Gavin Woodruff
@weirdworms.bsky.social
Development, evolution, worms, gene name etymology. I log interesting papers, questions, and ideas.
January 8, 2026 at 9:51 PM
Reposted by Gavin Woodruff
What a breakthrough! Such a puzzle for 30 years, this is real progress!
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers
The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...
www.biorxiv.org
January 7, 2026 at 7:46 PM
What a breakthrough! Such a puzzle for 30 years, this is real progress!
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
Reposted by Gavin Woodruff
New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...
January 6, 2026 at 3:01 AM
New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...
Reposted by Gavin Woodruff
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:30 AM
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
Systematic identification of oscillatory gene expression in single cell types
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Systematic identification of oscillatory gene expression in single cell types
Many biological cycles are driven by oscillatory gene expression coordinated across cell types. For example, larval development in Caenorhabditis elegans involves coordinated cyclic changes in cell di...
www.biorxiv.org
January 5, 2026 at 5:07 PM
Systematic identification of oscillatory gene expression in single cell types
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Gavin Woodruff
Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
January 5, 2026 at 8:53 AM
Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
Reposted by Gavin Woodruff
Another YouTube Tutorial – This one on Proximity Labeling and connected to our recent EMBO J. paper (PMID: 41381733). This is a recording of a talk at the IDeA National Resource for Quantitative Proteomics in Little Rock AR. One of the top facilities in the country!
www.youtube.com/watch?v=0T9P...
www.youtube.com/watch?v=0T9P...
Core Directors' Symposium - 2025 - David Fay
YouTube video by IDeA National Resource for Quantitative Proteomics
www.youtube.com
January 4, 2026 at 3:40 PM
Another YouTube Tutorial – This one on Proximity Labeling and connected to our recent EMBO J. paper (PMID: 41381733). This is a recording of a talk at the IDeA National Resource for Quantitative Proteomics in Little Rock AR. One of the top facilities in the country!
www.youtube.com/watch?v=0T9P...
www.youtube.com/watch?v=0T9P...
Reposted by Gavin Woodruff
Congrats Simon Han & @brugmannlab.bsky.social on your publication @cincyresearch.bsky.social
A dual role for GLI3 signaling in neural crest development
journals.biologists.com/dev/article/...
A dual role for GLI3 signaling in neural crest development
journals.biologists.com/dev/article/...
December 31, 2025 at 4:04 PM
Congrats Simon Han & @brugmannlab.bsky.social on your publication @cincyresearch.bsky.social
A dual role for GLI3 signaling in neural crest development
journals.biologists.com/dev/article/...
A dual role for GLI3 signaling in neural crest development
journals.biologists.com/dev/article/...
Reposted by Gavin Woodruff
Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2
www.youtube.com/watch?v=u63o...
www.youtube.com/watch?v=u63o...
David's AlphaFold WorkShop 2026
YouTube video by David Fay
www.youtube.com
January 2, 2026 at 11:03 PM
Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2
www.youtube.com/watch?v=u63o...
www.youtube.com/watch?v=u63o...
Mutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Laboratory Populations of Caenorhabditis elegans
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
Mutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Laboratory Populations of Caenorhabditis elegans
Abstract. Spontaneous mutations display biases in their relative frequencies with important consequences for genome structure and composition. While labora
academic.oup.com
January 1, 2026 at 3:49 PM
Mutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Laboratory Populations of Caenorhabditis elegans
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
How to measure, analyze, and interpret age-related changes in Caenorhabditis elegans: lessons for mechanistic and evolutionary theories of aging
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
How to measure, analyze, and interpret age-related changes in Caenorhabditis elegans: lessons for mechanistic and evolutionary theories of aging
Aging is characterized by progressive degenerative changes in tissue organization and function, some of which increase the probability of mortality. M…
www.sciencedirect.com
January 1, 2026 at 3:48 PM
How to measure, analyze, and interpret age-related changes in Caenorhabditis elegans: lessons for mechanistic and evolutionary theories of aging
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Hybridization and introgression between two fig trees with contrasting ecological preferences
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Hybridization and introgression between two fig trees with contrasting ecological preferences - BMC Ecology and Evolution
BMC Ecology and Evolution - Hybridization in plants with specialized pollination systems provides insights into the mechanisms of species boundary maintenance and breakdown. The significance of...
link.springer.com
January 1, 2026 at 3:45 PM
Hybridization and introgression between two fig trees with contrasting ecological preferences
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Reposted by Gavin Woodruff
Somatic and germline mutational processes across the tree of life https://www.biorxiv.org/content/10.64898/2025.12.28.691837v1
December 30, 2025 at 2:32 PM
Somatic and germline mutational processes across the tree of life https://www.biorxiv.org/content/10.64898/2025.12.28.691837v1
Reposted by Gavin Woodruff
This story is absolutely wild. Did you know that avocados change sex over the course of a day? And that it's controlled by a single ancient balanced polymorphism? This is flat our crazy
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
December 25, 2025 at 6:33 AM
This story is absolutely wild. Did you know that avocados change sex over the course of a day? And that it's controlled by a single ancient balanced polymorphism? This is flat our crazy
Reposted by Gavin Woodruff
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
December 24, 2025 at 3:51 PM
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
Reposted by Gavin Woodruff
Within a pitcher plant, bacteria break down prey to feed the plant. As the leaf ages, bacteria become less diverse, but more efficient at degrading insects. It appears that species that are strong degraders are weak competitors.
Read now ahead of print!
www.journals.uchicago.edu/doi/10.1086/...
Read now ahead of print!
www.journals.uchicago.edu/doi/10.1086/...
Opposing Effects of Succession on Bacterial Diversity and Function within Pitcher Plant (Sarracenia purpurea) Leaves | The American Naturalist
Abstract How biodiversity and ecosystem functions change with succession has proven to be difficult to predict. Generally, it is thought that species accumulation over time should increase function, y...
www.journals.uchicago.edu
December 24, 2025 at 12:45 AM
Within a pitcher plant, bacteria break down prey to feed the plant. As the leaf ages, bacteria become less diverse, but more efficient at degrading insects. It appears that species that are strong degraders are weak competitors.
Read now ahead of print!
www.journals.uchicago.edu/doi/10.1086/...
Read now ahead of print!
www.journals.uchicago.edu/doi/10.1086/...
Reposted by Gavin Woodruff
Biologists who teach: in what order do you teach the four forces of evolution? Genetic drift first or selection first? And I'm still struggling to smoothly fit in HWE so that its utility is emphasized (students focus so much on how likely it is that assumptions are violated).
#iteachbio 🧪 #Evolution
#iteachbio 🧪 #Evolution
December 22, 2025 at 2:00 PM
Biologists who teach: in what order do you teach the four forces of evolution? Genetic drift first or selection first? And I'm still struggling to smoothly fit in HWE so that its utility is emphasized (students focus so much on how likely it is that assumptions are violated).
#iteachbio 🧪 #Evolution
#iteachbio 🧪 #Evolution
Reposted by Gavin Woodruff
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
www.biorxiv.org
December 22, 2025 at 3:09 PM
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
Reposted by Gavin Woodruff
Interesting article on the evolution of views of Stephen Jay Gould in relation to punctuated equilibria.
www.cambridge.org/core/journal...
🧪 #Paleobio #EvoBio
www.cambridge.org/core/journal...
🧪 #Paleobio #EvoBio
December 22, 2025 at 3:06 PM
Interesting article on the evolution of views of Stephen Jay Gould in relation to punctuated equilibria.
www.cambridge.org/core/journal...
🧪 #Paleobio #EvoBio
www.cambridge.org/core/journal...
🧪 #Paleobio #EvoBio
Reposted by Gavin Woodruff
Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Decoding cnidarian cell type gene regulation - Nature Ecology & Evolution
This study reconstructs the gene regulatory networks that define cell types in the sea anemone Nematostella vectensis, providing a valuable resource for comparative regulatory genomics and the evoluti...
www.nature.com
December 22, 2025 at 10:12 AM
Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Gavin Woodruff
Happy to announce the publication of our foray into studying what happens to the transcriptomes of nuclei when cells fuse to form a syncytium. More to follow in the coming few years.
One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!
One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!
Epidermal cell fusion promotes the transition from an embryonic to a larval transcriptome in C. elegans
Highlighted Article:eff-1–mediated cell fusion drives transcriptomic progression from an embryonic to larval state in the C. elegans epidermis, without which developmental progression is delayed.
journals.biologists.com
December 22, 2025 at 2:59 PM
Happy to announce the publication of our foray into studying what happens to the transcriptomes of nuclei when cells fuse to form a syncytium. More to follow in the coming few years.
One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!
One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!
Reposted by Gavin Woodruff
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
December 21, 2025 at 3:10 AM
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
Reposted by Gavin Woodruff
"Range extender mediates long-distance
enhancer activity" by @evgenykvon.bsky.social 's team, led by @gracebower.bsky.social is one of my papers of the year. Discovery of a new class of cis-regulatory elements that modulate the regulatory activity and reach of enhancers.
doi.org/10.1038/s415...
enhancer activity" by @evgenykvon.bsky.social 's team, led by @gracebower.bsky.social is one of my papers of the year. Discovery of a new class of cis-regulatory elements that modulate the regulatory activity and reach of enhancers.
doi.org/10.1038/s415...
December 21, 2025 at 10:08 PM
"Range extender mediates long-distance
enhancer activity" by @evgenykvon.bsky.social 's team, led by @gracebower.bsky.social is one of my papers of the year. Discovery of a new class of cis-regulatory elements that modulate the regulatory activity and reach of enhancers.
doi.org/10.1038/s415...
enhancer activity" by @evgenykvon.bsky.social 's team, led by @gracebower.bsky.social is one of my papers of the year. Discovery of a new class of cis-regulatory elements that modulate the regulatory activity and reach of enhancers.
doi.org/10.1038/s415...
Reposted by Gavin Woodruff
Hey all, I reached out to the PO of my NIGMS MIRA to ask if the gov't shut down, and rescheduling of study sections, might allow for some accommodation to the standard rule that PIs cannot resubmit a MIRA while their MIRA (or other RPG) is under review (waiting in scores or summary statements) 🧪
December 19, 2025 at 7:17 PM
Hey all, I reached out to the PO of my NIGMS MIRA to ask if the gov't shut down, and rescheduling of study sections, might allow for some accommodation to the standard rule that PIs cannot resubmit a MIRA while their MIRA (or other RPG) is under review (waiting in scores or summary statements) 🧪
Reposted by Gavin Woodruff
Check out our preprint investigating host use in sympatric Caenorhabditis nematodes! We found three Caenorhabditis species in a local community are associated with different invert taxa, and document a strong association between one species and invasive nitidulid beetles.
doi.org/10.64898/202...
doi.org/10.64898/202...
December 19, 2025 at 8:03 AM
Check out our preprint investigating host use in sympatric Caenorhabditis nematodes! We found three Caenorhabditis species in a local community are associated with different invert taxa, and document a strong association between one species and invasive nitidulid beetles.
doi.org/10.64898/202...
doi.org/10.64898/202...