New preprint led by Hrushikesh Loya, me, and Simon Myers where we introduce GhostBuster! www.biorxiv.org/content/10.6...
The idea is to find all the different ways a target individual relates to reference groups in genealogies, to "bust the ghosts" in our ancestry.
Genome-wide genealogies reveal deep admixtures forming modern humans www.biorxiv.org/content/10.64898/2026.04...
My lab read this paper www.biorxiv.org/content/10.1... for journal club, and had some thoughts on the strong claims made about the number of signals of selection found.
They ended up choosing the (inflated) cutoff based on GWAS enrichment, which is different from just relaxing it. That being said, it of course can be done with previous studies too but this is I believe the first time it is actually done.
Spread the word! UChicago BSD is currently searching for an instructional professor (open rank) to help develop and support graduate training in quantitative biology at UChicago. This is an Instructional Professor position (open rank). apply.interfolio.com/183517.
Thrilled to see this out. What started out as a chat several years back with @drfejzo.bsky.social about leveraging publicly available data on hyperemesis gravidarum GWAS turned into a wonderful collaboration with April Shu, @mvaudel.bsky.social, @xwww.bsky.social and many others!
rdcu.be/fdl9k
Fantastic seminar from @deboraycb.bsky.social discussing some of the challenges and limitations of detecting balancing selection from genomic data and her ongoing work on developing a new ARG-based approach.
See preprint here: www.biorxiv.org/content/10.6....
Getting close to a robust pipeline for ARG inference for messy genomes.
1. get a vcf. Align short reads to a reference and GATK and pray, or use whole genome assemblies and github.com/baoxingsong/... followed by github.com/RILAB/argprep
Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes.
www.biorxiv.org/content/10.6...
We are destroying species' habitats, leading to a mass extinction event.
This habitat destruction also reduces the genetic diversity _within_ species.
Our latest work develops quantitative models to predict how much genetic diversity has been and _will be_ lost.
🧬🧪🧵
www.pnas.org/doi/10.1073/...
Delighted to share our latest preprint: Julie Zhu identifies a surprising reason why the genetic architecture of brain-related traits is so different than other traits. Check it out!
LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel.
Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL
Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n)
journals.plos.org/plosbiology/...
Why do schizophrenia GWAS signals look so flat across the genome?
In our recent preprint, we explored why psychiatric disorders — and, more broadly, brain-related traits involving the central nervous system — appear to have unusual genetic architectures.
🧵1/n
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens!
Read it in Science
dx.doi.org/10.1126/scie...
@ucberkeleyofficial.bsky.social
@hhmi-science.bsky.social
Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.
More on the Denisovan legacy in us: A Denisovan-derived Alu insertion in OCA2 contributes to pigmentation diversity in present-day Melanesians.
More evidence (validated in melanocytes) that introgressed structural variants contributed to adaptive & phenotypic diversity 🧪🧬
📣Our paper is out! 🤩 We found that local modification of H3K9me3 using CRISPR/dCas9 at hotspots changes crossover activity, bringing us closer to targeted recombination in plants.🌱
Huge thanks to @szymanskalejman.bsky.social, Wojtek, Ania, and Karolina!
www.science.org/doi/10.1126/...
NEE Focus issue on "Evolution in medicine", including a comment article from @alisonfeder.bsky.social and me.
Have you ever wondered how many archaic populations contributed DNA to modern humans? We know about Neanderthals and Denisovans, but the fossil and genetic evidence suggests a much more complex history!
www.biorxiv.org/content/10.6...
This is truly gold.
I'm so dang excited for #PEQG26 I've already started my talk. Registration and poster abstract submission open through March 10.
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).
If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...
How does the strength of genetic drift evolve over long times?
New preprint out 👇
www.biorxiv.org/content/10.6...
New preprint! with @a-solernunez.bsky.social
Rethinking a textbook example of human adaptation "AMY1 copy number evolution in light of demographic history"
Once population structure is accounted for, the classic starch–agriculture narrative becomes much less clear
www.biorxiv.org/content/10.6...
The next BAPG has been announced! April 11 at Davis organized by the inimitable @jrossibarra.bsky.social! bapg-conference.github.io
The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action:
Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...
Great news for anyone using ARGs in non-model species:
www.biorxiv.org/content/10.1...