Russ Corbett-Detig

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.

Disclaimer: I am a terrible web developer and this extension should not be used by anyone.

The chrome extension can do this for you! github.com/russcd/coreP...

Thanks so much, Ian! This means a lot coming from a mighty core-pivotal 17.

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.

Why this matters:

As biobanks + population sequencing projects scale into the hundreds of thousands (and millions), the bottleneck isn’t just inference. It’s exploration.

Feedback welcome 🌲

Truly, we harvest the truffulas standing on very tall shoulders.

On the visuals inspiration side: a huge thanks to @theo.io and Taxonium.

Taxonium showed the community that we can interactively explore enormous phylogenetic trees in the browser at pandemic scale.

Lorax brings a similar philosophy to ARGs.

Under the hood, Lorax runs on the incredibly powerful data model + API from tskit, developed by Jerome Kelleher and collaborators.

Tree sequences make it possible to store and traverse genome-wide genealogies efficiently, and Lorax uses that structure directly in the backend.

What does Lorax do?

It lets you dynamically explore tree sequences at massive scales - zooming through local trees, inspecting mutations, querying ancestry.

Built for *huge* datasets with up to millions of samples.

tl;dr:

Read about Lorax: www.biorxiv.org/content/10.6...

Try Lorax: lorax.ucsc.edu/view/1kg_chr...

Install Lorax: pypi.org/project/lora...

@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.

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.

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)

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

@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

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.

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

Thank you! I might need to steal this wonderful artwork!

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

More generally, my approach is a part of a "functional surveillance" paradigm where we infer changes in the functional properties of pathogens using genome sequence data.

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.

Comparison of allele frequency spectra for 3x coverage, with and without our bias model.

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...

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 ...

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!