Krishna Shrinivas
@shrinivaslab.bsky.social
Asst. prof at Northwestern ChBE Interested in how molecules and processes are organized and regulated in living cells | physics, math, engineering, and computation (mostly) for biology shrinivaslab.com
This is now published in PNAS! And double-treat, we also made the cover :) www.pnas.org/doi/10.1073/...
Krishna Shrinivas@shrinivaslab.bsky.social · 11mo agoPreprint! 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)
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.
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...
See our handy graphical abstract and article for free here: bit.ly/4vsl845
Jon Henninger@jhenninger.bsky.social · 2mo agoCheck out our new work in Cell Systems @cp-cellsystems.bsky.social! Much of the biochemistry in the cell is organized by biomolecular condensates, but what mechanisms control the distribution of a given condensate throughout the cell? And is this mesoscale organization important for function?
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.
Nature Computational Science@natcomputsci.nature.com · 2mo ago🚨Our May issue is now live, including a method to design dynamic unstructured proteins, a benchmark to evaluate spatial alignment methods for spatial transcriptomics, and much more! www.nature.com/natcomputsci... 📰Cover: www.nature.com/articles/s43...
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
Externally driven condensates show translation-induced polarization, directed coalescence, and anomalous diffusion in viscoelastic media
Phase separation into compositionally and physically distinct domains is ubiquitous in (non)living matter ranging from alloys and emulsions to biomolecular condensates in cells. The organization of th...
doi.org
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...
MirageBio technical report
jgreener64.github.io
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...
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.
nature.com
Borna Novak@bornanovak.bsky.social · last yr.Excited to announce the newest member of the flock - STARLING (conSTruction of intrinsicAlly disoRdered proteins ensembles efficientLy vIa multi-dimeNsional Generative models). www.biorxiv.org/content/10.1...
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.
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...
nature.com
Alex Holehouse@alexholehouse.bsky.social · 2y agoWe’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
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/...
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.
science.org
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...
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
nature.com
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...
Sequence-based prediction of condensate composition reveals that specificity can emerge from multivalent interactions among disordered regions - Communications Chemistry
Condensates composed of the disordered region of the mediator of RNA polymerase II transcription subunit 1 (MED1) are known to partition specific proteins, but whether this specificity arises from ord...
nature.com
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...
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)
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...
doi.org
📢 @shrinivaslab.bsky.social and colleagues introduce a method for designing unstructured proteins with tunable properties. www.nature.com/articles/s43... 🖥️ 🧬 🔓 rdcu.be/eJSuV
Generalized design of sequence–ensemble–function relationships for intrinsically disordered proteins - Nature Computational Science
The authors introduce a method that combines physics and machine learning to design dynamic unstructured proteins with tunable ensemble properties like size, shape, sensing and binding.
nature.com
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)
arXiv physics.bio-ph Biological Physics@physicsbioph-bot.bsky.social · 11mo agoAidan Zentner, Ethan V. Halingstad, Cameron Chalk, Michael P. Brenner, Arvind Murugan, Erik Winfree, Krishna Shrinivas: Information processing driven by multicomponent surface condensates https://arxiv.org/abs/2509.08100 https://arxiv.org/pdf/2509.08100 https://arxiv.org/html/2509.08100
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)
arXiv physics.bio-ph Biological Physics@physicsbioph-bot.bsky.social · 11mo agoAidan Zentner, Ethan V. Halingstad, Cameron Chalk, Michael P. Brenner, Arvind Murugan, Erik Winfree, Krishna Shrinivas: Information processing driven by multicomponent surface condensates https://arxiv.org/abs/2509.08100 https://arxiv.org/pdf/2509.08100 https://arxiv.org/html/2509.08100
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
Bioengineer Clifford Brangwynne wins Keio Medical Science Prize
Japan’s Keio University awards the prize annually to honor contributions in medicine and life sciences. Brangwynne is being recognized for groundbreaking work that has opened up a new field of cell bi...
princeton.edu
Our work highlighted in @science.org by L. Bryan Ray! www.science.org/doi/10.1126/...
Krishna Shrinivas@shrinivaslab.bsky.social · 11mo agoNew 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)
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
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...
pnas.org
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
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...
pnas.org
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
Design of intrinsically disordered region binding proteins
Intrinsically disordered proteins and peptides play key roles in biology, but a lack of defined structures and high variability in sequence and conformational preferences have made targeting such syst...
science.org
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...
A receptor-inactivation model for single-celled habituation in Stentor coeruleus
The single-celled ciliate Stentor coeruleus demonstrates habituation to mechanical stimuli, but the mechanism of learning in this single cell, which l…
sciencedirect.com
Deepa Rajan, PhD@deeparajan.bsky.social · 2y agoHow can a single cell learn without a brain or nervous system? We explore this in our new preprint with @wallaceucsf.bsky.social! We discovered that central features of learning in single cells can be accounted for by a model based on receptor inactivation bit.ly/3CDukfS 🧵 1/n
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
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...
rdcu.be
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...
