Krishna Shrinivas

This is now published in PNAS! And double-treat, we also made the cover :) www.pnas.org/doi/10.1073/...

Excited to share the first pre-print from our lab!! Check it out here! www.biorxiv.org/content/10.6... We found that many RNA-binding proteins canonically understood to regulate RNA processing can also function like transcription factors and cofactors to directly regulate transcription.

See our handy graphical abstract and article for free here: bit.ly/4vsl845

Our work made the cover! (and my very first one!) Congrats to co-authors as well as Ramanna Shrinivas for cover art and @natcomputsci.nature.com for editing/cover design.

Hey, I wrote a thing about AI in astrophysics ergosphere.blog/posts/the-ma...

Do different regions in the cell nucleus find each other by random motion or is there a directed component? In short: likely both. Below, I summarize a few predictions from a recently updated preprint from last June: doi.org/10.48550/arX.... (1/9) #biophysics #theory #active #chromatin #condensates

On this 1st April I'm happy to release a technical report from our startup MirageBio, describing a new protein structure model with state-of-the-art performance. jgreener64.github.io/posts/techni...

Papers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.

To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...

1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...

In collaboration with Hue Sun Chan and @jonaswessen.bsky.social, we present a polymer theory for sequence-based prediction of selective partitioning of charged IDRs. This method correctly predicted the partitioning of IDRs for which we had no experimental data. www.nature.com/articles/s42...

Happy to share our latest in @natcomputsci.nature.com led by (amazing) Ryan Krueger + colab w M. Brenner! We introduce a framework to directly design intrinsically disordered proteins (IDPs) from physics-based simulations. 🧬 doi.org/10.1038/s435... 📰 www.mccormick.northwestern.edu/news/article...

Our review on cell cycle – cell fate (de)coupling is out! doi.org/10.1242/dev.... Was a lot of fun writing this with Allon Klein, reading old papers(earliest from 1902), and speculating on why cell cycle progression is not necessary for differentiation across many many tissues and species. (1/3)

📢 @shrinivaslab.bsky.social and colleagues introduce a method for designing unstructured proteins with tunable properties. www.nature.com/articles/s43... 🖥️ 🧬 🔓 rdcu.be/eJSuV

A good day to remember John Gurdon’s school report from his biology master at Eton

Preprint! Inspired by condensates that form on specific DNA, we ask: can we design multicomponent fluids to form distinct condensates on diff. surfaces? i.e. perform classification by condensation ⚛️ 💻 exploiting phase transitions beyond compartmentalization! arxiv.org/abs/2509.08100 (1/2)

A tremendous honor! Thrilled & humbled to receive 2025 Keio Medical Science Prize for launching LLPS #phaseseparation field (= #softmatter + #cellbio) w collaborators esp @HymanLab. & Congrats to Akiko Iwasaki @virusesimmunity.bsky.social. www.princeton.edu/news/2025/09... #KeioMedicalSciencePrize

Our work highlighted in @science.org by L. Bryan Ray! www.science.org/doi/10.1126/...

Our paper on the spatial organization of nuclear paraspeckles is out in #PNAS! Excited to see what comes next from the teams of @shrinivaslab.bsky.social and @sneadlab.bsky.social at Northwestern! pnas.org/doi/10.1073/pnas.2504778122

The Baker lab @uwproteindesign.bsky.social apparently had a lot of fun 😂 some examples of sequences used in the paper www.science.org/doi/10.1126/... DAVIDLIKESPEPTIDE DAVIDITISTIME DANIELSILVA HIALIENFRIEND

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit! tinyurl.com/ydn6e3ac

Our paper on single-cell learning is now published in @currentbiology.bsky.social! @wallaceucsf.bsky.social sciencedirect.com/science/arti...

In the nucleus, many intrinsically disordered proteins (IDPs) form condensates. What IDP sequence features drive this behavior? We developed CondenSeq, a high-throughput approach to measure nuclear condensate formation, and applied it to ~14,000 IDPs to find out! rdcu.be/eq975

Start of 2025 @mblscience.bsky.social Physiology course! This is the second year of Amy @gladfelterlab.bsky.social and I co-Directing this absolutely amazing and life-changing course: www.mbl.edu/education/ad...

Join us for this week’s entry in the NITMB Seminar Series! Featuring Krishna Shrinivas (@shrinivaslab.bsky.social), Assistant Professor of Chemical and Biological Engineering at Northwestern University Learn more at www.nitmb.org/nitmb-semina...

I am excited to share the latest paper from my lab where we leverage the selection bias of condensate-promoting oncofusions to uncover molecular rules governing condensate specificity and function. www.cell.com/cell/fulltex....

AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...

Excited to share our first story on nuclear paraspeckles! Led by @sneadlab.bsky.social, this is the culmination of a ~4 year effort in collab. with @shrinivaslab.bsky.social. Can’t wait to see more paraspeckle stories from the future Snead Lab at Northwestern 🫧 www.biorxiv.org/content/10.1...

To all people who value science as a source of truth, cures for diseases, and hope for our climate and future, here are 2 hard truths: 1) our current research ecosystem is already strained and very fragile; 2) If it gets broken it will take a generation or longer to repair. Here’s why: 1/n

The answer is yes! Come hear about STARLING this afternoon at the Biophysical Society IDP subgroup symposium! Thread to follow later today... www.biorxiv.org/content/10.1...

Super excited to finally share PANCS-Binders: our group's decade-long quest to accelerate protein binder discovery. TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput. 1/n

My first post on bluesky!! Excited to see my PhD work featured on the cover of NCB @naturecellbiology.bsky.social December issue! This image shows a gorgeous #zebrafish embryo undergoing cell division (the green cells with condensed chromatin)—a fundamental process we study in development. 🧵1/2