Brief summary below:

Yours truly is a proper scientist now! TL;DR: we used AI to redesign parts of essential cell machinery with only 19 canonical amino acids instead of 20. Why? Great thread by @harriswang.bsky.social provides more context and details. Let me talk a bit about the AI design part of this. 1/

New work led by Hasan Cubuk: moving from interpreting variants individually to combining both alleles in recessive disease. DMS of >8000 ADSL variants → inferred enzyme activity → additive biallelic scores that track patient phenotypes. Great collab with the Kudla lab! www.cell.com/cell-systems...

Out Now! Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation #MicroSky

Very happy and proud that our paper “Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation” is out today in #NatureMicrobiology @natmicrobiol.nature.com Paper 👉 t1p.de/v42xb #microbiome #commensal #pathomechanism #T3SS #immune #health #IBD

delighted to share our review, out today in @cp-trendsgenetics.bsky.social! check it out if you're curious about how recent advances in technology & biology have contributed to our understanding of how alternative isoforms diversify the proteome.

I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel. We used ddPCA to map the genetic architecture of the entire human bZIP interaction network. www.biorxiv.org/content/10.1... Thanks to all our co-authors for the great collaboration!

Excited to share this collaborative review with @dsegre.bsky.social and @devmoy.bsky.social. We discuss common issues with context-specific genome-scale metabolic network models and provide recommendation for future model development.

Exited to share our recent work on viral cis-regulatory elements in collaboration with @tewhey.bsky.social! We identified >2000 CREs across the genomes of 27 human-infecting dsDNA viruses from the Herpesvirus, Adenovirus, Papillomavirus, and Polyomavirus families. www.biorxiv.org/content/10.1... 1/8

Variant characterization in the intrinsically disordered human proteome - here is how we did it using short linear motif prediction, AlphaFold, and experimentation. Check out our preprint: www.biorxiv.org/cgi/content/...

Congrats to Renata Goncalves who led a study in Gokhan Hotamisligil's lab that has just come out in Nature - ably assisted by Jillian Riveros! www.nature.com/articles/s41...

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Online Now: Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms Online now:

reposting the 🧵 from the other site that I wrote when the preprint came out: TFs, like most genes, are frequently expressed as a series of multiple distinct isoforms. these isoforms (by definition) differ in sequence -- often in annotated protein domain regions (e.g. DNA-binding & effector domains)

The published version of our transcription factor isoforms survey is online www.sciencedirect.com/science/arti... we cloned 100's of isoforms (that arise through alternative splicing etc.) testing them in high-throughput assays for DNA-binding, protein-binding, activation, and more.

our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell! key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity many are "negative regulators" & misexpressed in cancer www.sciencedirect.com/science/arti...

As the first measles death in the US since 2015--an unvaccinated child--is reported, let us read the thoughts of our new Secretary of Health and Human Services on this disease. www.reuters.com/world/us/fir... (Foreword to "The Measles Book", 2021)

On Wednesday 2/26, I’ll be in Boston to give a Harvard Science Book Talk. I’ll have a marvelous relic of aerobiological history to unveil. Details here: www.harvard.com/event/carl-z... 3/5

The STARLING has landed - excited to share new work from @bornanovak.bsky.social and @jefflotthammer.bsky.social in what is also Borna's first Bluesky post! If you're at BPS, I'll be speaking about this this afternoon in IDP SG, and Borna and Jeff both have posters (Sunday B112 and Wed B152).

Interested in learning about biases in protein-protein interface predictions with AlphaFold2? Check out our new review on this topic: authors.elsevier.com/a/1kbSa_,2Bd...

Btw, the abstract deadline has been extended to Jan 27!

🧪 If you are a network (or network-curious!) biologist, please consider attending the upcoming CSHL Network Biology Meeting. Details + abstract deadline below!

Can a single small molecule rescue the stability of nearly all mutations in a protein? Our new preprint by Taylor Mighell www.biorxiv.org/content/10.1... thread on the other place: x.com/taylor_mighe...