Justin Fay
@justinfay.bsky.social
Evolutionary genetics, University of Rochester
URochester Biology has a tenure-track position open in evolutionary genetics/genomics, particularly those with mathematical, computational, and/or quantitative approaches.
Deadline: Nov 10
apply.interfolio.com/173431
Bio Dept retreat photo for attention
Deadline: Nov 10
apply.interfolio.com/173431
Bio Dept retreat photo for attention
October 29, 2025 at 8:24 PM
URochester Biology has a tenure-track position open in evolutionary genetics/genomics, particularly those with mathematical, computational, and/or quantitative approaches.
Deadline: Nov 10
apply.interfolio.com/173431
Bio Dept retreat photo for attention
Deadline: Nov 10
apply.interfolio.com/173431
Bio Dept retreat photo for attention
Work is sometimes fun, having fun requires some work. I've found a blend of sampling yeast and riding that is a euphoric mix, and makes me wonder why its taken so many years to find. Route is via the finger lakes national forest, 16 miles round trip, 1hr biking straight out, 5 hours sampling back.
October 12, 2025 at 1:25 AM
Work is sometimes fun, having fun requires some work. I've found a blend of sampling yeast and riding that is a euphoric mix, and makes me wonder why its taken so many years to find. Route is via the finger lakes national forest, 16 miles round trip, 1hr biking straight out, 5 hours sampling back.
Great to hear back in the day stories, chum with alumns and progeny research at Roc-Fest, a celebration of Orr, Werren, Eickbush, and Jaenike and their contributions to adaptation, speciation, and selfish genetic elements. sites.google.com/view/rocfest...
I contributed wine:
I contributed wine:
October 5, 2025 at 3:10 PM
Great to hear back in the day stories, chum with alumns and progeny research at Roc-Fest, a celebration of Orr, Werren, Eickbush, and Jaenike and their contributions to adaptation, speciation, and selfish genetic elements. sites.google.com/view/rocfest...
I contributed wine:
I contributed wine:
Reposted by Justin Fay
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine.
1) Fundamental researc...
www.linkedin.com
September 23, 2025 at 10:31 PM
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Very pleased to share this long term (nearly 20 years) study of yeasts isolated from vineyards and forests, now up on biorxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 24, 2025 at 8:24 PM
Very pleased to share this long term (nearly 20 years) study of yeasts isolated from vineyards and forests, now up on biorxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Ella Al-Shamahi (muslim missionary turned evolutionary biologist, host of BBC human series) opinion piece on why follow the science fails.
www.washingtonpost.com/opinions/202...
www.washingtonpost.com/opinions/202...
September 23, 2025 at 10:44 AM
Ella Al-Shamahi (muslim missionary turned evolutionary biologist, host of BBC human series) opinion piece on why follow the science fails.
www.washingtonpost.com/opinions/202...
www.washingtonpost.com/opinions/202...
Reposted by Justin Fay
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Justin Fay
What killed the competitive renewal at NIH? drugmonkey.wordpress.com/2025/07/31/w...
What killed the competitive renewal at NIH?
Following up on yesterday’s whinesplaining about the relative difficulty of getting a NIH grant across pertinent career eras, I had some more thoughts on generational expectations and gasligh…
drugmonkey.wordpress.com
July 31, 2025 at 10:08 PM
What killed the competitive renewal at NIH? drugmonkey.wordpress.com/2025/07/31/w...
Reposted by Justin Fay
Walunjkar, @ghaemmaghamilab.bsky.social @justinfay.bsky.social et al. profiled the proteomes of two yeast species with differences in thermal tolerance, finding a proteome-wide shift in stability, driven by both sequence change and cellular context.
🔗 doi.org/10.1093/molbev/msaf137
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf137
#evobio #molbio
July 16, 2025 at 11:35 AM
Walunjkar, @ghaemmaghamilab.bsky.social @justinfay.bsky.social et al. profiled the proteomes of two yeast species with differences in thermal tolerance, finding a proteome-wide shift in stability, driven by both sequence change and cellular context.
🔗 doi.org/10.1093/molbev/msaf137
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf137
#evobio #molbio
Reposted by Justin Fay
New paper w/ @plos.org! @chaochihl.bsky.social identifies a unique mutational pattern among sodium azide-induced mutants. SNPs in 'CC' context and indels. Thanks to @justinfay.bsky.social @lilei0051.bsky.social @giuliafrascarelli.bsky.social @nanoporetech.com et al
journals.plos.org/plosgenetics...
journals.plos.org/plosgenetics...
Sodium azide mutagenesis induces a unique pattern of mutations
Author summary Sodium azide is frequently used as a mutagen for experimental studies in plants. It induces primarily C → T changes. We find that these most often occur when a cytosine (C) is followed ...
journals.plos.org
June 5, 2025 at 4:09 PM
New paper w/ @plos.org! @chaochihl.bsky.social identifies a unique mutational pattern among sodium azide-induced mutants. SNPs in 'CC' context and indels. Thanks to @justinfay.bsky.social @lilei0051.bsky.social @giuliafrascarelli.bsky.social @nanoporetech.com et al
journals.plos.org/plosgenetics...
journals.plos.org/plosgenetics...
Reposted by Justin Fay
"We believe that mapping the damage done and its human costs—and the pushback and resilience work already underway—is necessary groundwork for building and retaining political agency"
May 31, 2025 at 12:08 AM
"We believe that mapping the damage done and its human costs—and the pushback and resilience work already underway—is necessary groundwork for building and retaining political agency"
Abstract submission and early registration for Evolution and core processes of gene expression www.asbmb.org/meetings-eve...
June 26–29, 2025
June 26–29, 2025
Evolution and core processes in gene expression
June 26–29, 2025 | Kansas City, Mo.
www.asbmb.org
May 1, 2025 at 10:49 AM
Abstract submission and early registration for Evolution and core processes of gene expression www.asbmb.org/meetings-eve...
June 26–29, 2025
June 26–29, 2025
Hitchhiking in facultative sexuals e.g. baker's yeast: can reduce diversity across the genome and contribute to Lewontin’s paradox. Results relevant to anyone (e.g. me) who has looked but found few if any strong sweeps. www.biorxiv.org/content/10.1...
Beyond Recombination: Exploring the Impact of Meiotic Frequency on Genome-wide Genetic Diversity
An important aim of population genetics is to elucidate the processes affecting genetic diversity across regions of the genome and across species. Canonical population genetic models of sexually repro...
www.biorxiv.org
March 19, 2025 at 12:31 PM
Hitchhiking in facultative sexuals e.g. baker's yeast: can reduce diversity across the genome and contribute to Lewontin’s paradox. Results relevant to anyone (e.g. me) who has looked but found few if any strong sweeps. www.biorxiv.org/content/10.1...
Reposted by Justin Fay
A model for background selection in non-equilibrium populations https://www.biorxiv.org/content/10.1101/2025.02.19.639084v1
February 21, 2025 at 11:39 AM
A model for background selection in non-equilibrium populations https://www.biorxiv.org/content/10.1101/2025.02.19.639084v1
Reposted by Justin Fay
1of3 Our new preprint now online: www.biorxiv.org/content/10.1... Commercial #Saccharomyces cerevisiae baker's yeasts: strain redundancy, genome plasticity, and colonization of the sourdough environment and the human body
February 9, 2025 at 2:15 PM
1of3 Our new preprint now online: www.biorxiv.org/content/10.1... Commercial #Saccharomyces cerevisiae baker's yeasts: strain redundancy, genome plasticity, and colonization of the sourdough environment and the human body
Reposted by Justin Fay
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
January 22, 2025 at 8:46 PM
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
Reposted by Justin Fay
Our work, which shows statistical issues with the previous claim of a severe ancient bottleneck in the ancestry of African populations, has been selected as a Featured article in Genetics.
doi.org/10.1093/gene...
doi.org/10.1093/gene...
A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact
Hu et al. (Science, 2023) recently inferred a severe ancient bottleneck around 900 thousand years (kya) ago in African ancestry but found no similar eviden
doi.org
January 8, 2025 at 8:23 PM
Our work, which shows statistical issues with the previous claim of a severe ancient bottleneck in the ancestry of African populations, has been selected as a Featured article in Genetics.
doi.org/10.1093/gene...
doi.org/10.1093/gene...
Reposted by Justin Fay
And another MIRA from @gutengroup.mcb.arizona.edu ! Please send along successful grant proposals and job apps. Seeing these is enormously helpful to folks applying for grants or jobs the first time!
New! @jenncoughlan.bsky.social kindly shared their MIRA NIH award with our github repo. If you have a successful grant app you're willing to share, please contribute! github.com/RILAB/statem...
GitHub - RILAB/statements: Successful Job Applications and Grants
Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.
github.com
January 3, 2025 at 6:44 AM
And another MIRA from @gutengroup.mcb.arizona.edu ! Please send along successful grant proposals and job apps. Seeing these is enormously helpful to folks applying for grants or jobs the first time!
Reposted by Justin Fay
Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Diverse phage communities are maintained stably on a clonal bacterial host
Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...
www.science.org
December 16, 2024 at 11:38 AM
Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Very proud of Nilima Walunjkar’s preprint reporting her work on evolution of protein stability.
www.biorxiv.org/content/10.1...
This work was very fruitful collaboration with multiple members of the Fay lab, along with the Ghaemmaghami @ghaemmaghamilab.bsky.social and Phizicky labs at U. Rochester.
www.biorxiv.org/content/10.1...
This work was very fruitful collaboration with multiple members of the Fay lab, along with the Ghaemmaghami @ghaemmaghamilab.bsky.social and Phizicky labs at U. Rochester.
Pervasive divergence in protein thermostability is mediated by both structural changes and cellular environments
Temperature is a universal environmental constraint and organisms have evolved diverse mechanisms of thermotolerance. A central feature of thermophiles relative to mesophiles is a universal shift in p...
www.biorxiv.org
December 13, 2024 at 4:22 PM
Very proud of Nilima Walunjkar’s preprint reporting her work on evolution of protein stability.
www.biorxiv.org/content/10.1...
This work was very fruitful collaboration with multiple members of the Fay lab, along with the Ghaemmaghami @ghaemmaghamilab.bsky.social and Phizicky labs at U. Rochester.
www.biorxiv.org/content/10.1...
This work was very fruitful collaboration with multiple members of the Fay lab, along with the Ghaemmaghami @ghaemmaghamilab.bsky.social and Phizicky labs at U. Rochester.
Reposted by Justin Fay
Great! Loved the preprint 😀, look forward to the final version. 👏 @gsherloc.bsky.social @petrovadmitri.bsky.social
In a cool twist on their previous work, @grantkinsler.bsky.social Yuping Li @gsherloc.bsky.social & @petrovadmitri.bsky.social use yeast to reveal that #evolution involves a) early large-effect pleiotropic mutations, b) a shift towards more modular adaptation @plosbiology.bsky.social plos.io/4glXoXJ
December 6, 2024 at 4:37 PM
Great! Loved the preprint 😀, look forward to the final version. 👏 @gsherloc.bsky.social @petrovadmitri.bsky.social
Reposted by Justin Fay
How best to avoid the costs of bearing a #plasmid? Rosanna Wright @brockhurstlab.bsky.social @jpjhall.bsky.social &co find that #bacteria benefit from compensating plasmids by chromosomal (rather than plasmid-borne) mutations @plosbiology.bsky.social plos.io/3ODbXdN
A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation
Plasmids spread important traits in microbiomes but impose fitness costs on their hosts. This study of the ecological consequences of plasmid-bacterial compensatory evolution reveals benefits to bacte...
plos.io
December 3, 2024 at 12:19 PM
How best to avoid the costs of bearing a #plasmid? Rosanna Wright @brockhurstlab.bsky.social @jpjhall.bsky.social &co find that #bacteria benefit from compensating plasmids by chromosomal (rather than plasmid-borne) mutations @plosbiology.bsky.social plos.io/3ODbXdN
Reposted by Justin Fay
For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...
Hybrid adaptation is hampered by Haldane’s sieve - Nature Communications
Hybrids have complex genomes that influence their adaptive potential. This study reveals that yeast hybrids adapt slower than their parental species in a new environment, primarily due to a reduced ra...
www.nature.com
November 28, 2024 at 12:18 PM
For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...
Reposted by Justin Fay
🤩🦠 A new #preprint #openscience recommendation just out: Yeast consortia for novel wine fermentations by E. Pourcelot, et al.
Check here: microbiol.peercommunityin.org/articles/rec...
Thanks to @fcocubillosr.bsky.social for handling and @pablo-villa.bsky.social, C. Varela and 3 anonymous reviewers
Check here: microbiol.peercommunityin.org/articles/rec...
Thanks to @fcocubillosr.bsky.social for handling and @pablo-villa.bsky.social, C. Varela and 3 anonymous reviewers
Yeast consortium for novel wine fermentations
microbiol.peercommunityin.org
November 28, 2024 at 8:04 AM
🤩🦠 A new #preprint #openscience recommendation just out: Yeast consortia for novel wine fermentations by E. Pourcelot, et al.
Check here: microbiol.peercommunityin.org/articles/rec...
Thanks to @fcocubillosr.bsky.social for handling and @pablo-villa.bsky.social, C. Varela and 3 anonymous reviewers
Check here: microbiol.peercommunityin.org/articles/rec...
Thanks to @fcocubillosr.bsky.social for handling and @pablo-villa.bsky.social, C. Varela and 3 anonymous reviewers