Jiayue Yang
@stjarnaa.bsky.social
Grad student of Whitaker Lab at UIUC studying CRISPR ecology and evolution in archaea metapopulations ♨️
Reposted by Jiayue Yang
An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 21, 2025 at 4:20 PM
An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs
Reposted by Jiayue Yang
The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.
Dynamics of dN/dS within recombining bacterial populations
The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often decline...
www.biorxiv.org
November 16, 2025 at 3:26 PM
The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.
Reposted by Jiayue Yang
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Jiayue Yang
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 10:28 AM
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Reposted by Jiayue Yang
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
www.biorxiv.org
October 12, 2025 at 9:16 PM
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Reposted by Jiayue Yang
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
October 6, 2025 at 6:27 AM
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Reposted by Jiayue Yang
A new theme issue of #PhilTransB examines the evolutionary history of bacterial immune systems, their modes of action, and the patterns how different bacterial immune systems are distributed across different ecosystems. Read: buff.ly/Z4qdxY1
September 5, 2025 at 4:01 PM
A new theme issue of #PhilTransB examines the evolutionary history of bacterial immune systems, their modes of action, and the patterns how different bacterial immune systems are distributed across different ecosystems. Read: buff.ly/Z4qdxY1
Reposted by Jiayue Yang
Our EEB department at the University of Illinois at Urbana-Champaign is hiring an assistant professor in evo-devo. See go.illinois.edu/EEBAsstProf for details. Please share!
August 26, 2025 at 10:10 PM
Our EEB department at the University of Illinois at Urbana-Champaign is hiring an assistant professor in evo-devo. See go.illinois.edu/EEBAsstProf for details. Please share!
Reposted by Jiayue Yang
Have you ever wondered what increasing environmental stress will do to microbial communities?
In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts
Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...
www.biorxiv.org
August 25, 2025 at 2:33 PM
Have you ever wondered what increasing environmental stress will do to microbial communities?
In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
Reposted by Jiayue Yang
I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
1/n
1/n
August 21, 2025 at 4:57 PM
I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
1/n
1/n
Reposted by Jiayue Yang
Special issue in @science.org on #EvolvingImmunity (great illustrations!), with themes addressed by the ERC #IDEM @philinbiomed.bsky.social 10+ years ago: the need to rethink the function of immunity in the context of its physiological roles & co-evo with microbes
www.science.org/toc/science/...
www.science.org/toc/science/...
Contents | Science 389, 6760
www.science.org
August 13, 2025 at 7:50 PM
Special issue in @science.org on #EvolvingImmunity (great illustrations!), with themes addressed by the ERC #IDEM @philinbiomed.bsky.social 10+ years ago: the need to rethink the function of immunity in the context of its physiological roles & co-evo with microbes
www.science.org/toc/science/...
www.science.org/toc/science/...
Reposted by Jiayue Yang
I am happy to announce that the Midwest Mathematical Biology Seminar will be returning for the Fall 2025 semester. Our talks will be held on Tuesdays at 11am US/Canada Eastern time (10am Central time).
Please see the link below for more information.
sites.google.com/view/midwest...
Please see the link below for more information.
sites.google.com/view/midwest...
Midwest Mathematical Biology Seminar
The Midwest Mathematical Biology Seminar will be a series of virtual talks on mathematical biology featuring speakers from the Midwest region and beyond. All areas of mathematical biology will be repr...
sites.google.com
August 6, 2025 at 11:42 PM
I am happy to announce that the Midwest Mathematical Biology Seminar will be returning for the Fall 2025 semester. Our talks will be held on Tuesdays at 11am US/Canada Eastern time (10am Central time).
Please see the link below for more information.
sites.google.com/view/midwest...
Please see the link below for more information.
sites.google.com/view/midwest...
Reposted by Jiayue Yang
Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...
www.jobbnorge.no/en/available...
Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway
Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025
www.jobbnorge.no
August 8, 2025 at 7:52 AM
Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...
www.jobbnorge.no/en/available...
Reposted by Jiayue Yang
Hello new phage phollowers!
I am shamelessly self-promoting mine and Angus Buckling's relatively new review "Critically evaluating the relative importance of phage in shaping microbial community composition"
www.cell.com/trends/micro...
I am shamelessly self-promoting mine and Angus Buckling's relatively new review "Critically evaluating the relative importance of phage in shaping microbial community composition"
www.cell.com/trends/micro...
Critically evaluating the relative importance of phage in shaping microbial community composition
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological
impacts they can have on their microbial hosts has resulted in phages often cited
as key drivers shaping microbial com...
www.cell.com
November 15, 2024 at 3:52 PM
Hello new phage phollowers!
I am shamelessly self-promoting mine and Angus Buckling's relatively new review "Critically evaluating the relative importance of phage in shaping microbial community composition"
www.cell.com/trends/micro...
I am shamelessly self-promoting mine and Angus Buckling's relatively new review "Critically evaluating the relative importance of phage in shaping microbial community composition"
www.cell.com/trends/micro...
Reposted by Jiayue Yang
Excited 🥳 to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓
July 28, 2025 at 8:41 AM
Excited 🥳 to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓
Reposted by Jiayue Yang
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
July 17, 2025 at 8:32 PM
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601