Tim Dunn

New vcfdist paper on bioRxiv! Key Takeaways: 1) Jointly evaluating small and structural variants decreases measured FN+FP by 20-50% 2) 43-92% of phasing flip "errors" are FP due to variant representations More below Code: github.com/TimD1/vcfdist Paper: biorxiv.org/content/10.110…

Climate experts were increasingly saying that keeping heating below 1.5C is near impossible, yet it remains the global goal. So I asked hundreds of top IPCC scientists what they thought. What they said shocked even me… 🧵 1/n #ClimateCrisis

🚨Apparently all NIH Study Sections have been suspended indefinitely. For those who don’t know, this means there won’t be any review of grants submitted to NIH Depending on how long this goes on for, this could lead to an interruption in billions in research funding.

Finally took the time to create a BlueSky account, you can follow me @timd.one

After nearly six months waiting for review, our extension to vcfdist was finally published in BMC Genome Biology this week! genomebiology.biomedcentral.com/articles/10.11…

Jointly benchmarking small and structural variant calls with vcfdist genomebiology.biomedcentral.com/articles/10.11… 🧬🖥️ github.com/TimD1/vcfdist

I'm thrilled to announce that I successfully defended my PhD thesis today, "Improving select applications of long-read DNA sequencing"! After graduating, I'll be joining @fulcrumgenomics as a Senior Bioinformatics Scientist. I can't wait to see what this next chapter brings!

Excited to see a new benchmarking analysis using vcfdist!

Mandatory reading and surprising results from Michael Hall and colleagues - much better SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work biorxiv.org/content/10.110…

Finally got around to adding vcfdist into bioconda. Installation is now as easy as `conda install vcfdist`. github.com/TimD1/vcfdist

Google is donating $1M to the @rust_foundation to improve C++/Rust interoperability. This is big news!

Excited to announce that our accompanying paper on HiPhase has been published today, I'll highlight some of the additions in this thread! #PacBio #HiFi “HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing”: doi.org/10.1093/bioinf…

Jointly benchmarking small and structural variant calls with vcfdist biorxiv.org/content/10.110…

Jointly benchmarking small and structural variant calls with vcfdist biorxiv.org/cgi/content/sh… #biorxiv_bioinfo