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Louise Huuki-Myers

@lahuuki.bsky.social
293 followers 577 following 42 posts

Staff Scientist at LIBD studying brain transcriptomics with #RStats 🧠 PhD Student in Neuroscience at University of Cambridge lahuuki.github.io

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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
And of course thanks to @lcolladotor.bsky.social @kr-maynard.bsky.social @martinowk.bsky.social
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
Thank you to all of our collaborators at the @lieberinstitute.bsky.social for their excellent work on this project! 🧑‍🔬 @heenadivecha.bsky.social @svitlanabach.bsky.social @madelinevalentine.bsky.social @nick-eagles.bsky.social @berniejmulvey.bsky.social and UK collaborators @jamesrevans.bsky.social
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two men sitting next to each other with the words " teamwork makes the dream work " on the bottom
ALT: two men sitting next to each other with the words " teamwork makes the dream work " on the bottom
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
This dataset is paired with a spatial transcriptomic analysis of the locus coeruleus from the same donors. This work led by @berniejmulvey.bsky.social is also now in pre-print! bsky.app/profile/berniejmulvey.bsky.social/post/3m4isvuqabm2v www.biorxiv.org/content/10.1...
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
Many exciting findings here inspire future work! Next we'll explore Oligo.3 to see if this signal is present in AD donors and check how upstream events in the circuit connecting the locus coeruleus and the ERC may drive disease. Keep an eye on @lieberinstitute.bsky.social for more AD research! 🧠
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
This ERC SRT and snRNA-seq data is available to explore via our interactive websites research.libd.org/LFF_spatial_ERC/ and available for download via #spatialLIBD 💻 🔓 #opendata
Screenshot from spatial LIBD web-app for exploring ERC SRT data
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
The risk effect of #APOE is ancestry dependent, and the diverse set of donors in our study allowed us to assess this in our data. Oligo.3 was the major source of DEGs in both African and European ancestry, but DEGs were quite different between the two ancestries
barplot of number of ancestry-specific DEGs. Venn diagram of overlap between African and European ancestry DEGs in Oligo.3. Scatter plot of DE t-statistics from each ancestry group.
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
This pattern of downregulation of #oligodendrocyte maturation genes in pre-mylenating Oligo.3’s led us to hypothesize that the maturation of oligos is reduced in the #APOE E4+ ERC, which could lead to reduced myelination, rendering neurons more vulnerable to degradation in #Alzheimers disease
Proposed model for oligodendrocyte subcluster classification and maturation trajectory in APOE E2+ and E4+ carriers
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
Examining the gene expression changes in Oligo.3 between #APOE carriers, genes up-regulated in E4+ were enriched in synaptic signaling & metal ion transport, down-regulated genes enriched in myelination & #oligodendrocyte development
Volcano plot of Oligo.3, boxplots of select DEGs, heatmap of top up and downregulated DEGs in Oligo subtypes, top DEG enriched GO terms from Oligo.3
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
The strong AD risk signal in this #oligodendrocyte subtype prompted a closer look at the identity of Oligo.3. Marker genes and a trajectory analysis suggest Oligo.3 is a pre-myelinating oligodendrocyte, perhaps the earliest stage of oligos differentiating from OPCs
tSNE plot of OPC and Oligo subclusters with trajectory analysis, Centered and scaled log-normalized gene expression of Oligo subcluster marker genes, cartoon of subclusters along oligo maturation process.
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
To explore gene expression changes in AD risk, we performed differential expression analysis with #voomLmFit on ERC clusters between high risk #APOE E4+ and low risk E2+. We found a large number of differential expressed genes in an oligodendrocyte subcluster Oligo.3 #edgeR #limma
Design of differential expression analysis in clusters between APOE E4+ and E2+ donors. Bar plot of number of DEGs from each cluster in SRT and snRNA-seq data, subcluster Oligo.3 had the majority of DEGs.
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
In addition we generated the largest public ERC #snRNAseq dataset, 122k nuclei clustered into 38 fine resolution sub-clusters. Taking a close look at the cellular diversity of the brain region 🔍 🦠
TSNE plot and hierarchical clustering of cell types in snRNA-seq data from human ERC
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
We used #Visium to generate the FIRST spatial transcriptomics dataset of the human #entorhinal cortex. By profiling gene expression across ERC layers with #BayesSpace and #spatialLIBD we uncovered gene expression patterns that could be useful in #Alzheimers research 🧠
Three representative SRT ERC samples, showing histology, expression of marker genes MBP, PCP4, and SNAP25, and spatial domains
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Louise Huuki-Myers @lahuuki.bsky.social · 11/12/2025
Excited to share our latest preprint from @lieberinstitute.bsky.social spatial + single-cell RNA-seq map the ERC & explore how AD risk shapes gene expression doi.org/10.1101/2025... Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
Experimental design for LIBD LFF Spatial ERC project
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
For more, check the @lieberinstitute.bsky.social announcements at 🔗 www.libd.org/tiny-brain-r... 🔗 www.libd.org/inside-the-h... As well as the American Psychiatry Association press release 🔗 www.psychiatry.org/News-room/Ne...
libd.org
Inside the Habenula: Lieber Institute Researchers Uncover a Hidden Player in Schizophrenia
About the size of a pea, the habenula serves as a hub connecting key brain systems that regulate motivation, mood, and reward — all of which are disrupted in schizophrenia. Yet until now, the habenula...
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Thanks to @nataliematosin.bsky.social and Sophie Debs for highlighting our work in their editorial “Unlocking the Molecular Secrets of the Human Habenula” 🔗 doi.org/10.1176/appi...
doi.org
Unlocking the Molecular Secrets of the Human Habenula | American Journal of Psychiatry
PsychiatryOnline.org is the platform for all American Psychiatric Association Publishing journals, DSM, and bestselling textbooks, as well as APA Practice Guidelines, and continuing medical education.
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
This data provides a foundation for future work into molecular changes that occur in the #Habenula in disease 🧠🧬 Keep an eye on @lieberinstitute.bsky.social for future work on the Hb spatially resolved transcriptomics with @10xgenomics.bsky.social tech #Visium and #Xenium 👀 #HabenulaLIBD
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Our #Habenula #singlecell and differential expression data is available to explore via our interactive websites 💻 #opendata github.com/LieberInstit...
github.com
GitHub - LieberInstitute/Habenula_Pilot: habenulaPilot project code repository
habenulaPilot project code repository. Contribute to LieberInstitute/Habenula_Pilot development by creating an account on GitHub.
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
We used #eQTL analysis to examine how SNPs relate to gene expression in #Habenula, 7 eQTLS genes were identified in differential expression, and 16 eSNPs were schizophrenia GWAS risk SNPs. Nine new schizophrenia colocalized genes with genetic risk were identified
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
We investigated whether the DEGs we found were unique to the #Habenula vs. other brain regions studied in schizophrenia (Caudate, Dentate Gyrus, dlPFC, Hippocampus) and found 75% of our DEGs were unique to habenula 🦄
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Differential gene expression yielded 173 differentially expressed genes between schizophrenia and control donors, some of which support the neurodevelopmental hypothesis of schizophrenia 🌋
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
To refine habenula signal from neighboring thalamus we utilized our #snRNAseq data to perform #deconvolution on our bulk samples, estimating proportion of habenula. These proportions were used to control for dissection differences in the differential expression analysis
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
We also profiled habenula-enriched tissue from schizophrenia and control donors using bulk RNA-seq #Transcriptomics, generating a unique dataset to identify disease associated molecular changes. PCA with bulk data from other regions shows #Habenula as an outlier
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
To provide cross-species context we integrated our human Hb snRNA-seq dataset with a previously published mouse #Habenula #singlecell dataset from @gstuber.bsky.social. Some neuronal subclusters such as human OPRM1-enriched LHb.2 appeared to be conserved across species 🐁
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Single molecule fluorescence in situ hybridization #RNAScope and HALO from @indicalabs.bsky.social was used to visualize the spatial organization of these human Hb neuronal populations. 🔬 For example, MHb.2 neurons that highly expressed CHAT clustered separately from other MHb cell types
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
We’ve created a #snRNAseq molecular atlas of the human Habenula to understand neuronal diversity on a molecular level in this unique brain region. Our snRNA-seq data on 7 control donors yielded 16k nuclei and 17 clusters, including 7 lateral & 3 medial Hb neuron populations 🧪
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Thank you to all of our collaborators at the @lieberinstitute.bsky.social for their dedication and hard work on this project! 🧑‍🔬 #HabenulaLIBD @freneegf.bsky.social @nick-eagles.bsky.social @lcolladotor.bsky.social @kr-maynard.bsky.social @martinowk.bsky.social
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...
doi.org
Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry
Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...
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Louise Huuki-Myers @lahuuki.bsky.social · 28/05/2025
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
doi.org
Redirecting
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Reposted by Louise Huuki-Myers
Manisha Barse @mbarse.bsky.social · 22/05/2025
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
youtu.be
[2025-04-23] Journal club on "[...] deconvolution of pooled snRNA-seq using sex-dependent gene expr"
YouTube video by Leonardo Collado Torres
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Louise Huuki-Myers @lahuuki.bsky.social · 25/04/2025
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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...
lahuuki.github.io
Deconvolution Benchmark: TL;DR – Louise A. Huuki-Myers
A high level overview of the Deconvolution Benchmark project, now published in Genome Biology!
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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...
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
To assess method accuracy, we compared the estimated proportions to the #RNAScope proportions for correlations and rmse 📈 #BisqueRNA and #hspe were the top performers 🏆
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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 📊
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
The resulting cell type proportions had a large range across the different #DLPFC samples, and were not always correlated with the paired #snRNAseq proportions ⚠️
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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)
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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 🔬
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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
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two men sitting next to each other with the words " teamwork makes the dream work " on the bottom
ALT: two men sitting next to each other with the words " teamwork makes the dream work " on the bottom
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Louise Huuki-Myers @lahuuki.bsky.social · 11/04/2025
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
doi.org
Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex - Genome Biology
Cellular deconvolution of bulk RNA-sequencing data using single cell/nuclei RNA-seq reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as the h...
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Louise Huuki-Myers @lahuuki.bsky.social · 14/02/2025
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...
doi.org
Fast, flexible analysis of differences in cellular composition with crumblr
Changes in cell type composition play an important role in human health and disease. Recent advances in single-cell technology have enabled the measurement of cell type composition at increasing cell ...
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Reposted by Louise Huuki-Myers
🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 12/02/2025
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
Highlight image from YouTubeZoom AI summary screenshot
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Louise Huuki-Myers @lahuuki.bsky.social · 04/12/2024
Reading the instructions first next time 😅 completed "Ceres Search" - Day 4 - Advent of Code 2024 #AdventOfCode adventofcode.com/2024/day/4
adventofcode.com
Day 4 - Advent of Code 2024
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Louise Huuki-Myers @lahuuki.bsky.social · 02/12/2024
I've completed "Red-Nosed Reports" - Day 2 - Advent of Code 2024 🔴 #AdventOfCode adventofcode.com/2024/day/2
adventofcode.com
Day 2 - Advent of Code 2024
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Reposted by Louise Huuki-Myers
🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 12/11/2024
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
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Louise Huuki-Myers @lahuuki.bsky.social · 12/11/2024
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 🦋
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