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
Interested in how molecules and processes are organized and regulated in living cells | physics, math, engineering, and computation (mostly) for biology
shrinivaslab.com
Pinned
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...
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...
Reposted by Krishna Shrinivas
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.
www.nature.com
October 28, 2025 at 4:02 PM
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...
Reposted by Krishna Shrinivas
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...
www.nature.com
October 22, 2025 at 6:30 PM
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...
Reposted by Krishna Shrinivas
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...
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...
October 10, 2025 at 6:16 PM
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...
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...
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...
October 10, 2025 at 6:16 PM
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...
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...
Reposted by Krishna Shrinivas
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)
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
October 9, 2025 at 2:08 PM
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)
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)
Reposted by Krishna Shrinivas
📢 @shrinivaslab.bsky.social and colleagues introduce a method for designing unstructured proteins with tunable properties. www.nature.com/articles/s43... 🖥️ 🧬
🔓 rdcu.be/eJSuV
🔓 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.
www.nature.com
October 7, 2025 at 3:03 PM
📢 @shrinivaslab.bsky.social and colleagues introduce a method for designing unstructured proteins with tunable properties. www.nature.com/articles/s43... 🖥️ 🧬
🔓 rdcu.be/eJSuV
🔓 rdcu.be/eJSuV
Reposted by Krishna Shrinivas
A good day to remember John Gurdon’s school report from his biology master at Eton
October 7, 2025 at 8:45 PM
A good day to remember John Gurdon’s school report from his biology master at Eton
Reposted by Krishna Shrinivas
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)
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)
September 22, 2025 at 9:38 PM
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)
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)
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)
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)
September 22, 2025 at 9:38 PM
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)
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)
Reposted by Krishna Shrinivas
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
#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...
www.princeton.edu
September 20, 2025 at 6:16 PM
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
#KeioMedicalSciencePrize
September 12, 2025 at 2:50 AM
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)
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
September 4, 2025 at 2:44 AM
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)
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)
Reposted by Krishna Shrinivas
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
August 7, 2025 at 4:10 PM
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
Reposted by Krishna Shrinivas
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
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...
www.science.org
July 18, 2025 at 7:55 AM
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
some examples of sequences used in the paper www.science.org/doi/10.1126/...
DAVIDLIKESPEPTIDE
DAVIDITISTIME
DANIELSILVA
HIALIENFRIEND
Reposted by Krishna Shrinivas
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
tinyurl.com/ydn6e3ac
June 30, 2025 at 9:15 PM
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
tinyurl.com/ydn6e3ac
Reposted by Krishna Shrinivas
Our paper on single-cell learning is now published in
@currentbiology.bsky.social!
@wallaceucsf.bsky.social
sciencedirect.com/science/arti...
@currentbiology.bsky.social!
@wallaceucsf.bsky.social
sciencedirect.com/science/arti...
June 24, 2025 at 5:13 PM
Our paper on single-cell learning is now published in
@currentbiology.bsky.social!
@wallaceucsf.bsky.social
sciencedirect.com/science/arti...
@currentbiology.bsky.social!
@wallaceucsf.bsky.social
sciencedirect.com/science/arti...
Reposted by Krishna Shrinivas
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/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
June 17, 2025 at 3:26 AM
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/eq975
Reposted by Krishna Shrinivas
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...
June 9, 2025 at 3:03 PM
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...
Reposted by Krishna Shrinivas
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...
Featuring Krishna Shrinivas (@shrinivaslab.bsky.social), Assistant Professor of Chemical and Biological Engineering at Northwestern University
Learn more at www.nitmb.org/nitmb-semina...
April 28, 2025 at 8:22 PM
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...
Featuring Krishna Shrinivas (@shrinivaslab.bsky.social), Assistant Professor of Chemical and Biological Engineering at Northwestern University
Learn more at www.nitmb.org/nitmb-semina...
Reposted by Krishna Shrinivas
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....
April 25, 2025 at 5:43 PM
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....
Reposted by Krishna Shrinivas
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...
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...
April 17, 2025 at 7:11 PM
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...
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...
Reposted by Krishna Shrinivas
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...
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. ...
www.biorxiv.org
March 19, 2025 at 7:09 PM
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...
Reposted by Krishna Shrinivas
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
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
February 20, 2025 at 7:04 PM
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
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
Reposted by Krishna Shrinivas
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...
Thread to follow later today...
www.biorxiv.org/content/10.1...
February 15, 2025 at 5:23 PM
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...
Thread to follow later today...
www.biorxiv.org/content/10.1...
Reposted by Krishna Shrinivas
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
TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.
1/n
While everyone esle has been concentrating on generative binder design, this group has demonstrated screening libraries in vivo! www.biorxiv.org/content/10.1...
#biosky
#biosky
High-throughput protein binder discovery by rapid in vivo selection
Proteins that selectively bind to a target of interest are foundational components of research pipelines, diagnostics, and therapeutics. Current immunization-based, display-based, and computational ap...
www.biorxiv.org
January 7, 2025 at 8:50 PM
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
TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.
1/n