Nick Dimonaco
@nickdimonaco.bsky.social
PostDoc in 'Computational Biology' | Queen's University Belfast | Abersytwyth University | github.com/NickJD
Reposted by Nick Dimonaco
It was really fun and hopeful, describing the potential for a better future with @nickdimonaco.bsky.social (QUB) and Martin Vickers (JIC). Although bioRxiv doesn't accept review paper preprints, here it is on Figshare figshare.com/articles/pre... 6/6
Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution
For the past 25 years, genomic data has been distributed in two key file formats, FASTA and GFF. These files are used across nearly all genomic analyses and encode both the data of genomic sequences ...
figshare.com
December 1, 2025 at 7:07 PM
It was really fun and hopeful, describing the potential for a better future with @nickdimonaco.bsky.social (QUB) and Martin Vickers (JIC). Although bioRxiv doesn't accept review paper preprints, here it is on Figshare figshare.com/articles/pre... 6/6
PyamilySeq (built for another purpose 😇) reveals how tiny tweaks (output flags, CPU/mem, decimal precision) warp core/accessory calls and how pangenome tools spit out misleading 'representative' sequences. If you care about transparent, reproducible gene clustering & pangenomes, check it out!
July 22, 2025 at 10:42 AM
PyamilySeq (built for another purpose 😇) reveals how tiny tweaks (output flags, CPU/mem, decimal precision) warp core/accessory calls and how pangenome tools spit out misleading 'representative' sequences. If you care about transparent, reproducible gene clustering & pangenomes, check it out!
Reposted by Nick Dimonaco
Using these proteins as a base, the magnificent Matt Schmitz developed a tool to study the prevalence of proteins within the human gut. This is InvestiGUT: github.com/Matt-Schmitz.... To allow its instant use we have made InvestiGUT accessible on our Galaxy instance: protologger.bi.denbi.de
GitHub - Matt-Schmitz/InvestiGUT: Lineage-specific microbial protein prediction facilitates exploration of protein ecology within the human gut.
Lineage-specific microbial protein prediction facilitates exploration of protein ecology within the human gut. - Matt-Schmitz/InvestiGUT
github.com
April 4, 2025 at 12:03 PM
Using these proteins as a base, the magnificent Matt Schmitz developed a tool to study the prevalence of proteins within the human gut. This is InvestiGUT: github.com/Matt-Schmitz.... To allow its instant use we have made InvestiGUT accessible on our Galaxy instance: protologger.bi.denbi.de
It isn't technically wrong... Just not technically correct either.. No? (I do not call myself a microbiologist!)
March 31, 2025 at 6:38 PM
It isn't technically wrong... Just not technically correct either.. No? (I do not call myself a microbiologist!)
Please mark this with a trigger warning.
November 21, 2024 at 5:00 PM
Please mark this with a trigger warning.
Reposted by Nick Dimonaco
With rORForise (similar to ORForise) we aim to enumerate/tabulate all the possibilities, and to use these to let users know which predictors are more suitable for their task. It's still work in progress but here's early release code to keep an eye on github.com/NickJD/rORFo... (preprint coming soon)
GitHub - NickJD/rORForise: Read-based gene coverage evaluation
Read-based gene coverage evaluation. Contribute to NickJD/rORForise development by creating an account on GitHub.
github.com
November 15, 2024 at 10:15 AM
With rORForise (similar to ORForise) we aim to enumerate/tabulate all the possibilities, and to use these to let users know which predictors are more suitable for their task. It's still work in progress but here's early release code to keep an eye on github.com/NickJD/rORFo... (preprint coming soon)