Yang I Li
@yang_i_li
Human genomics, gene regulation, RNA. Associate Professor @UChicago.
Excited to share our new preprint! CACTI boosts cQTL(or caQTL) discovery by leveraging correlation between nearby peaks, uncovering 51%-255% more signals than single-peak methods. Plus, a version of CACTI,CACTI-S, skips peak calling & works great when peak calling is challenging.
Improved chromatin QTL mapping with CACTI biorxiv.org/content/10.110… #biorxiv_genetic
Super thrilled to see @ZepengMu's work out in preprint form! See thread for summary of his thorough mapping and analysis of caQTLs from PBMC scATAC-seq data.
Excited to share the final chapter my PhD research on @medrxivpreprint! eQTLs only explain 30% of GWAS loci and 11% of trait heritability. Here we investigate if epigenetic QTL can provide new insights at the remaining GWAS loci. medrxiv.org/content/10.110…
Staff scientist position (computational): I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record. #sciencejobs
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.
We are excited to share our new preprint on LeafCutter2! Our new method clusters, quantifies, and classifies splice junctions and intron clusters according to their molecular functionality (e.g., protein-coding or NMD-splicing). @yang_i_li doi.org/10.1101/2025.0…
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
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).
Our work is out in AJHG! I wholeheartedly thank all the co-authors @marie_saitou @andywdahl @qbw_128 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.
📢Online now! 📰Allele frequency impacts the cross-ancestry portability of gene expression prediction in lymphoblastoid cell lines 🧑🤝🧑@marie_saitou @XuanyaoLiu & co cell.com/ajhg/abstract/…
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!
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 🙏
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.
🚨New Preprint Alert: Our work led by @JinghuiLi14637 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🧵👇
Protein-protein interactions shape trans-regulatory impact of genetic variation on protein expression and complex traits biorxiv.org/cgi/content/sh… #biorxiv_genetic
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…
I'm delighted to release the first half of my new open-access online textbook in human population genetics: web.stanford.edu/group/pritchar…
Really impressive paper from @skoyamamd, @pnatarajanmd, 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.
"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 @JExpMed doi.org/10.1084/jem.20…
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.
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…
Hmm, splicing might be important
Mutations in the U2 snRNA gene RNU2-2P cause a severe neurodevelopmental disorder with prominent epilepsy #RareDisease #Genetics #morbidgene medrxiv.org/content/10.110…
Very useful resource for validating methods for predicting mutational effects on splicing. Looking forward to using this in our next project!
We’re thrilled to announce the publication of SpliceVarDB: A comprehensive database of experimentally validated human splicing variants in @AJHGNews 🧬 📖 cell.com/ajhg/fulltext/… #splicing #GeneChat
We’re thrilled to announce the publication of SpliceVarDB: A comprehensive database of experimentally validated human splicing variants in @AJHGNews 🧬 📖 cell.com/ajhg/fulltext/… #splicing #GeneChat