Yuya Karita
@yuyakarita.bsky.social
Studying microbial populations in spatial structures. UTokyo, Japan.
Reposted by Yuya Karita
Allele-frequency time series as a window into gene flow and transmission in COVID / influenza is now out in PNAS
www.pnas.org/doi/10.1073/...
Huge thanks to three reviewers altruistically improving our paper!
Below is the thread from the preprint.
www.pnas.org/doi/10.1073/...
Huge thanks to three reviewers altruistically improving our paper!
Below is the thread from the preprint.
November 26, 2025 at 7:18 PM
Allele-frequency time series as a window into gene flow and transmission in COVID / influenza is now out in PNAS
www.pnas.org/doi/10.1073/...
Huge thanks to three reviewers altruistically improving our paper!
Below is the thread from the preprint.
www.pnas.org/doi/10.1073/...
Huge thanks to three reviewers altruistically improving our paper!
Below is the thread from the preprint.
Reposted by Yuya Karita
New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well
New online! Experimental evolution in an era of molecular manipulation
Experimental evolution in an era of molecular manipulation
Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00867-6In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the underlying genetics and forces that shape phenotypic evolution.
www.nature.com
July 21, 2025 at 5:30 PM
New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well
Reposted by Yuya Karita
📣Book alert📣
Finally out with Cambridge University Press: the book by Udo Seifert on "Stochastic thermodynamics". It comprehensively covers many topics, from an introduction to statistical physics to many special subjects such as reaction networks and active particles. Highly recommended 👍👍👍
Finally out with Cambridge University Press: the book by Udo Seifert on "Stochastic thermodynamics". It comprehensively covers many topics, from an introduction to statistical physics to many special subjects such as reaction networks and active particles. Highly recommended 👍👍👍
July 17, 2025 at 3:12 PM
📣Book alert📣
Finally out with Cambridge University Press: the book by Udo Seifert on "Stochastic thermodynamics". It comprehensively covers many topics, from an introduction to statistical physics to many special subjects such as reaction networks and active particles. Highly recommended 👍👍👍
Finally out with Cambridge University Press: the book by Udo Seifert on "Stochastic thermodynamics". It comprehensively covers many topics, from an introduction to statistical physics to many special subjects such as reaction networks and active particles. Highly recommended 👍👍👍
Reposted by Yuya Karita
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
July 17, 2025 at 6:36 AM
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
Reposted by Yuya Karita
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬
www.science.org/doi/full/10....
www.science.org/doi/full/10....
June 24, 2025 at 4:52 PM
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬
www.science.org/doi/full/10....
www.science.org/doi/full/10....
Reposted by Yuya Karita
This is a bizarre discovery by Kyosuke. He introduces an active binary mixture model and finds bubbles, typically found in very large MIPS simulations, appearing in smaller setups. Then observes that even the mean-field deterministic ver. of the model also produces bubbles.
arxiv.org/abs/2505.08637
arxiv.org/abs/2505.08637
Bubble formation in active binary mixture model
Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of self-propelled elements, active phase se...
arxiv.org
May 15, 2025 at 12:32 AM
This is a bizarre discovery by Kyosuke. He introduces an active binary mixture model and finds bubbles, typically found in very large MIPS simulations, appearing in smaller setups. Then observes that even the mean-field deterministic ver. of the model also produces bubbles.
arxiv.org/abs/2505.08637
arxiv.org/abs/2505.08637
Excited to share my postdoc work with @paulbrainey.bsky.social !
Common adaptive types in air-liquid-interface colonization turn out to grow slowly and colonize the niche inefficiently. They even fail when monocultured from low inocula. How can they reliably succeed in laboratory evolution? [1/5]
Common adaptive types in air-liquid-interface colonization turn out to grow slowly and colonize the niche inefficiently. They even fail when monocultured from low inocula. How can they reliably succeed in laboratory evolution? [1/5]
May 6, 2025 at 5:51 AM
Excited to share my postdoc work with @paulbrainey.bsky.social !
Common adaptive types in air-liquid-interface colonization turn out to grow slowly and colonize the niche inefficiently. They even fail when monocultured from low inocula. How can they reliably succeed in laboratory evolution? [1/5]
Common adaptive types in air-liquid-interface colonization turn out to grow slowly and colonize the niche inefficiently. They even fail when monocultured from low inocula. How can they reliably succeed in laboratory evolution? [1/5]
Reposted by Yuya Karita
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
May 1, 2025 at 6:41 PM
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
Reposted by Yuya Karita
A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!
April 22, 2025 at 4:36 PM
A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!
Reposted by Yuya Karita
It’s increasingly clear that the language of microbial communities is one of resources. Conserved metabolism leads to regular, reliable resource flows across ecosystems—from the gut to wastewater. In complex communities, one serious challenge is: who is eating what?
March 24, 2025 at 8:27 PM
It’s increasingly clear that the language of microbial communities is one of resources. Conserved metabolism leads to regular, reliable resource flows across ecosystems—from the gut to wastewater. In complex communities, one serious challenge is: who is eating what?
Reposted by Yuya Karita
Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n
Homepage - openRxiv
openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
openrxiv.org
March 11, 2025 at 1:20 PM
Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n
Reposted by Yuya Karita
+Our paper now out in @nature.com. We designed and built at AMOLF a robot that maps & tracks fungal networks as they trade nutrients with plants. We discovered how fungi build and operate hyper-efficient 'supply chains' for underground ecosystems.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
March 1, 2025 at 10:37 PM
+Our paper now out in @nature.com. We designed and built at AMOLF a robot that maps & tracks fungal networks as they trade nutrients with plants. We discovered how fungi build and operate hyper-efficient 'supply chains' for underground ecosystems.
www.nature.com/articles/s41...
www.nature.com/articles/s41...