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Pratik Katte

@pratikkatte.bsky.social
15 followers 19 following 7 posts

PhD in computational bio @UCSC • Understanding evolution• building ARGs at scale • lorax.ucsc.edu • pratikkatte.github.io

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Reposted by Pratik Katte
alex ioannidis @alexgioannidis.bsky.social · 03/09/2026
ARGformer is out in Bioinformatics! doi.org/10.1093/bioi... Just as PCA reduces dimensionality from genotypes, ARGformer can do this now for ARGs...yielding a representation that comes directly from inferred genealogical topologies & at a haplotype level across each individual genome.
doi.org
ARGformer: learning on ancestral recombination graphs with transformers
AbstractMotivation. Recent advances in inference of the ancestral recombination graph (ARG), which describes how segments of chromosomes trace back through
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Pratik Katte @pratikkatte.bsky.social · 04/09/2026
I’ve been reading statistical mechanics for molecular dynamics alongside coalescent theory for evolution, and noticed an idea they share: Sometimes, taking a system toward infinity makes it simpler to understand. Here’s a beautiful example from evolution ↓
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Reposted by Pratik Katte
Russ Corbett-Detig @russcd.bsky.social · 27/08/2026
Hard to beat days when I have time to walk/hike home.
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Pratik Katte @pratikkatte.bsky.social · 09/06/2026
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
lorax.ucsc.edu
Lorax
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Reposted by Pratik Katte
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026
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...
biorxiv.org
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Reposted by Pratik Katte
Pratik Katte @pratikkatte.bsky.social · 07/04/2026
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...
biorxiv.org
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Pratik Katte @pratikkatte.bsky.social · 07/04/2026
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...
biorxiv.org
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Reposted by Pratik Katte
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/03/2026
Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!
github.com
GitHub - RILAB/argprep: Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files.
Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep
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Reposted by Pratik Katte
Russ Corbett-Detig @russcd.bsky.social · 24/02/2026
@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.
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Molecular Biology and Evolution @molbioevol.bsky.social · 30/04/2025
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
doi.org
A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum
Abstract. The molecular processes that generate new mutations evolve, but the causal mechanisms are largely unknown. In particular, the relative rates of m
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Reposted by Pratik Katte
UC Santa Cruz Genomics Institute @ucscgenomics.bsky.social · 03/12/2025
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...
Next Wave of Faculty in Genomics Symposium call for submissions. Submission deadline January 15, 2026, Symposium date April 7, 2026
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