Gavin Woodruff
@weirdworms.bsky.social
Development, evolution, worms, gene name etymology. I log interesting papers, questions, and ideas.
Reposted by Gavin Woodruff
Do contest-related traits evolve faster? A test of the exaggerated evolution hypothesis in a clade of Neotropical arachnids royalsocietypublishing.org/rsbl/article... | #BiologyLetters #Evolution
January 25, 2026 at 10:00 AM
Do contest-related traits evolve faster? A test of the exaggerated evolution hypothesis in a clade of Neotropical arachnids royalsocietypublishing.org/rsbl/article... | #BiologyLetters #Evolution
Reposted by Gavin Woodruff
gonna do the old science twitter thing and post my reading here this year
January 12, 2026 at 4:36 PM
gonna do the old science twitter thing and post my reading here this year
Reposted by Gavin Woodruff
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 23, 2026 at 11:10 AM
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
Reposted by Gavin Woodruff
PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5!
*Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.
*Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.
Homepage - 2026 Population, Evolutionary, and Quantitative Genetics Conference
Visit our website to learn more.
genetics-gsa.org
January 23, 2026 at 2:37 PM
PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5!
*Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.
*Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.
Reposted by Gavin Woodruff
OUT NOW! Parasex generates highly recombinant progeny in Candida albicans with increased virulence
By Robert Fillinger, Scott Filler, Anna Selmecki, Richard Bennett,
Matthew Anderson & colleagues.
#microsky @annaselmecki.bsky.social
www.nature.com/articles/s41...
By Robert Fillinger, Scott Filler, Anna Selmecki, Richard Bennett,
Matthew Anderson & colleagues.
#microsky @annaselmecki.bsky.social
www.nature.com/articles/s41...
Parasex generates highly recombinant progeny in Candida albicans with increased virulence - Nature Microbiology
An alternative mating system, termed parasex, produces progeny with high levels of genotypic diversity and is able to fulfil the roles of meiosis when it is absent in the fungal pathobiont Candida alb...
www.nature.com
January 21, 2026 at 4:38 PM
OUT NOW! Parasex generates highly recombinant progeny in Candida albicans with increased virulence
By Robert Fillinger, Scott Filler, Anna Selmecki, Richard Bennett,
Matthew Anderson & colleagues.
#microsky @annaselmecki.bsky.social
www.nature.com/articles/s41...
By Robert Fillinger, Scott Filler, Anna Selmecki, Richard Bennett,
Matthew Anderson & colleagues.
#microsky @annaselmecki.bsky.social
www.nature.com/articles/s41...
Reposted by Gavin Woodruff
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...
www.nature.com
October 16, 2025 at 7:49 AM
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Gavin Woodruff
An extensive ER network develops in the olfactory hair cells of Drosophila. Inagaki et al. @riken-bdr.bsky.social report that the transmembrane protein Gore-tex controls a novel ER to the plasma membrane trafficking pathway essential for the cuticular nanopore formation. rupress.org/jcb/article/...
January 20, 2026 at 2:45 PM
An extensive ER network develops in the olfactory hair cells of Drosophila. Inagaki et al. @riken-bdr.bsky.social report that the transmembrane protein Gore-tex controls a novel ER to the plasma membrane trafficking pathway essential for the cuticular nanopore formation. rupress.org/jcb/article/...
A protein language model unveils the E. coli pangenome functional landscape regulating host proteostasis
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 18, 2026 at 8:47 PM
A protein language model unveils the E. coli pangenome functional landscape regulating host proteostasis
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
!
Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids
www.nature.com/articles/s41...
Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids
www.nature.com/articles/s41...
Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids - Nature Communications
Haldane’s rule suggests that in hybrid crosses, the heterogametic sex is often rare or sterile. This study crosses Caenorhabditis nematodes, and determines that an underlying feature of Haldane’s rule...
www.nature.com
January 16, 2026 at 4:40 PM
!
Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids
www.nature.com/articles/s41...
Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids
www.nature.com/articles/s41...
!
More heroic work from Zhongying Zhao's group
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses
www.biorxiv.org/content/10.6...
More heroic work from Zhongying Zhao's group
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses
www.biorxiv.org/content/10.6...
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses
Toxin-antidote (TA) systems are selfish genetic elements that promote their own inheritance by selectively eliminating offspring lacking the module, thereby establishing post-zygotic genetic incompati...
www.biorxiv.org
January 12, 2026 at 5:17 PM
!
More heroic work from Zhongying Zhao's group
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses
www.biorxiv.org/content/10.6...
More heroic work from Zhongying Zhao's group
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses
www.biorxiv.org/content/10.6...
Reposted by Gavin Woodruff
The tutorial for how to assemble organellar genomes from nuclear-targeted long reads is ready to be used. Please check it out
bioinformaticsworkbook.org/dataAnalysis...
#Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria
bioinformaticsworkbook.org/dataAnalysis...
#Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria
Extracting and Assembling a Mitochondrial and Chloroplast Genome from Nuclear-targeted Nanopore Reads
A workbook to help scientists working on bioinformatics projects
bioinformaticsworkbook.org
April 30, 2025 at 9:57 PM
The tutorial for how to assemble organellar genomes from nuclear-targeted long reads is ready to be used. Please check it out
bioinformaticsworkbook.org/dataAnalysis...
#Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria
bioinformaticsworkbook.org/dataAnalysis...
#Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria
Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation
Abstract. Prototypical PUF proteins are known for modular, sequence-specific RNA recognition. A single PUF protein in Drosophila melanogaster Pumilio and t
academic.oup.com
January 9, 2026 at 5:49 PM
Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Gavin Woodruff
Interesting new multi-population aDNA selection scan from Colbran, Terhorst, Mathieson. Loci that are estimated to be under selection in one population also show enrichment in other populations, consistent with parallel or pre-split selection.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
January 9, 2026 at 2:37 PM
Interesting new multi-population aDNA selection scan from Colbran, Terhorst, Mathieson. Loci that are estimated to be under selection in one population also show enrichment in other populations, consistent with parallel or pre-split selection.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
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...