Natural Selection in Transcription Factor–DNA Interaction Motifs: A Comparative and Population Genomics Perspective Abstract. Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype-to-phenotype transitions. On the molecu

📄 Joshi et al. (2025)
Natural selection in transcription factor–DNA interaction motifs from comparative & population genomics perspectives.

GLADE: Accurate inference of Gains, Losses, Ancestral genomes, and Duplication Events for comparative genomics www.biorxiv.org/content/10.64898/2026.01...

Excited to share our newest preprint!

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Picture of five people wearing berets and costume jewelry.

Happened to wear black today, so I got sucked into a lab Louvre heist Halloween dress up.

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

www.biorxiv.org/content/10.1...

Proud of the latest edition of my free intro biostats book.

gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/

Not complete but at a good point to take a break, and I think its quite usable

dm me with comments , ideas etc

Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...

Three schematic diagrams. The first illustrates selective publishing of internal resection, the second selective causal focus, and the third selective access and funding for researchers.

1. We ( @jbakcoleman.bsky.social, @cailinmeister.bsky.social, @jevinwest.bsky.social, and I) have a new preprint up on the arXiv.

There we explore how social media companies and other online information technology firms are able to manipulate scientific research about the effects of their products.

GitHub - RILAB/statements: Successful Job Applications and Grants Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

Lunch today halfway around the world in Hangzhou and met a new asst professor who was very thankful for this resource. Please help out folks like them and other early career scientists with examples of job apps. Submit yours!
github.com/RILAB/statem...

Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes - Nature Genetics Ctyper is a genotyping method for copy number variation and complex genes that produces sequence-resolved genotypes by directly comparing sequencing reads to pangenome haplotypes, achieving increased ...

www.nature.com/articles/s41...

A deep-time landscape of plant cis-regulatory sequence evolution Developmental gene function is conserved over deep time, but cis -regulatory sequence conservation is rarely found. Rapid sequence turnover, paleopolyploidy, structural variation, and limited phylogen...

From @kirkamundson.bsky.social this looks pretty amazing. www.biorxiv.org/content/10.1...

Movi 2: Fast and Space-Efficient Queries on Pangenomes www.biorxiv.org/content/10.1101/2025.10....

We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories...

New preprint led by grad student, Yu Mo! We introduce new software to calculate evolutionary rates of quantitative characters in the presence of discordance

1/

www.biorxiv.org/content/10.1...

We are excited to share our new preprint describing the inclusion of selection models to stdpopsim, our community-maintained library with an extensive catalog of population genetic models. 1/n
www.biorxiv.org/content/10.1...

Artistic image of male and female Caenorhabditis briggsae nematodes against a backdrop of multi-species genome alignments.

New paper early online at GBE: Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genome assembly of the hyper-polymorphic nematode Caenorhabditis brenneri. doi.org/10.1093/gbe/...