Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

Just an outrageous amount of structural variation in pennycress. While not yet reproductively isolated, its likely these shredded pericentromeres contribute to some reproductive incompatibilities.

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

Don't forget to apply to our position in Evolutionary Genetics at U of South Carolina! In my experience it is a fantastic place to start a new lab, with friendly and supportive colleagues and many junior faculty in EEB! Review starts in 1 week (Oct 1)!

And yes, now is the right time. New for @undark.org "The fundamental problem with the tenure process is that it has struggled to recognize that knowledge is curated, created, and consumed differently today than even a decade ago." undark.org/2025/09/11/o...

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts. We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

Motherfucker wrote one sloppy paper in April 2020 and instead of being like oops, shit, my bad, he has kept doubling down until now he's killing most promising medical technology of the past quarter century rather than going to therapy.

This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'. Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:

🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨 Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics Apply by 18-Aug Apply here: jobs.ornl.gov/job/Oak-Ridg...

@jrossibarra.bsky.social your kind of street art

Wow, the cover looks great! Nice work Patrice and @roederlab.bsky.social The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome

The PLANTS program (funded by NSF) at @botsocamerica.bsky.social was a cornerstone of the conference each year, bringing together new-to-science scholars with more experienced mentors. It helped provide community, support, and connection to new scientists. The grant was terminated last week.

We begin reviewing applications next week!

Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv. 🧵with some background and a few things we found 👇 bsky.app/profile/bior...

So long San Diego! Here’s my opinionated meeting report from #PAG2025 | #PAG32. What else did I miss???

My work on a pangenome for the hexaploid oilseed crop Camelina sativa is now out early access in Genetics! This young polyploid genome has a small pangenome to match it's low SNP diversity, but regained lost diversity by packing in all the unique genes from its 3 diploid progenitors.

Last week we published a peanut genome that was much more complex than it originally appeared. A 🧵 about 🥜 genomes and what we found ... Find the article as a ‘featured’ genome report in G3: academic.oup.com/g3journal/ar....

Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWU

@carlbergstrom.com you had a post about making 🐦‍⬛ friends a while back - mind linking it here? We’re gonna try it out with the magpies on our street. Got the 🥜 ready to go

Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...

The All of Us paper is rightly being criticized for its UMAP figure, which suggests an overly discrete view of human variation—a problem that is compounded by colouring the plot with self-identified race and then omitting the “self-identified” from the title & legend. 1/n

I can confirm the appalling news that Duke intends to close its 800K specimen herbarium as part of an embarrassing plan to delete its position as a leader in biodiversity research. This is despite successful fundraising efforts with a donor secured to save the herbarium.

Excellent postdoc right at the cutting edge of genomics; the Harkess lab is great! “collab w/ Loren Honaas (USDA) & Stephen Ficklin (WSU) labs to sequence 1000s of apple/pear RNAs to develop biomarker assays for maturity and post-harvest traits. $60,000.” hudsonalpha.applicantpro.com/jobs/3238779

🚨We're hiring🚨 We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO. Pls share! hudsonalpha.applicantpro.com/jobs/3211389

We are trying to come up with subgenome IDs for a new genome. Need to be single uppercase character for each of two subgenomes. Any suggestions of characters to NOT USE? Right now we are avoiding: ABCDEIOPQUVWXYZ

I'm pulling double duty this year at #PAG31. On Sunday, check out the Polyploid session for some amazing talks on the biological & evolutionary impacts of polyploidy across plants & animals. On Monday evening I'm presenting our work on a pangenome of hexaploid Camelina sativa in the DOE-BER session

The 2nd biennial meeting of the North American Forest Genetics Society (June 10-14th 2024) will take place in Oaxaca, Mexico! Researchers at all levels are encouraged to attend - nafgs24.org for info on confirmed speakers, preliminary schedule, & training workshops. Registration opens Jan 19th! 🌲🌳

Inaugural Bluesky post (👋 Everyone!): The Ecology, Evolution, and Organismal Biology Dept. at Iowa State U. (my dept!) is conducting an open search at the rank of Professor for a new Dept. Chair! isu.wd1.myworkdayjobs.com/en-US/IowaSt...

I am recruiting a manager/tech for our plant evolutionary genetics lab, looking for someone interested in learning ancient DNA techniques psu.wd1.myworkdayjobs.com/PSU_Staff/jo...

@cbcuconn.bsky.social is offering 2 virtual #bioinformatics training workshops in Jan! Genome Assembly (Jan 8-11) and Genome Annotation (Jan 22-25). 1/2 days, real instructors, real data examples! Learn more & register here: bioinformatics.uconn.edu/cbc-workshops/

If you review a genome paper and state that the major flaw is that it is not "T2T" ... please justify why a couple gaps in highly repetitive regions is such a problem. For the same $$ we can learn so much more from multiple nearly gapless genomes than a single gap-patched reference.

We're working on a viz tool to show differences btw genome assemblies, both due to biology and assembly quality. Currently, the output looks like this for Human Hg38 vs. CHM13-T2T: orange = gene density, blue = repeats, red = gaps, grey ribbons = GENESPACE synteny any thoughts for improvements?

So excited to announce our search for an Assistant Professor focused on understanding plant response to climate change! Come join us at UC Riverside aprecruit.ucr.edu/JPF01827

SMBE 2024 Puerto Vallarta website is live! The call for symposia opens soon! www.smbe2024.org

Great integration of genomics, quant gen and breeding. Great story too. doi.org/10.1038/s414...

Question for the #genomics hive mind: I want to test whether a transcription factor binds better to one of two sequences … is there a tool that can do this statistical test?