Very sad to hear about the passing of Peer Bork, one of true giants of computational biology www.embl.org/news/embl-an...

Video introduction to our new “Conformational Biasing” method for computational design of mutations that bias proteins towards desired conformational states CB part starts at 14:55 Thanks to Peter Cavanagh and Andrew Xue – amazing graduate students who co-led this work

Link to paper: www.science.org/doi/10.1126/...

This appeared today: www.asbmb.org/asbmb-today/...

Modern biology research is biased towards investigating genes that are widely conserved and present in humans. What about genes that ARE widely conserved but NOT present in humans? Can genes missing from humans tell us something about what makes our biology different from that of other animals? 1/8

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...

RFpeptides made it to the cover of Nature Chemical Biology December issue! Credit to Stephen Rettie for leading the work and making this very cool graphic!

Very happy to share our latest led by the relentless @shawnfayer.bsky.social! We developed multiplexed assays to measure variant effects across diverse genetic and cell contexts in stem cell and differentiated cells. 🧵 👇

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Congratulations to the newly minted Dr. Brittney Voigt! After defending a fantastic thesis spanning work in my lab and the @edwardmarcotte.bsky.social lab.

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

Last week, the research of Rui Gao and lab was published by @Science.org and featured on the issue's cover! Dr. Rui Gao is an Assistant Professor in Biological Sciences and Chemistry. science.org/doi/10.1126/...

The Gao lab at #UIC reports a breakthrough in volumetric fluorescence imaging, featured on the cover of Science Magazine! Their new technique, VIPS (Volumetric Imaging via Photochemical Sectioning), enables reconstruction of 3D images of whole tissues with unprecedented detail.

#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years. www.cell.com/cell-reports...

Congrats Qian www.science.org/doi/full/10....

I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

Excited for you to join us!

🚨The Bits to Binders Competition has concluded!🧬 One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors Spoiler: They work!

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell. www.biorxiv.org/content/10.1...

‼️🚨Preprint alert! 🚨‼️ Excited to have some of my first works as a postdoc, and first corresponding author (!!), on biorxiv! This was a fun side quest of a project marrying a few things I deeply love, development, cilia, and hormones in the pituitary! Happy reading! www.biorxiv.org/content/10.1...

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬 www.science.org/doi/full/10....

BioEmu now published in @science.org !! What is BioEmu? Check out this video: youtu.be/LStKhWcL0VE?...

Cilia Alert! So excited to finally have this paper on the CPLANE complex out in @natcomms.nature.com! We show that RSG1 is a human ciliopathy protein and links CPLANE to the transition zone. 1/n www.nature.com/articles/s41...

Much appreciated support from biotech execs and investors 🙏 www.statnews.com/2025/06/27/b...

@bmoore-beth.bsky.social We are delighted to announce that Dr. Teresa O'Meara ‪was awarded the Henry Russel award at U-M. Our highest honor for an early-mid career faculty member for her outstanding research and teaching! @teresaomeara.bsky.social ‬ @umichmicroimmuno.bsky.social

New lab preprint - Delora Baptista tested AlphaFold 2 and 3 for the prediction of structures of host-pathogen interactions and then applied these to study convergence of binding and molecular mimicry in host-pathogen vs. host-host interactions. www.biorxiv.org/content/10.1...

How do tiny worm embryos decide which cells become muscle, nerve, or gut - all without reading any new DNA? 🤔 Our new Cell Reports paper explores this fascinating question using C. elegans embryos. cell.com/cell-reports/fulltext/S2211-1247(25)00549-2 🧵 Thread below 👇

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments #MolSystBiol #MassSpec www.embopress.org/doi/full/10....

Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights: www.nature.com/articles/s41...

Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes. www.embopress.org/doi/full/10....

BioRxiV is very slow, so this appeared in Authorea before www.authorea.com/users/436643...

Chicago #handsoff

@jbwallingford.bsky.social talks about the importance of science research. #standupforscience

We are doing this in Chicago!!! #syandupforscience

Stand up for Science Chicago! I’ll be there. Scientists, if not now, when???

Great piece about our upcoming rally in the Sun-Times by @neilsteinberg.bsky.social Meet the organizers behind Chicago's Stand Up for Science Rally #standupforscience #scienceforall @standupforscience.bsky.social chicago.suntimes.com/columnists/2...

Check out our web tool for searching for interactors of your favorite cell surface protein, developed by undergrad Pinyu Liao and postdoc postdoc Brendan Floyd @stanford-chemh.bsky.social cellsurfacemap.org

I'll post more about this later. But for a long time, we've observed odd behavior of AlphaFold's ipTM in the presence of disorder and accessory domains. Looking into the math points a way to solving the problem. There are other solutions besides ours. But I think understanding the math is key.

This will gut the #UniversityofTexas, the largest recipient of NIH funds in #Texas, along with every other US research university and biomedical institute "Indirect costs" aren't padding. They fund core infrastructure for biomed research, from shared staff to keeping lights on

The article on the 1st Int'l Society for Computational Biology LGBTQI+ Symposium is out. Many thanks to @gonzaparra.bsky.social for organizing & putting the article together & to @iscb.bsky.social for sponsoring & hosting the online symposium. We won't give in to the hate. tinyurl.com/2v7mn6j5

Fox Chase Cancer Center’s Roland Dunbrack Appointed Co-Leader of the Cancer Signaling and Microenvironment Program @rolanddunbrack.bsky.social #oncology www.onclive.com/view/fox-cha...

This was lots of fun to work on! Beyond what we learned, I think this set of stabilizing indels is a great challenge set for methods that predict stability. Our first paper from a (former) undergrad researcher! @yuliagutierrez.bsky.social is going places!! 🚀💫

We had shown that network propagation of trait associated genes can identify related traits based on GWAS data. With the Bachmann-Gagescu lab we (Ellen Aarts) tested the same concept on a family of rare disorders (ciliopathies) and their related mouse phenotypes www.biorxiv.org/content/10.1...

Structural and energetic analysis of stabilizing indel mutations https://www.biorxiv.org/content/10.1101/2024.12.18.629072v1

I am excited to share some of my PhD work on the motile cilia interactome revealed by XL/MS with @jbwallingford.bsky.social @edwardmarcotte.bsky.social Ophelia Papoulas, Chanjae Lee, David Taylor, and @builab.bsky.social www.cell.com/developmenta...

Complex Portal release 249 is out! 4,940 manually curated biological complexes. www.ebi.ac.uk/complexporta... (in sync with UniProt release 2024_05)

We have two exciting job openings! 1. Open Rank Teaching Faculty (Genetics), Non-Tenure Track: go.uic.edu/TeachingFacu... 2. Tenure Track Asst Professor in #Genetics and/or #Epigenetics : go.uic.edu/AsstProfGene... Both postings will close 12/16 @ 5pm 📣Spread the word!📣