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...
1/ BRAKER4 hatched!
The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
Dear letter writers, study sections, grant panels, etc…..(though expecting little will resonate)….
Congrats Maitreya!!!! 🎉🥳 A wonderful scientist, mentor, teacher, and leader
@maitreya.bsky.social
A comment from the story:It's a colorful pangenome world . From: It’s a colorful pangenome world... When digging into pangenomics methods to avoid reference bias, a hurdle is that “when you represent a lot of variations, it becomes, paradoxically, harder to correctly place the ‘nonaligners,’” says Camille Marchet. Aligning sequence to graphs offers “no trivial answer.” She and her team use the De Bruijn graph and her lab’s latest method is Vizitig.
From my pangenomics story in @natmethods.nature.com, It's a colorful pangenome world, which is here www.nature.com/articles/s41... and here: rdcu.be/e8ZYC
A comment from @camillemrcht.bsky.social
Trippy Memphis bridge https://pangenome.github.io/MemPanG26/
Level up your #pangenomics game! Workshop, conference & biohackathon in #Memphis, May 11-15, 2026. Join us and get your hands dirty with sequence alignment, explicit and implicit graphs, cutting-edge methods, and AI. Register now! pangenome.github.io/MemPanG26/ #Bioinformatics #MemPanG26
Need to annotate transposons in fungal genomes? 🧬
Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg...
Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social!
w/ @danielcroll.bsky.social
We just launched flyRoom — modern web-based stock management for Drosophila labs. No more spreadsheets, no more messy labels, no more lost stocks. Free to start, built by researchers for researchers.
www.flyroom.net
Remembering Phil Bourne. Personal reflections on a legendary scientist, leader, builder, and mentor. blog.stephenturner.us/p/rememberin...
Haven’t read the paper yet, but the pattern shown would be my expectation under a reward system that favors chasing trends. Like baby name or dog breed popularity, scientists collectively follow trends at scale that I’d expect to be highly auto correlated but drift over time.
Well deserved. Congratulations Joseph 🎉
Thrilled and honored to be part of the 2026 GSA Award recipient! This honor reflects years of teamwork - huge thanks to everyone who has been part of the #haploteam. Proud to share this with you all! @genetics-gsa.bsky.social
genestogenomes.org/the-2026-gsa...
26.3 (25D125). I think you need to click "Use as Defaults" after you check "always open in list view" and "browse in list view"
View -> Show view options -> always open in list view
Sad to learn that David Botstein has passed away. Few people truly shape how you think and do science, and David was definitely one of them. I had a fun and influential time at Princeton with the Botstein, Kruglyak and co gangs. It shaped the way I do science.
www.online-tribute.com/DavidBotstein
So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).
how LLMs change incentives for research - a great talk by @carlbergstrom.com , had to watch in parts, a lot to digest. #institutional_epistemology at its best! www.youtube.com/watch?v=9Mj3... #philsci
One of my favorite tools to introduce to new students. Thanks for developing and maintaining!
Can't wait to release a 10-year-old birthday version for SeqKit!
- 10 years
- 2 papers, 3500 citations
- 20 contributors
- 40 subcommands
- 880 commits
- 500 issues
- 685.5K Bioconda total downloads
Thank you all, dear contributors and users!
I'll keep maintaining it.
github.com/shenwei356/s...
Amazing peppered moth story from Saccheri lab - same locus, but different structural variants, underly parallel evolution of industrial melanism in the UK and across continental Europe.
@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.
With @litinice.bsky.social, we built a haploid resource from 33 wild Taiwanese Saccharomyces cerevisiae strains — including some of the most genetically divergent Asian lineages — to bring natural yeast diversity into a genetically tractable framework. www.biorxiv.org/content/10.6...
Time-calibrated phylogeny of the family Drosophilidae showing major species groups, surrounded by representative adult flies that highlight the remarkable morphological diversity of this model insect group. The composite image was created using Microsoft PowerPoint. Fly photographs were taken by Darren J. Obbard and are published under the Creative Commons Attribution License with permission.
The #fly community aims to achieve a comprehensive genomic study of the Drosophilidae family. @pankajd.bsky.social @bernardkim.bsky.social @petrovadmitri.bsky.social @darrenobbard.bsky.social present a comparative gene annotation for 301 #Drosophilidae species @plosbiology.org 🧪 plos.io/4c3pyrI
Our paper is now out in Nature:
“Ancient co-option of LTR retrotransposons as yeast centromeres”
www.nature.com/articles/s41...
A short thread on how retrotransposons helped give rise to yeast point centromeres.
1/14
🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
Thanks, we’re still waiting on a submission from September. Trying to contact the general NCBI help desk now.
We were all very sad to learn the death of Pierre Capy. Pierre was a professor at University Paris Saclay, in the 1990s, he started a group working on the evolutionary genomics of transposable elements; this group is still very active today. He was a great teacher, mentor, and colleague.
How does the piRNA pathway solve the self vs. non-self problem? 🧬
Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
👏
Looking for a postdoc to build my new lab at TGen (Phoenix, AZ) focused on pangenome methods for cancer and complex disease. Full stack — from pangenome assembly and compression to association studies and somatic variant discovery. Reach out if interested! guarracinolab.github.io#join