Pangenomes, but scalable. Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social www.biorxiv.org/content/10.6...

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...

Open question for anyone that develops/maintains of bioinformatics tools, especially those used for public health - what do you think is the right way to fund this long term? Grants are great for new research directions, but aren't really appropriate for most tool dev/maintenance.

I’m already getting community feedback on the core-pivotal index. I truly appreciate it. But in the spirit of core-pivoteering, I will only implement suggestions from whoever has the highest core-pivotal index.

@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.

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza. Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

@cademirch.bsky.social @erikenbody.bsky.social TB Sackton & @russcd.bsky.social introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST). 🔗 doi.org/10.1093/molbev/msaf282 #evobio #molbio #compbio

Genetti & @russcd.bsky.social investigated Puerto Rico honeybees, suggesting that local pressures on bee behavior may have induced changes in alleles linked to different ancestries at loci involved in neuronal development, behavior, and mating. 🔗 doi.org/10.1093/gbe/evaf217 #genome #evolution

I am 100% stoked to lead this effort again this year! Come on out to beautiful Santa Cruz and show off your awesome-est science.

Our lab has an opening for a research technician to contribute to our efforts to understand RSV evolution & its impact on antibody countermeasures (see journals.asm.org/doi/full/10....). The tech will also help w lab management. If interested, apply here: careers-fhcrc.icims.com/jobs/29940/job

Super glad to see this out ! Lovely collaboration with @russcd.bsky.social @crouxevo.bsky.social and the groups of @meauxjuliette.bsky.social @plantadaptation.bsky.social

Hey! That's me! Check out my latest where I develop a method for pinpointing where mutation spectra change along phylogenies. Striking, nodes with large changes are significantly enriched for protein changes in the RdRp (catalytic domain of the polymerase) suggesting a causal role.

Would you consider applications from a slightly more senior postdoc? ... Asking for a friend, of course. :)

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released! (Most credit to Minh Bui and @roblanfear.bsky.social and their labs) ecoevorxiv.org/repository/v...

This is absolutely fascinating! Impressive analysis (3.2M TEs in 1.9K samples) and super interesting examples of locally adaptive TE insertions. Congrats to @tobybarilbio.bsky.social and all the authors.

Our paper on fitting population genetic models to low-pass sequencing data is now out in Molecular Biology and Evolution! doi.org/10.1093/molb...

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome: [1/N] www.biorxiv.org/content/10.1...

Delighted to organize the Next-Wave Symposium again this year! If you are an awesome postdoc in genomics---very broadly defined---come tell us about your amazing science!

There's a lot of uncertainty about the future right now. I'd like to do something constructive: if you teach students in #publichealth, #microbiology, #genomics, #bioinformatics, I'd be happy to talk about CDC AMD, #fellowships, gov sci and career paths. #microsky #blackinmicro 🧬🖥️ www.cdc.gov/amd

Got milk virus genomes? (or any H5N1?) Throw them at usher.bio and see where they land in per-segment trees of tens of thousands of public Influenza A H5N1 sequences!

Excited to dig into this - very cool work from @russcd.bsky.social‘s lab! 🙌 #TEworldwide #TEsky

So glad our paper on lethal hybrid incompatibilities is out at Nature today: rdcu.be/dvFcM ! @ben-moran.bsky.social moved mountains for this project: we identified two new incompatibilities in swordtail hybrids , characterize mechanisms of lethality, and their evolutionary history.

The Ecology & Evolution department at UC Santa Barbara is searching for an Assistant Professor of Evolutionary Biology. Please apply and/or spread the word! recruit.ap.ucsb.edu/JPF02635

Are you a postdoc doing awesome research in genomics?! Apply to present at the NextWave of Faculty in Genomics symposium! Also, please repost!

UShER has been an amazing project, but we never really documented exactly how we maintain the 16M sample SARS-CoV-2 tree 😬... In a paper the came out over the break, we go back through our server logs to retrospectively walk through the major choices we made. Check it out here: rdcu.be/du5q5

I'm pleased to share our new article in MBE! We dug deep into the molecular details of the classic Ruff inversion that mediates different plumage and mating display phenotypes. w/ Jason Hill and Huijan Bi and others with Leif Andersson

Registration for BAPG at Stanford Dec. 2, 2023 is now open. The registration is free but required: docs.google.com/forms/d/14ne...