Learning more about APOE differences in the cell types of the brain 🧠

I presented "APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease" from @zhaonaa.bsky.social at our team journal club, check it out!

doi.org/10.1016/j.ne...

▶️ youtu.be/L4J9jFS-Pic

Hi! Check my journal club talk: smart ML method to deconvolute pooled snRNA-seq using sex-specific expression🧬

Thanks @daylab.bsky.social & @rphillips3.bsky.social for this approach🙌

🎥 youtu.be/zpeCFwYfV3o
🛝 speakerdeck.com/manishabarse

#snRNAseq #ML #Bioinformatics @lieberinstitute.bsky.social

This paper was an exciting culmination of a lots of exploration with #deconvolution ! Check-out my blog post on this work for the TL;DR version: lahuuki.github.io/posts/2025-0...

We also propose and evaluate a new method for selecting cell type specific #markergenes for deconvolution: #MeanRatio implemented in #DeconvoBuddies
@bioconductor.bsky.social #rstats
🛠️ research.libd.org/DeconvoBuddi...

To assess method accuracy, we compared the estimated proportions to the #RNAScope proportions for correlations and rmse 📈 #BisqueRNA and #hspe were the top performers 🏆

We ran #deconvolution on the 110 bulk RNA-seq samples, with six selected methods: #DWLS, #bisqueRNA, #MuSiC, #BayesPrism, #hspe, and #CIBERSORTx. The methods returned a wide range of proportion estimates 📊

The resulting cell type proportions had a large range across the different #DLPFC samples, and were not always correlated with the paired #snRNAseq proportions ⚠️

We designed an #RNAScope/IF experiment to measure six broad cell types in the #DLPFC. We used #HALO from Indica Labs to count the occurrence of the cell types across the tissue sections 🔬 #ImmunoFlourescence (awesome work from Kelsey Montgomery)

Testing these #deconvolution methods was made possible by a really cool multi-assay dataset from consecutive slices of #DLPFC tissue blocks 🧠1. Bulk RNA-seq 🧬 2. #snRNAseq as the reference 🦠 3. #RNAScope serving as a orthogonal measurement of cell type proportions 🔬

This #deconvolution project was a group effort! Thanks to the whole team including: @shkwon-bcmbneuro.bsky.social @nick-eagles.bsky.social @daiannaglez.bsky.social @metamaden.bsky.social @stephaniehicks.bsky.social @kr-maynard.bsky.social @lcolladotor.bsky.social

Hey #deconvolution fans! 👀 We’ve got an exciting new publication for you: a benchmark of 6 popular deconvolution methods on a multimodal human brain #DLPFC dataset 🧠🧬
Now out in Genome Biology: doi.org/10.1186/s130...

@lieberinstitute.bsky.social @jhubiostat.bsky.social

Check out my journal club presentation on the crumblr pre-print from Hoffman and Roussos, a new method to analyze differential composition in #singlecell data 🍪
Looks very useful for single cell RNA-seq data with case/control study design 🤔
📄 doi.org/10.1101/2025...
▶️ www.youtube.com/watch?v=Hi5E...

Check our recent video "[2025-01-29] R/Bioconductor-powered Team Data Science: TLDR version 2025"
youtu.be/alL-g2roXxM

We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻

Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...

👥 go.bsky.app/53gy4UP

Reading the instructions first next time 😅

completed "Ceres Search" - Day 4 - Advent of Code 2024 #AdventOfCode adventofcode.com/2024/day/4

I've completed "Red-Nosed Reports" - Day 2 - Advent of Code 2024 🔴 #AdventOfCode adventofcode.com/2024/day/2

I decided to make a starter pack for members/alumni of @lieberinstitute.bsky.social "Data Science Team 1" 💻

Initially led by @aejaffe.bsky.social until 2020/09; then by me. In 2024, the team became part of the Division of Translational Neuroscience led by @martinowk.bsky.social

go.bsky.app/53gy4UP

Hi Bluesky! 👋 I'm Louise Huuki-Myers I work on transciptomic research in the brain 🧠🧬 @lieberinstitute.bsky.social and am Studying for my PhD in #neuroscience at the University of Cambridge. Excited to share more about neurosci research and #Rstats here 🦋