Darius

Check out largest scale analysis of bacterial DNA polymerases! Diversity and distribution of bacterial DNA polymerases academic.oup.com/nar/article/54…

@wet2drylab Sure 😉

Now looking forward to work with DNA language models 👏🙏congratulations @DariusBio and your teams 👏

Finally published. Still SotA. TemStaPro: protein thermostability prediction using sequence representations from protein language models academic.oup.com/bioinformatics…

@mkrupovic Well deserved! Congrats.

Not all CRISPR-Cas systems cleave nucleic acids! Our recent study at @NAR_Open explores miniature Cas12m effectors, showcasing a nuclease-free DNA interference mechanism that can be utilized in the development of compact base editors. academic.oup.com/nar/advance-ar…

GTalign: High-performance protein structure alignment, superposition, and search biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

At #NeurIPS conference to find new ideas on using AI in computational biology. Grateful to @BAFFScholarship for financial support!

@duguyuan @sokrypton ESM-1b has a protein length limit (<1023 aa), thus, we use ProtTrans in our works. I'll guess we'll move to ESM-2 or your method soon 🙂.

@DariusBio @sokrypton thanks, in this manuscript, we have not compared to ProtTrans but mainly with ESM family as they share the same experimental settings. We will consider add ProtTrans later not sure since there are a few differences with this model. ProtTrans-BERT's comparison makes sense.

A novel protein language model has outperformed Meta ESM models in 10 protein function tasks. Huge thanks to @sokrypton his invaluable help and contribution. Sergey deserves authorship recognition. biorxiv.org/content/10.110…

Origins and evolution of Rep-encoding ssDNA (CRESS-DNA) viruses - nature.com/articles/s4146… Developing an AI predictor to investigate thermostability of Cas9/Cas12/Cas13 proteins - biorxiv.org/content/10.110…

If you're interested and want to familiarize with what we do, please check out our notable works: Structure and sequence analysis of Cas12/TnpB family - nature.com/articles/s4158… Diversity of Cas9 PAM-interacting domain - nature.com/articles/s4146…

We have a #PhD position in #bioinformatics to study diversity, origins and evolution of CRISPR-Cas effector proteins ( tinyurl.com/uuwsrukp ). It is desirable that the candidate has a degree in life sciences and is familiar with programming.

We are happy to report @Nature the cryo-EM structures of IS200/IS605-associated TnpB nuclease by Sasnauskas, Tamulaitiene, Druteika et al! nature.com/articles/s4158…

@wet2drylab Thanks!

@DariusBio Congratulation @DariusBio

Congrats to Ieva Pudžiuvelytė, Kliment Olechnovič and @CasZyme team on developing TemStaPro - a method to predict thermostability of proteins using protein language models: doi.org/10.1101/2023.0… #LanguageModels #ML #Bioinformatics

Thermal stability varies in C2EPs. More than a half of the members of groups Cas12b, Cas12f1, Cas12f2, Cas12g, TnpB2 and TnpB-Kra have predicted temperatures of ≥50 ℃. In contrast, members of Cas12a, Cas9, and Cas13 groups might function at lower temperatures. #CRISPR

The program was tested on CRISPR-Cas Class II effector proteins (C2EPs) that have experimentally-characterized temperatures and in most cases (35 out of 38) predicted thermostability varied no more than 10 ℃.