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Much of the impact of alternative splicing is mediated by nonsense-mediated decay-induced changes in gene expression rather than diversification of the proteome Nature Genetics Yang I Li nature.com/articles/s4158…

We’re thrilled to announce the publication of SpliceVarDB: A comprehensive database of experimentally validated human splicing variants in AJHG 🧬 📖 cell.com/ajhg/fulltext/… #splicing #GeneChat

Very useful resource for validating methods for predicting mutational effects on splicing. Looking forward to using this in our next project!

Hmm, splicing might be important

Yang I Li @BenjaminFair3 Carlos Buen Abad very interesting. Our 10y effort (though very low throughput) of characterizing many isoform-level functions seems to agree with that. isoforms differ in stability either at RNA or PROTEIN levels to affect total protein outputs 👇sciencedirect.com/science/articl… nature.com/articles/s4146…

Changes in RNA abundance are most often attributed solely to changes in RNA production (transcription). Remember RNA degradation. Changes in RNA abundance also reflect changes in RNA degradation.

"stay curious and excited about science, especially about what’s happening outside your field. You never know where your next good idea will come from." -Judy Lieberman Journal of Experimental Medicine doi.org/10.1084/jem.20…

Really impressive paper from Satoshi Koyama, Pradeep Natarajan, and co. looking at rare exome variants in 1.15M (MVP, UKB, AoU) individuals for blood lipids. Fig. 2a provides pretty strong support for including cryptic splice variants (from Illumina's SpliceAI) in gene-based tests.

Two new chapters from my free online book in human genetics out this weekend! These complete Part 3 of the book, on human population structure and history: 3.3: Inferring human prehistory from genetic data [this thread] 3.4: Ancient DNA [next thread] web.stanford.edu/group/pritchar…

🚨New Preprint Alert: Our work led by Jinghui Li is up on bioRxiv. We re-analyzed large maps of trans-pQTLs, and found that protein–protein interactions shape trans-regulatory impact of genetic variation on protein expression and complex traits. A brief thread🧵👇

We found that proteins with trans-pQTLs but without cis-pQTLs are under much stronger selective constraints than those with cis-pQTLs, and they are highly enriched in GWAS loci. Therefore, trans-pQTLs are an important resource for interpreting GWAS loci.

Looking for postdoc candidate, who is interested in RNA-protein interactions, RNA localization and gene regulation. Candidates with backgrounds in biophysics (particularly single-molecule imaging), chemical biology and cell biology are all welcome to apply! Please help retweet 🙏

My guidelines for exploratory data analysis

I am very excited to share my study, trans-regulation of proteome through protein-protein interactions, at #ASHG2024 ! Please check my poster number 6077 on Wednesday (11/6) afternoon!

Our work is out in AJHG! I wholeheartedly thank all the co-authors marie.saitou Andy Dahl Qingbo Seiha Wang for their time and effort! All four of us started our own labs between 2019 and 2021 and the pandemic didn't make things easy. Super proud of everyone.

Super thrilled to see Zepeng (Phoenix) Mu's work out in preprint form! See thread for summary of his thorough mapping and analysis of caQTLs from PBMC scATAC-seq data.

My Chinese American colleagues in Texas public universities such as the whole U Texas including MD Anderson are now required to report family visit trip to China ahead of trip, and provide a post-travel briefing detailing the trip. Land of the free (your experience may differ).

Science’s secret weapon is that it cannot be subject to authority. There is no hierarchy when making discoveries which only happens when scientists treat each other as intellectual peers. #standupforscience

Happy to share our update to LeafCutter, which allows the study of unproductive splicing from short-read RNA-seq. We report findings from analysis of 3 large datasets (GTEx, multi-tissue development in 7 species, Alzheimer brains from AD FunGen consortium). See thread by Carlos.