Check out our just-published AI-based (temporal convolutional network) system, PSAURON, for predicting eukaryotic proteins, from @markusjsommer. We used a similar method in BALROG, our bacterial gene finder. Note: the "P" is silent in PSAURON 🤣 https://t.co/WBBS7vDezh
@nickdimonaco@StevenSalzberg1 Since it scores each amino acid in the protein (with a fairly small receptive field), any piece that looks like a protein would likely get a high score regardless of the overall structure, so definitely not the best tool to detect relatively small differences in isoforms
“One Model to rule them all, One Model to find them, One Model to score them all, and in the Paper cite them.” 🧬🧙♂️The eye of PSAURON seeks spurious proteins in your genome annotation! New paper with Aleksey Zimin and @StevenSalzberg1 https://t.co/xZJdA196wu
@StevenSalzberg1 Closed source code? 10 free predictions per day? That seems a bit too evil, even for a dark lord. Unleash the power of PSAURON via “pip install psauron” Code freely available at GitHub https://t.co/tSMME7Kai8
Three @biorxivpreprint releases from my lab last week, and one more today! From postdoc @markusjsommer, his new eukaryotic gene recognizer, PSAURON (the "p" is silent), a successor to his bacterial gene finder Balrog #LOTR https://t.co/z5HfQrmAMz
@JakobHeinz9@StevenSalzberg1@NatlAquarium One short year (and one talented former undergrad intern) later we are a bit closer to understanding our delicate and essential coral ecosystem.
Mystery disease decimating coral reefs off the coast of Florida? Sounds like a job for @JakobHeinz9 and novel metagenomics methods in the @StevenSalzberg1 lab, with guidance from Stephanie Rosales & Lindsay Huebner! Check out the paper! https://t.co/ZVn5pDRXgE
@JakobHeinz9@StevenSalzberg1 Thank you to the @NatlAquarium Animal Care and Rescue Center for raising awareness of coral disease. This collaboration would not have happened without the tour I took in Oct. 2022 (shout-out to Duncan!)
How does alternative splicing regulate protein structure to enable cell-type-specific protein functions? With @momeara, we used AlphaFold2 + scRNA-seq to investigate this question in our latest preprint. https://t.co/JnRhcGNipD🧵
Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With @elapertea@av_sparrow @thesteinegger @markusjsommer@ErdogduBeril @IliaMinkin and others: https://t.co/pDvDfPjtcT
watch out SpliceAI, there's a new kid on the block, Splam! More accurate at predicting splice sites and much faster too. Check out the code and the pre-print in the thread from @KuanHaoChao below.
ORFanage is new system by @av_sparrow@ErdogduBeril and @elapertea that finds protein-coding regions in RNA-seq assemblies, guided by annotation. Just published today in @NatComputSci:
https://t.co/mumLqMN4BV
Accurate DTU detection in complex diseases with SPIT by @ErdogduBeril,@stephaniehicks,@StevenSalzberg1,@elapertea! Findings include previously unreported DTU events in 6 genes associated with schizophrenia. Also available on Google Colab -> Learn more at https://t.co/9hmVgzEZmW
ORFanage is new system by @av_sparrow@ErdogduBeril and @elapertea that finds protein-coding regions in gene annotation, esp. in RNA-seq assemblies. See what it can do in our new preprint https://t.co/pITSPpHy81
first paper of 2023 for us: a gap-free, fully annotated genome of a southern Han Chinese individual, led by @KuanHaoChao, with @AlekseyZimin5 and @elapertea. We used the #T2T CHM13 genome to fill gaps https://t.co/VFv7ZmCrXY
The final version of our paper on using protein structure to determine functionality is out in @eLife: https://t.co/Tuyx3hKXuk. Some of the prettiest figures we've had in any recent paper, like the one here. Led by @markusjsommer, plus @elapertea @thesteinegger et al.