We have a machine learning scientist opening in my group to tackle problems in gene regulation and single cell genomics! Apply here calicolabs.com/careers?gh_jid…

Yifei HUANG (Yifei Huang), our dear colleague, Asst Prof Penn State Biology, passed away from cancer in October at the age of 40. We are collecting donations for his daughter's education. All donations are tax-deductible. Penn State Research Please RT. gofund.me/ef82effe

Links to the recordings: Day 1: nih.zoomgov.com/rec/play/9o8-x… nih.zoomgov.com/rec/play/YZutj… Day 2: nih.zoomgov.com/rec/play/V1meR… nih.zoomgov.com/rec/play/tr_e8…

A few thoughts on the recent set of papers torture testing genomic deep learning for predicting individual-level gene expression [ pubmed.ncbi.nlm.nih.gov/38036790/ , pubmed.ncbi.nlm.nih.gov/38036778/ , pubmed.ncbi.nlm.nih.gov/38036789/ ]. First a brief summary 🧵: x.com/SashaGusevPost…

It's 2024 and there are many great tutorials for single-cell analysis. One frustrating thing to follow any R-based tutorial is package installation (of course)! With all sorts pkg managers, it should be easy to install pkgs, right? Well, no, especially if you are a beginner. 1/9

Excited to share our latest work (nature.com/articles/s4146…) in Nature Communications. We conducted TWAS focusing on blood pressure traits using PUMICE, complemented by multi-omics follow-up analyses. Kudos to Xiaoguang Xu, James Eales, and Maciej Tomaszewski for leading this amazing work.

Hi friends! We are looking to hire a postdoc to join our group Ray and Stephanie Lane Computational Biology Dept. CMU School of Computer Science, to work on exciting projects related to identifying disease genes by integrating GWAS and functional genomics. mzhanglab.github.io/openings/

Excited to share our latest work in Nature Communications. We extended our previous PUMICE's framework (nature.com/articles/s4146…) to allow the utilization of publicly available single-cell eQTL summary statistics. Kudos to Lida Wang and Dajiang Liu for leading this important work.

Really excited to share our latest work in Nature Communications! We developed a method called EXPRESSO to conduct TWAS using single-cell eQTL summary statistics. Special thanks to Dajiang Liu for the guidance and the help from Poom Khunsriraksakul 🇹🇭 and lab members.

Excited to share our latest work describing a spatial mixed linear effect (SMILE) model that refines the estimates of genetic heritability and air pollution causal effects using EHR in Nature Communications. Huge thanks to Dan McGuire and my PI Dajiang Liu! nature.com/articles/s4146…

Thrilled to share our work to analyze insurance claim datasets to dissect genetic and environmental contributions to 1083 human diseases. We developed a spatial linear mixed model SMILE, using geolocations as a proxy for the environment. nature.com/articles/s4146…

Excited to share our recent publication in Communications Biology! We explored how genetic variation shapes T cell receptor (TCR) diversity and its impact on diseases such as autoimmune disorders and cancer. nature.com/articles/s4200… (1/11)

I am happy to share our new work that predicts the progression of autoimmune diseases, integrating EHR and GWAS datasets Nature Communications . nature.com/articles/s4146…

Beyond excited to share this new paper with all of you . It's the most fun we've ever had. We figured out how to study a latent index driving partner choice without measuring it directly🥂 Qinwen Zheng Preprint📰: biorxiv.org/content/10.110… Sumstats⬇️: qlu-lab.org/data.html

🧠🔥"Put on your 3D glasses...oh wait, you don't need them!"😝 Brain Metabolome just got an upgrade-why look at slices when you can see the whole picture in 3D? Check out our latest work in Nature Metabolism .🚀🔬 🔗doi.org/10.1038/s42255…

I'm excited to share a wonderful collaboration with Lida Wang: JOBS integrates bulk and single-cell eQTLs to boost eQTL discovery. Integrated with GWAS, it identified more disease-linked loci for 14 immune disorders & fueled drug-repurposing. #immunology #drugdiscovery #genomics

Check out our scPrediXcan paper cell.com/cell-genomics/… Led by talented Yichao (Charles) Zhou, supervised by Mengjie Chen and me, with thanks to many contributors scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.