iiinova — where your digital self keeps evolving

Reposted by Tim Dunn

Fulcrum Genomics @fulcrumgenomics.com · 05/08/2026

A CRISPR off-target search cannot report a sequence it was never given. @ameynert.bsky.social explains how DivRef brings common human variants and haplotypes into the search space—and how her rebuild complements @timd.one work on Sassy. Read Alison’s post: blog.fulcrumgenomics.com/p/a-crispr-o...

blog.fulcrumgenomics.com

A CRISPR off-target search is only as good as the sequences it searches

Rebuilding DivRef so CRISPR off-target searches can account for human variation

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Tim Dunn @timd.one · 22/07/2026

CRISPR off-target search can find the right locus while hiding plausible alignments within it. I wrote about how Sassy v0.2.5 uses recursive backtracking to report every reasonable alignment—more than 9× as many in under 30 seconds. blog.fulcrumgenomics.com/p/why-crispr...

blog.fulcrumgenomics.com

Why CRISPR Off-Target Search Should Report Multiple Alignments Per Locus

How Sassy enumerates every reasonable alignment without sacrificing runtime

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Reposted by Tim Dunn

Fulcrum Genomics @fulcrumgenomics.com · 31/03/2026

We built fgbio years ago to support UMI-aware sequencing. As datasets grew, the single-threaded design started to show its limits. fgumi is the next iteration: same expected outputs, rewritten for performance and scale. github.com/fulcrumgenom... Blog post details below👇

github.com

GitHub - fulcrumgenomics/fgumi: High-performance UMI tools for NGS data analysis

High-performance UMI tools for NGS data analysis. Contribute to fulcrumgenomics/fgumi development by creating an account on GitHub.

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Reposted by Tim Dunn

Matt Holt @holtjma.bsky.social · 16/09/2025

Question for the rust-bio folks: any recommendations on a dynamic de-bruijn graph crate? I found some DBG crates but they seem to be A) unmaintained and/or B) not for dynamic applications.

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Tim Dunn @timd.one · 16/05/2025

Finally, some better syntax parsing in Nextflow! seqera.io/blog/nextflo...

The new syntax parser highlights exactly where in the code a compilation error is

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Tim Dunn @timd.one · 06/04/2025

Finally got around to fixing the main limitation of the current vcfdist release: exploding memory usage and runtime in regions with high-density variants. A new `--max-supercluster-size` parameter limits this. Release v2.6.0 is out on [Github](github.com/timd1/vcfdist), DockerHub, and bioconda!

github.com

GitHub - TimD1/vcfdist: vcfdist: Accurately benchmarking phased variant calls

vcfdist: Accurately benchmarking phased variant calls - TimD1/vcfdist

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Reposted by Tim Dunn

Ragnar {Groot Koerkamp} @curiouscoding.nl · 27/03/2025

New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes

Schematic figures showing global pairwise alignment algorithms

Schemetic figures showing various modes, such as semi-global, local, and extension alignment

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Reposted by Tim Dunn

Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · 03/03/2025

🧪🚨 NSF's Directorate for STEM Education (EDU) has halted making nearly all new awards since inauguration day. Among *many* other things, EDU runs the Graduate Research Fellowship Program (GRFP). We need to protect the education & training of the next gen of scientists #StandUpForScience Thread👇🧵

Graph between 1/20 and 2/28 of fiscal year 2024 and 2025 new awards in the EDU directorate.

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Reposted by Tim Dunn

openRxiv @openrxiv.bsky.social · 11/03/2025

openRxiv has arrived! We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences. openrxiv.org/introducing-... #openRxiv #OpenScience #Preprints #bioRxiv #medRxiv

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Reposted by Tim Dunn

Zamin Iqbal @zaminiqbal.bsky.social · 24/02/2025

Roche's SBX sequencing by expansion - preprint out! www.biorxiv.org/content/10.1...

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Reposted by Tim Dunn

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 08/02/2025

Another assault on US competitiveness at a time when biomedicine is roaring with innovation, an own-goal in a high-stakes international tournament. Of course the real losers are American people needing medicines and cures. www.washingtonpost.com/health/2025/...

washingtonpost.com

NIH cuts billions of dollars in biomedical funding, effective immediately

The move halts a large slice of money for most universities and research institutions virtually overnight, imperiling vital research in everything from cancer to heart disease.

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Reposted by Tim Dunn

Thiago Carvalho @cyrilpedia.bsky.social · 05/02/2025

'Almost all of these actions are illegal, and many are actually unconstitutional. The administration is obviously daring someone to try to stop them, and as mentioned in Part Six below, right now that's the Federal Judiciary.' www.science.org/content/blog...

science.org

Revised and Extended: What's Happening Inside the NIH and NSF

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Tim Dunn @timd.one · 30/11/2024

Finally took the time to migrate from Twitter/X over to BlueSky!

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