Jim Shaw

@jim_elevator

Postdoc with Heng Li at Dana-Farber/Harvard Med School. Math PhD from @UofT with @YunWilliamYu. Working on methods for analyzing (metagenomic) sequencing data.

jim-shaw-bluenote.github.io Joined April 2018

356 Following 592 Followers 233 Posts

Latest posts 5

Jim Shaw @jim_elevator 3d

Update: I will be starting in Fall 2027 as an Assistant Professor at UNC Chapel Hill in the CS department.

My lab will build algorithms for large-scale microbial and meta-omics sequence analysis. I'll be recruiting PhD students. More info at jshaw-lab-compbio.github.io 1/2

jshaw-lab-compbio.github.io Research The JShaw Lab will be starting in the Fall of 2027 in the Department of Computer Science at the University of North Carolina at Chapel Hill.

Jim Shaw @jim_elevator Oct 12

Skani (github.com/bluenote-1577/…) is now v0.4.0!

Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes.

The database format has changed (breaks forward compatibility; watch out!).

github.com GitHub - bluenote-1577/skani: Fast average nucleotide identity (ANI) calculator for bacterial... Fast average nucleotide identity (ANI) calculator for bacterial genomes, MAGs, and contigs. Supports genome comparisons and large-scale database searches. - bluenote-1577/skani

Jim Shaw @jim_elevator Mar 27

Myloasm, our long-read metagenome assembler, is now published! w/ Max Marin & @lh3lh3

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers for helpful feedback.

Link: rdcu.be/famFj

Nature Biotechnology Verified account @NatureBiotech Mar 27

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3 go.nature.com/3PBEwvR

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Jim Shaw @jim_elevator Sep 7, 2025

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin and supervised by Heng Li @lh3lh3

bioRxiv Bioinfo @biorxiv_bioinfo Sep 7, 2025

High-resolution metagenome assembly for modern long reads with myloasm biorxiv.org/content/10.110… #biorxiv_bioinfo
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Jim Shaw @jim_elevator Sep 3, 2025

Stunning feat of applied sequencing bioinformatics. Congrats to the authors!!

Rayan Chikhi @RayanChikhi Sep 3, 2025

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024.0…

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