Tim Dunn
@timd.one
Staff Bioinformatics Scientist at Fulcrum Genomics. Recent UMich CS PhD grad. Views are my own. https://timd.one
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...
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
blog.fulcrumgenomics.com
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...
Why CRISPR Off-Target Search Should Report Multiple Alignments Per Locus
How Sassy enumerates every reasonable alignment without sacrificing runtime
blog.fulcrumgenomics.com
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 - 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.
github.com
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.
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 - TimD1/vcfdist: vcfdist: Accurately benchmarking phased variant calls
vcfdist: Accurately benchmarking phased variant calls - TimD1/vcfdist
github.com
New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes
🧪🚨 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👇🧵
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
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/...
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.
washingtonpost.com
'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...
Revised and Extended: What's Happening Inside the NIH and NSF
science.org
