Kalki Kukreja
@kkukreja.bsky.social
Stem cell and devbio scientist
Reposted by Kalki Kukreja
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 Kalki Kukreja
Coupling and decoupling of the cell cycle from cell differentiation in development
In this Spotlight, @kkukreja.bsky.social & Allon Klein discuss the dependence of animal cell differentiation on cell cycle, and how their decoupling facilitates development
journals.biologists.com/dev/article-...
In this Spotlight, @kkukreja.bsky.social & Allon Klein discuss the dependence of animal cell differentiation on cell cycle, and how their decoupling facilitates development
journals.biologists.com/dev/article-...
October 10, 2025 at 4:00 PM
Coupling and decoupling of the cell cycle from cell differentiation in development
In this Spotlight, @kkukreja.bsky.social & Allon Klein discuss the dependence of animal cell differentiation on cell cycle, and how their decoupling facilitates development
journals.biologists.com/dev/article-...
In this Spotlight, @kkukreja.bsky.social & Allon Klein discuss the dependence of animal cell differentiation on cell cycle, and how their decoupling facilitates development
journals.biologists.com/dev/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)
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 Kalki Kukreja
📢 @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 Kalki Kukreja
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 Kalki Kukreja
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 Kalki Kukreja
Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw
shorturl.at/2LHbw
July 6, 2025 at 10:11 PM
Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw
shorturl.at/2LHbw
Reposted by Kalki Kukreja
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
www.cell.com/cell-systems...
July 7, 2025 at 5:27 PM
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
www.cell.com/cell-systems...
Loved this! Using devbio to engineer embryo models with notochord – neat and cool study. Lot of careful characterization of the embryo model.
Our latest: how to generate the notochord
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
Timely TGFβ signalling inhibition induces notochord - Nature
Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.
www.nature.com
December 19, 2024 at 7:19 PM
Loved this! Using devbio to engineer embryo models with notochord – neat and cool study. Lot of careful characterization of the embryo model.
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
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
December 12, 2024 at 4:22 PM
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
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
Really liked reading this interview with @karalmckinley.bsky.social , so frank and honest! My favorite part "I think it's easy to get caught up in saying what we think is ‘the right thing’ to succeed, so much so that we can lose sight of what we are truly passionate about".
Transitions in development– an interview with Kara McKinley
Here, @karalmckinley.bsky.social talks about her transition to becoming a PI, her insights on navigating the tenure-track market in biology and her dedication to promoting gender diversity within academia
https://doi.org/10.1242/dev.204456
Here, @karalmckinley.bsky.social talks about her transition to becoming a PI, her insights on navigating the tenure-track market in biology and her dedication to promoting gender diversity within academia
https://doi.org/10.1242/dev.204456
December 4, 2024 at 7:15 PM
Really liked reading this interview with @karalmckinley.bsky.social , so frank and honest! My favorite part "I think it's easy to get caught up in saying what we think is ‘the right thing’ to succeed, so much so that we can lose sight of what we are truly passionate about".
Reposted by Kalki Kukreja
🔊
We are recruiting PhD students and Postdocs!
We are seeking highly motivated, talented, and creative researchers, with strong background in cell and developmental biology, who are looking to spearhead original interdisciplinary investigations, addressing overlooked biology.
1/5
We are recruiting PhD students and Postdocs!
We are seeking highly motivated, talented, and creative researchers, with strong background in cell and developmental biology, who are looking to spearhead original interdisciplinary investigations, addressing overlooked biology.
1/5
November 30, 2024 at 5:55 PM
🔊
We are recruiting PhD students and Postdocs!
We are seeking highly motivated, talented, and creative researchers, with strong background in cell and developmental biology, who are looking to spearhead original interdisciplinary investigations, addressing overlooked biology.
1/5
We are recruiting PhD students and Postdocs!
We are seeking highly motivated, talented, and creative researchers, with strong background in cell and developmental biology, who are looking to spearhead original interdisciplinary investigations, addressing overlooked biology.
1/5
Reposted by Kalki Kukreja
New work from @kkukreja.bsky.social & Klein Lab
Cell division is NOT a must for differentiation during early zebrafish embryogenesis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cell state transitions are decoupled from cell division during early embryo development - Nature Cell Biology
Kukreja et al. show that blocking cell division in zebrafish does not affect differentiation of major cell types during gastrulation and segmentation, but it does decelerate differentiation of particu...
www.nature.com
November 23, 2024 at 8:34 AM
New work from @kkukreja.bsky.social & Klein Lab
Reposted by Kalki Kukreja
🥂Congratulations to Klein & co for their new study in our journal (@naturecellbiology.bsky.social) showing that blocking cell division does not affect major cell type differentiation during development, but it does decelerate differentiation of particular cell types.
rdcu.be/d0Ry3
rdcu.be/d0Ry3
Cell state transitions are decoupled from cell division during early embryo development
Nature Cell Biology - Kukreja et al. show that blocking cell division in zebrafish does not affect differentiation of major cell types during gastrulation and segmentation, but it does decelerate...
rdcu.be
November 21, 2024 at 1:35 PM
🥂Congratulations to Klein & co for their new study in our journal (@naturecellbiology.bsky.social) showing that blocking cell division does not affect major cell type differentiation during development, but it does decelerate differentiation of particular cell types.
rdcu.be/d0Ry3
rdcu.be/d0Ry3