iiinova — where your digital self keeps evolving

Krishna Shrinivas @shrinivaslab.bsky.social · 07/07/2026

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

Reposted by Krishna Shrinivas

Jon Henninger @jhenninger.bsky.social · 08/06/2026

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.

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Krishna Shrinivas @shrinivaslab.bsky.social · 08/06/2026

Intrinsically disordered proteins (IDPs) flit between diverse shapes and interact in fuzzy ensembles whose collective properties shape function. Q: Can we rationally design emergent properties of IDPs? Our newest preprint takes a stab at this 🧵 biorxiv.org/content/10.6...

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Jon Henninger @jhenninger.bsky.social · 03/06/2026

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

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Krishna Shrinivas @shrinivaslab.bsky.social · 28/05/2026

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.

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Joe Greener @jgreener64.bsky.social · 01/04/2026

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...

jgreener64.github.io

MirageBio technical report

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Alex Holehouse @alexholehouse.bsky.social · 19/02/2026

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...

nature.com

Accurate predictions of disordered protein ensembles with STARLING - Nature

The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.

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Alex Holehouse @alexholehouse.bsky.social · 12/02/2026

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.

nature.com

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology

Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...

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Kyogo Kawaguchi @kyogok.bsky.social · 20/11/2025

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/...

science.org

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.

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Bruno Di Stefano @distefanolab.bsky.social · 28/10/2025

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...

nature.com

Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology

Stem cell differentiation is controlled by manipulating RNA condensates.

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Krishna Shrinivas @shrinivaslab.bsky.social · 10/10/2025

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...

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Krishna Shrinivas @shrinivaslab.bsky.social · 10/10/2025

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Kalki Kukreja @kkukreja.bsky.social · 09/10/2025

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)

doi.org

Coupling and decoupling of the cell cycle from cell differentiation in development

Summary: This Spotlight surveys investigations of the dependence of cellular differentiation on the cell cycle in animals. Strict dependence is uncommon. The decoupling of the cell cycle and different...

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 07/10/2025

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

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Krishna Shrinivas @shrinivaslab.bsky.social · 22/09/2025

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)

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Krishna Shrinivas @shrinivaslab.bsky.social · 22/09/2025

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Krishna Shrinivas @shrinivaslab.bsky.social · 12/09/2025

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

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Krishna Shrinivas @shrinivaslab.bsky.social · 04/09/2025

New in @pnas.org with @gladfelterlab.bsky.social @sneadlab.bsky.social ! 📢 Cells use condensates (dynamic compartments without membranes) to organize key reactions. Some condensates have core & shell layers… but how do such layers form? 🤔 👉 pnas.org/doi/10.1073/pnas.2504778122 (1/6)

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Dave Shechner @shechnerlab.bsky.social · 30/06/2025

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

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Kalli Kappel @kallikappel.bsky.social · 17/06/2025

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

rdcu.be

Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq

Nature Methods - CondenSeq is an imaging-based, high-throughput platform for characterizing condensate formation within the nuclear environment, uncovering the protein sequence features that...

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brangwynnelab.bsky.social @brangwynnelab.bsky.social · 09/06/2025

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...

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NSF-Simons NITMB @nitmb.bsky.social · 28/04/2025

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...

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Ben Sabari @bsabari.bsky.social · 25/04/2025

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....

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025

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...

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Gladfelter Lab @gladfelterlab.bsky.social · 19/03/2025

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...

biorxiv.org

Immiscible proteins compete for RNA binding to order condensate layers

Biomolecular condensates mediate diverse and essential cellular functions by compartmentalizing biochemical pathways. Many condensates have internal subdomains with distinct compositional identities. ...

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Abby Dernburg @adernburg.bsky.social · 20/02/2025

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

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Bryan Dickinson @chembiobryan.bsky.social · 07/01/2025

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

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Kalki Kukreja @kkukreja.bsky.social · 12/12/2024

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

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Frank Noe @franknoe.bsky.social · 06/12/2024

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

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Michaela Müller-McNicoll @mixmue.bsky.social · 30/11/2024

#Paraspeckles look surprisingly different when you look at them in 3D and using multiple probes. We would be interested to her your ideas on potential functional implications.

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Dave Shechner @shechnerlab.bsky.social · 21/11/2024

It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture. If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)

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Wallace Marshall @wallaceucsf.bsky.social · 21/11/2024

Single cells can learn without a brain, but how? Our new preprint from @deeparajan.bsky.social describes a model for habituation in Stentor coeruleus, based on receptor internalization and recycling, along with new experiments inspired by the model. 1/n www.biorxiv.org/content/10.1...

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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024

Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)

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Mark Peifer (He, him) @peiferlabunc.bsky.social · 16/11/2024

In September the world lost one of the great biologists of our time: Joe Gall. He bridged the transition from the histology era of cell biology to our molecular present, contributing a remarkable set of insights in his 9 decades 1/n 🧪 rupress.org/jcb/article-...

Title and abstract of the memoriam in the Journal of Cell Biology in the link

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 15/11/2024

go.bsky.app/FdHEYR3

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Krishna Shrinivas @shrinivaslab.bsky.social · 15/11/2024

A new starter pack for condensates :) i am obviously missing many, pls ping and I'll add go.bsky.app/FdHEYR3

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Krishna Shrinivas @shrinivaslab.bsky.social · 15/11/2024

Just started this, would love to add more people i missed go.bsky.app/FdHEYR3

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Jon Henninger @jhenninger.bsky.social · 11/11/2024

First post! I am a new Assistant Professor at Carnegie Mellon University exploring how RNA molecules regulate transcription and cell fate. Check out our recent review in this space! www.cell.com/molecular-ce...

cell.com

An RNA-centric view of transcription and genome organization

RNA molecules are involved in diverse regulatory mechanisms that contribute to gene activation, gene repression, and genome structure. Henninger and Young discuss how the more traditional DNA-protein-...

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