My abiding memory of a wonderful #SMBE2026:

Excited to be presenting my poster on Lorax at #PEQG26! Lorax is a GPU-accelerated, web-native tool for real-time interactive visualization of Ancestral Recombination Graphs. If you're at Asilomar this week, come check it out. Would love to chat about scalable ARG exploration and get your feedback

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.

Molecular Biology and Evolution@molbioevol.bsky.social · 5mo ago

@russcd.bsky.social ushers in a new era of academic metrics with the core-pivotal author index, which assigns all credit to authors that occupy the exact center of the author list, while non-central peripheral authors receive no credit whatsoever. 🔗 doi.org/10.1093/molbev/msag026 #evobio #molbio

@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)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

nature.com

@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

Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)

Abstract. The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversi

doi.org

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

Signals of Ancestry-Specific Selection in Gentle Africanized Honey Bees

Abstract. Understanding the genetic basis of adaptive responses to environmental and human mediated pressures is a central concern in evolutionary biology.

doi.org

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.

UC Santa Cruz Genomics Institute@ucscgenomics.bsky.social · 8mo ago

POSTDOCS: We're hosting our fourth-annual Next Wave of Faculty in Genomics symposium in beautiful Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants ✈️😎🏖 APPLY BY JAN 15: genomics.wordpress.ucsc.edu/calendar_eve...

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

Evolution Letters@evolletters.bsky.social · last yr.

Diverging Arabidopsis populations quickly accumulate pollen-acting genetic incompatibilities doi.org/10.1093/evle... Now in @evolletters.bsky.social by Christopher Condon et al.

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.

Molecular Biology and Evolution@molbioevol.bsky.social · last yr.

Using ~8M SARS-CoV-2 genomes, a new phylogenetic algorithm by @russcd.bsky.social detects 10 shifts in mutation patterns, some of them linked to changes in viral polymerase. This provides new perspectives on the evolution of mutational processes. 🔗 doi.org/10.1093/molb... #molbio #evobio #covid

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

Daniel Croll@danielcroll.bsky.social · last yr.

Excited to do a postdoc in beautiful Neuchatel / Switzerland🇨🇭? We have several postdoc positions open at the moment! Check our website for the full ads here: pathogen-genomics.org/jobs Happy to answer any question and please spread the word to anyone who might be interested!

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

Michael Baym@baym.lol · last yr.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/

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.

Toby Baril@tobybarilbio.bsky.social · last yr.

Excited to share our latest preprint 🥳 Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen @danielcroll.bsky.social #TESky www.biorxiv.org/content/10.1...

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...

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure

RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

biorxiv.org

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!

UC Santa Cruz Genomics Institute@ucscgenomics.bsky.social · 2y ago

Calling all postdocs! We're hosting a symposium in beautiful Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants ✈️😎🏖 The event will be held on April 15. Applications due Feb 15: bit.ly/NextWave25

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

Advanced Molecular Detection (AMD)

CDC’s Advanced Molecular Detection program leads national efforts to develop and expand the use of

cdc.gov

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

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y ago

Horizontal transmission of functionally diverse transposons is a major source of new introns https://www.biorxiv.org/content/10.1101/2024.06.04.597373v1

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!

UC Santa Cruz Genomics Institute@ucscgenomics.bsky.social · 3y ago

DEADLINE APPROACHING! We're hosting a postdoc symposium in beautiful beachside Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants. The event will be held on March 12. Applications due Jan 12: genomics.ucsc.edu/calendar_eve...

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