Angli Xue

I am thrilled to have been awarded @nhmrc Investigator Grant (EL1). My research will be focused on understanding the genetic regulation of autoimmune diseases at the cellular level by building a population-scale single-cell atlas of immune cells. @GarvanInstitute @UNSWMedicine

Thrilled to share that my second project during my PhD has now been published in Nature! We introduced gsMap, a method that integrates genome-wide association studies and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

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Check out our scPrediXcan paper cell.com/cell-genomics/… Led by talented @Charles_Zhou12, supervised by @MengjieChen6 and me, with thanks to many contributors scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.

Using chromatin accessibility data from 170 human livers, @AJHGNews' latest study demonstrates that variants associated with transcription factor binding can be used to fine-map causal variants at disease-associated loci: cell.com/ajhg/abstract/… #ASHG

8 Resources to study Transcription factor binding, enhancers and histone modification distribution  1. ENCODE encodeproject.org

🧬Oz Single Cell Hackathon 2025🧬 Join us at the Uni of Sydney 19-21 May before the Oz Single Cell conference! Join us to tackle challenges in scMultiomics integration, viz & predictive modeling. Details 👉 petercallen.github.io/2025-OSC-hacka… #OzSingleCell #ozsinglecell25 @ozsinglecells

Most genetic variants associated with human disease are assumed to act by influencing gene expression. Expression is regulated at the cell level, but most resources linking variants to expression come from tissue-level data Two advances in the world of single-cell eQTLs🧵 1/9

📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬medrxiv.org/content/10.110… 🧵👇 (1/n)

gsMap paper online. Source code: github.com/JianYang-Lab/g…. Results visualisation website: yanglab.westlake.edu.cn/gsmap.

📣Excited to share my last postdoc paper with @soumya_boston on eQTL mechanisms depending on where the RNA is in the cell! @BrighamResearch @broadinstitute TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵👇

New online! Epigenetics and individuality: from concepts to causality across timescales bit.ly/4haZkCL

@ozsinglecells, #ozsinglecell25 has a new web address. ozsinglecell.com See the current list of invited speakers and stay tuned for registration details. Sponsors reach out to [email protected]

Super excited to share our new study from the @JD_Buenrostro Lab in @Nature! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: nature.com/articles/s4158…

The genetics of diabetes is likely better studied than that of any other complex human disease🧬 For reference, the largest GWAS for type 2 diabetes included 2,535,601 individuals (428,452 cases)❗️ 👇this review covers all aspects of human genetics in complex diseases

Gene expression is regulated at cell level. However, most eQTL studies use bulk-tissue RNAseq. scRNAseq is still very expensive and not scalable🧬 👉A new method (IBSEP) provides a framework for cell-type eQTL detection using bulk eQTL and scRNAseq summary stats📊 1/5🧵

nature.com/articles/s4158… (1/n) Ever wonder how transcription factors locate, "invade," and activate their enhancers during cell fate acquisition? 🧬🚀Check out our latest collaborative work with the Soufi lab, now published in @Nature!

Pre-existing chromatin accessibility and gene expression differences among naive CD4+ T cells influence effector potential cell.com/cell-reports/f…

Chromatin-based memory as a self-stabilizing influence on cell identity genomebiology.biomedcentral.com/articles/10.11…

🌟 Exciting news: The Leena Peltonen School of Human Genetics returns in 2025! We're excited to bring PhD students together with an all-star list of leaders in human genetics. 📅 July 27-31, 2025 📍 Wellcome Genome Campus, UK 📝 Apply by March 7 at lpshg.com

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…