Aaron Kwok

Flexible and efficient count-distribution and mixed-model methods for eQTL mapping with quasar Identifying genetic variants that affect gene expression, expression quantitative trait loci (eQTLs), is a major focus of modern genomics. Today, various methods exist for eQTL mapping, each using dif...

Very excited to share new work from my PhD on a new software package for eQTL mapping: quasar. The quasar software package is a C++ program designed to provide a flexible and efficient eQTL mapping. www.medrxiv.org/content/10.1...

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses!

@davisjmcc.bsky.social

www.biorxiv.org/content/10.1...

Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...

Biologist, stop putting UMAP plots in papers!

Blogpost here: simplystatistics.org/posts/2024-1...

EpiAgent: Foundation model for single-cell epigenomic data Large-scale foundation models have recently opened new avenues for artificial general intelligence. Such a research paradigm has recently shown considerable promise in the analysis of single-cell sequ...

EpiAgent: Foundation model for single-cell epigenomic data | bioRxiv
www.biorxiv.org/content/10.1101/2024.12.19.629312v1

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

What do GWAS and rare variant burden tests discover, and why?

Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?

Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)

www.biorxiv.org/content/10.1...

Many thanks to my supervisors @davisjmcc.bsky.social and Heejung who encouraged me to write this piece up! It is not a style of writing that I am the most familiar with so it took a lot of experimenting and also valuable feedback from @jeffreypullin.bsky.social on some earlier versions

New work! Wherein we (as in, the AVE ODIC working group) looked at clinical variant classification across genetic ancestry groups in gnomAD and AoU and what we found... is exactly what you might expect, after decades of Eurocentric research. But we also show there's a better way forward! 🧬🖥️

Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data? Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...

Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)

Luckily for you, @aaronkwc.bsky.social has!

Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?

Check it out 👇
www.biorxiv.org/content/10.1...

🧪🧬💻