BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA biorxiv.org/content/10.110…

VEuPathDB data will remain available beyond the day NIAID meant it to go dark, but no new data will be brought in. Get involved with VEuPathDB in the conversation about the future of shared data.

Our parasite genome databases are really gone! The lack of communication and scientific vision ⁦NIH⁩ is hard to follow. Colossal mistake! ⁦parasitesrule⁩ ⁦British Society for Parasitology⁩ ⁦National Academy of Sciences⁩ ⁦Science Magazine⁩ ⁦nature⁩ ⁦NIAID News⁩

SVbyEye: A visual tool to characterize structural variation among whole genome assemblies biorxiv.org/content/10.110…

Check out SVbyEye: A new visualization tool to characterize structural variation among whole-genome assemblies (biorxiv.org/content/10.110…)

Fantastic new paper on phosphodiestarase inhibitors as potential treatment for cryptosporidiosis. Tour de force paper from screening, to modelling, to genetic target validation. Great work from the lab of Chris Huston University of Vermont nature.com/articles/s4146… Trends in Parasitology

Welcome back! VEuPathDB resources are back online today! We will continue to provide bioinformatics services under a new organizational structure. Read more here: veupathdb.org/veupathdb/app/…

Great news ... but a stable model has to be found ... and I don't feel that we should give @NIAIDFunding a free pass on this. I am still puzzled that one would cut funding to something we urgently need and replace it with something few of us have asked for or need for.

Building pangenome graphs biorxiv.org/content/10.110…

v0.8.1 dorado bug fix release 🐛⛔️ github.com/nanoporetech/d…

We just launched Circa 2.0! Create beautiful circos plots in minutes, without a single line of code. You can try it for free with sample data now! circa.omgenomics.com

Gordon Research Seminar in Tropical Infectious Diseases, Lucca, Italy, Feb 1-2 2025. Speaker Abstract Deadline: October 28, 2024. Excellent opportunity for early career scientists to present your projects on Tropical Infectious Diseases. Check it out: grc.org/tropical-infec…

Characterization of a new protein (LiaY) involved in phospholipid remodeling in DAP-R enterococci. Work from April Nguyen, MD PHD and now proud IM resident at BCM and future ID doc!! #IDWeek2024 insight.jci.org/articles/view/…

SKA is no longer just a preprint! Thanks to John Lees, Romain and Johanna especially for taking it on, making it better and getting it published!

noMapper: A mapping-free natural language processing-based technique for sequence search in nanopore long-reads bmcbioinformatics.biomedcentral.com/articles/10.11…

Targeted CRISPR Screens Reveal Genes Essential for Cryptosporidium Survival in the Host Intestine (full thread in the other place!) Lucy Watson biorxiv.org/content/10.110…

The Ken Kennedy Institute, OIT Rice, and NIH NIAID P01AI15299 are offering an opportunity on reading, assembling, analyzing, and deciphering #MicrobialGenomes. Registration is open; limited spots are available. Ticket sales end January 8th: lnkd.in/gAg-zMzQ.

BEAST GAME EPISODE 3 IS OUT NOW! To celebrate, I'm giving away $100,000 total to 10 random people who like and retweet this post! Go watch it here: amazon.com/beastgames

Really proud to share the PhD thesis work of Rui Xiao. One day, while using long-read RNA-seq for annotation of the genome, he discovered polycistronic transcripts in Cryptosporidium parvum. Read all about it at: biorxiv.org/content/10.110…

Happy to work the amazing team at KRG to get this out for the Cryptosporidium research community! Rodrigo Baptista, PhD Yiran Li