Our RNA-linked CRISPR approach is now published! Work led by fantastic graduate student in the lab, Patrick Nugent.

The era of coding agents is here. How do we approach this as scientists? Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned ( https://t.co/LpeqQ58xT2) about how to leverage agentic coding to do rigorous science. https://t.co/N4bfZVkVyl

The Mahan postdoctoral fellowship offers 21 months of support to develop your own research with Fred Hutch computational biology faculty-- lots of excellent labs to choose from! Apply: https://t.co/pzPWKcbIjr Faculty:

We are hiring a postdoc to work on ribosome quality control and ribosome-mediated stress signaling. Start date is expected to be Fall- Winter 2025. More information can be found here:

Biorxiv preprint:

Excited to share the work of postdoc Rachael Bakker in collaboration with @C_P_Lapointe lab! We show that RNA base editors can be repurposed for deep mutational scanning of RNA-RBP interactions at scale both in vitro and in vivo.

Our latest preprint, regarding endogenous RQC substrates, is online! This is a wonderful collaboration with Taku Ito lab from RIKEN BDR!

We think this GitHub-based workflow will make bench research more reproducible, collaborative, and efficient—saving time and money. We found this to be the case after 9+ years of using it in our group!

You can find examples of these steps and more in our demo GitHub repository: https://t.co/qIjGiGXZWd. Feel free to copy it to your GitHub account, ping us for help, or provide feedback by opening a new issue in the repo.

3. Use GitHub packages to share software environments for data analysis, writing manuscripts, and preparing grant proposals. https://t.co/XpQl8xc7mh

2. Use Git version control to track lab notebooks, data analysis code, figures, and tables. https://t.co/f3HDHDgvU3

1. Use GitHub issues to brainstorm ideas, plan experiments, troubleshoot steps, and discuss data. https://t.co/vxf9UFQyBP

In our new manuscript with @klathrin_chen and Maria Toro-Moreno https://t.co/7mcy8AbvG1, we show how wet-lab research groups can use GitHub to replace electronic lab notebooks, Slack-like collaboration tools, and software package managers. Here are the first three steps:

Thanks to our wonderful co-authors and collaborators including @klathrin_chen and @HsiehLab ! 11/

You can find more details in our bioRxiv manuscript: https://t.co/73UcUsBpdS. 10/

We think that ReLiC will be broadly useful for studying all aspects of RNA metabolism in different cell types and states. ReLiC plasmids can be publicly requested at https://t.co/dQ73VIo8Qz. 9/

Using ReLiC, we find that that the ribosome collision sensor protein GCN1 mediates the cellular response to the anti-leukemic drug homoharringtonine (HHT). 8/

We can perform chemogenomic ReLiC screens to identify factors that mediate the cellular response to different drugs. 7/

Isoform-specific ReLiC shows that differenet SF3b complex members have distinct effects on intron retention and exon skipping. 6/

We can use ReLiC to identify factors that regulate different alternative splicing events simply by changing RT-PCR primers! 5/