Will Macnair
@willmacnair.bsky.social
Amateur neuroscientist, quite a bit of experience in single cell analysis, working on #neurodegeneration in Basel. Formerly postdoc with @markrobinsonca.bsky.social at UZH.
Pinned
Will Macnair
@willmacnair.bsky.social
· Nov 14
I made a bot that posts pre-prints of single cell papers:
@prepub-singlecell.bsky.social
(I posted about it a little while ago when no one was here, so posting again now :D)
It's pretty dumb so very open to suggestions for improvements!
@prepub-singlecell.bsky.social
(I posted about it a little while ago when no one was here, so posting again now :D)
It's pretty dumb so very open to suggestions for improvements!
Reposted by Will Macnair
I'm looking for top-notch candidate for a fully-funded PhD working on role of somatic mutations in ageing immune decline. Ideal for wet-lab or quantitative candidates. Fantastic collaboration with Prof Martin Taylor in Edinburgh THE UK expert in mutations.
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com
November 23, 2025 at 10:38 AM
I'm looking for top-notch candidate for a fully-funded PhD working on role of somatic mutations in ageing immune decline. Ideal for wet-lab or quantitative candidates. Fantastic collaboration with Prof Martin Taylor in Edinburgh THE UK expert in mutations.
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Reposted by Will Macnair
Journalist challenge: Use “Machine Learning” when you mean machine learning and “LLM” when you mean LLM. Ditch “AI” as a catch-all term, it’s not useful for readers and it helps companies trying to confuse the public by obscuring the roles played by different technologies. 🧪
November 22, 2025 at 4:50 PM
Journalist challenge: Use “Machine Learning” when you mean machine learning and “LLM” when you mean LLM. Ditch “AI” as a catch-all term, it’s not useful for readers and it helps companies trying to confuse the public by obscuring the roles played by different technologies. 🧪
Reposted by Will Macnair
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Will Macnair
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Reposted by Will Macnair
Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1
November 21, 2025 at 2:46 PM
Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1
Reposted by Will Macnair
ApoE lipidation, not isoform, is the key modulator of Aβ interaction, uptake, and cytotoxicity #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.11.19.685371v1
https://www.biorxiv.org/content/10.1101/2025.11.19.685371v1
November 20, 2025 at 5:02 PM
ApoE lipidation, not isoform, is the key modulator of Aβ interaction, uptake, and cytotoxicity #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.11.19.685371v1
https://www.biorxiv.org/content/10.1101/2025.11.19.685371v1
Reposted by Will Macnair
Very happy to share our latest manuscript about TCR-epitope recognition specificity: www.biorxiv.org/content/10.1...
www.biorxiv.org
November 18, 2025 at 7:21 AM
Very happy to share our latest manuscript about TCR-epitope recognition specificity: www.biorxiv.org/content/10.1...
Reposted by Will Macnair
I work with large collections of AnnDatas for single-cell work and got tired of opening notebooks for simple operations. Built a CLI tool to handle some common stuff directly from the terminal.
Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc.
github.com/noamteyssier...
Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc.
github.com/noamteyssier...
GitHub - noamteyssier/anntools: a cli-driven anndata toolkit
a cli-driven anndata toolkit. Contribute to noamteyssier/anntools development by creating an account on GitHub.
github.com
November 18, 2025 at 8:14 PM
I work with large collections of AnnDatas for single-cell work and got tired of opening notebooks for simple operations. Built a CLI tool to handle some common stuff directly from the terminal.
Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc.
github.com/noamteyssier...
Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc.
github.com/noamteyssier...
Reposted by Will Macnair
Excellent new review on the blood-brain barrier, by Alon Friedman and colleague @natureportfolio.nature.com #Cerebrovascular #BloodBrainBarrier
Dynamic modulation of the blood–brain barrier in the healthy brain - Nature Reviews Neuroscience
The blood–brain barrier was conventionally seen as a static protective structure, but a more complex, dynamic view of this barrier has now emerged. In this Review, Friedman et al. discuss the dynamic ...
www.nature.com
November 16, 2025 at 3:48 PM
Excellent new review on the blood-brain barrier, by Alon Friedman and colleague @natureportfolio.nature.com #Cerebrovascular #BloodBrainBarrier
Reposted by Will Macnair
The challenges of single cell transcriptomics on difficult human tissue: the placenta #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
November 16, 2025 at 8:01 AM
The challenges of single cell transcriptomics on difficult human tissue: the placenta #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
Reposted by Will Macnair
CSF Proteomics and Machine Learning Reveal Distinct Stages Across the Alzheimer's Disease Continuum #NeuroDegeneration 🧪🧠
http://medrxiv.org/cgi/content/short/2025.11.05.25339138v1
http://medrxiv.org/cgi/content/short/2025.11.05.25339138v1
November 14, 2025 at 8:01 AM
CSF Proteomics and Machine Learning Reveal Distinct Stages Across the Alzheimer's Disease Continuum #NeuroDegeneration 🧪🧠
http://medrxiv.org/cgi/content/short/2025.11.05.25339138v1
http://medrxiv.org/cgi/content/short/2025.11.05.25339138v1
Reposted by Will Macnair
Whoah
EBV not only causes multiple sclerosis, it also might be the root of SLE
www.science.org/doi/10.1126/...
An EBV vaccine to rid ourselves of these horrible autoimmune conditions (and many cancers)?
#lupus #medsky #RheumSky
@christosargyrop.bsky.social
EBV not only causes multiple sclerosis, it also might be the root of SLE
www.science.org/doi/10.1126/...
An EBV vaccine to rid ourselves of these horrible autoimmune conditions (and many cancers)?
#lupus #medsky #RheumSky
@christosargyrop.bsky.social
Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells in systemic lupus erythematosus
Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells to promote pathogenic antinuclear T and B cell responses in lupus.
www.science.org
November 13, 2025 at 11:05 PM
Whoah
EBV not only causes multiple sclerosis, it also might be the root of SLE
www.science.org/doi/10.1126/...
An EBV vaccine to rid ourselves of these horrible autoimmune conditions (and many cancers)?
#lupus #medsky #RheumSky
@christosargyrop.bsky.social
EBV not only causes multiple sclerosis, it also might be the root of SLE
www.science.org/doi/10.1126/...
An EBV vaccine to rid ourselves of these horrible autoimmune conditions (and many cancers)?
#lupus #medsky #RheumSky
@christosargyrop.bsky.social
Reposted by Will Macnair
Oligodendroglia as functional effectors of Multiple Sclerosis risk variants #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.11.11.687640v1
https://www.biorxiv.org/content/10.1101/2025.11.11.687640v1
November 13, 2025 at 8:01 AM
Oligodendroglia as functional effectors of Multiple Sclerosis risk variants #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.11.11.687640v1
https://www.biorxiv.org/content/10.1101/2025.11.11.687640v1
Reposted by Will Macnair
Astrocytes distress triggers brain pathology through induction of δ secretase in a murine model of Alzheimer’s disease
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Astrocytes distress triggers brain pathology through induction of δ secretase in a murine model of Alzheimer’s disease - Nature Communications
The role of astrocytes in Alzheimer’s disease pathology remains insufficiently characterized. Here, the authors show that aggravated astrocyte response to Aβ causes brain inflammation, and amyloid and...
www.nature.com
November 5, 2025 at 12:42 PM
Astrocytes distress triggers brain pathology through induction of δ secretase in a murine model of Alzheimer’s disease
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Will Macnair
Required reading for cell biologists to get a sense of basic statistical principles!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Ten essential tips for robust statistics in cell biology - Nature Cell Biology
Statistical thinking is a core part of solid, trustworthy biology. However, many studies still include insufficient sample sizes, have poor experimental design or select an incorrect statistical metho...
www.nature.com
November 4, 2025 at 7:23 PM
Required reading for cell biologists to get a sense of basic statistical principles!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Will Macnair
🚀Excited to share our new preprint: “Programming human cell type-specific gene expression via an atlas of AI-designed enhancers”
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
Programming human cell type-specific gene expression via an atlas of AI-designed enhancers
Differentially active enhancers are key drivers of cell type specific gene expression. Active enhancers are found in open chromatin, which can be mapped at genome scale across tissue and cell types. T...
www.biorxiv.org
October 6, 2025 at 4:57 PM
🚀Excited to share our new preprint: “Programming human cell type-specific gene expression via an atlas of AI-designed enhancers”
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
Reposted by Will Macnair
Now I'm also looking for a research software engineer to implement a pile of research results to R packages loo, posterior, bayesplot, projpred, priorsense, brms or/and Python packages ArviZ, Bambi and Kulprit. Apply by email with no specific deadline (see contact info at users.aalto.fi/~ave/)
I'm now also looking for a postdoc with strong Bayesian background and interest in developing Bayesian cross-validation theory, methods and software. Apply by email with no specific deadline (see contact information at users.aalto.fi/~ave/).
Others, please share
Others, please share
I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
November 3, 2025 at 11:13 AM
Now I'm also looking for a research software engineer to implement a pile of research results to R packages loo, posterior, bayesplot, projpred, priorsense, brms or/and Python packages ArviZ, Bambi and Kulprit. Apply by email with no specific deadline (see contact info at users.aalto.fi/~ave/)
Reposted by Will Macnair
Thank you Alzforum for featuring our new preprint identifying regulators of disease states of #microglia.
Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs.
Alzforum
www.alzforum.org/news/researc...
Preprint
www.biorxiv.org/content/10.1...
Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs.
Alzforum
www.alzforum.org/news/researc...
Preprint
www.biorxiv.org/content/10.1...
October 22, 2025 at 6:28 PM
Thank you Alzforum for featuring our new preprint identifying regulators of disease states of #microglia.
Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs.
Alzforum
www.alzforum.org/news/researc...
Preprint
www.biorxiv.org/content/10.1...
Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs.
Alzforum
www.alzforum.org/news/researc...
Preprint
www.biorxiv.org/content/10.1...
Reposted by Will Macnair
Happy to share our latest work led by @kevincziegler.bsky.social and Aydan Askarova, examining cell type contributions of vascular cell types to dementia risk. Many thanks to the donors, and for support from @ukdri.ac.uk and @alzassociation.bsky.social.
www.cell.com/neuron/fullt...
www.cell.com/neuron/fullt...
October 31, 2025 at 10:10 AM
Happy to share our latest work led by @kevincziegler.bsky.social and Aydan Askarova, examining cell type contributions of vascular cell types to dementia risk. Many thanks to the donors, and for support from @ukdri.ac.uk and @alzassociation.bsky.social.
www.cell.com/neuron/fullt...
www.cell.com/neuron/fullt...
Reposted by Will Macnair
Got with the times + made a BSky to share our new, large-scale spatial RNAseq study of adult human #locuscoeruleus! Co-1st auth and cryostat wizard @heenadivecha.bsky.social squeezed 85 tissue sections into 43 Visium arrays. (1/8)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus
The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections across the brain regulating sleep, arousal, attention, stress responses, and some forms of cognition...
www.biorxiv.org
October 31, 2025 at 3:42 PM
Got with the times + made a BSky to share our new, large-scale spatial RNAseq study of adult human #locuscoeruleus! Co-1st auth and cryostat wizard @heenadivecha.bsky.social squeezed 85 tissue sections into 43 Visium arrays. (1/8)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Will Macnair
Thrilled to share our latest preprint using single nuq sequencing and Xenium to define neuron organisation and sex differences in glia within human spinal cord. Truly a collaborative effort, with a big shoutout to Katherin Gabriel and @tedpricethepainguy.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A molecular map of the human spinal dorsal and ventral horn defines arrangement of neuronal types and glial sex differences
The spinal cord is the gateway for sensory information from the body as it ascends to the brain, as well as a major motor output center of the nervous system. It is also a key location for sensory-mot...
www.biorxiv.org
November 1, 2025 at 10:46 AM
Thrilled to share our latest preprint using single nuq sequencing and Xenium to define neuron organisation and sex differences in glia within human spinal cord. Truly a collaborative effort, with a big shoutout to Katherin Gabriel and @tedpricethepainguy.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Will Macnair
Excited to share our newest project using spatial transcriptomics with novel image analysis approaches to investigate the impact of biological risk factors for Alzheimer's disease (AD) - APOE haplotype, sex, and genomic ancestry - on molecular states in the locus coeruleus (LC 🔵) of the human 🧠.
Got with the times + made a BSky to share our new, large-scale spatial RNAseq study of adult human #locuscoeruleus! Co-1st auth and cryostat wizard @heenadivecha.bsky.social squeezed 85 tissue sections into 43 Visium arrays. (1/8)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus
The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections across the brain regulating sleep, arousal, attention, stress responses, and some forms of cognition...
www.biorxiv.org
October 31, 2025 at 5:24 PM
Excited to share our newest project using spatial transcriptomics with novel image analysis approaches to investigate the impact of biological risk factors for Alzheimer's disease (AD) - APOE haplotype, sex, and genomic ancestry - on molecular states in the locus coeruleus (LC 🔵) of the human 🧠.
Reposted by Will Macnair
Consensus meta-analysis of genome-wide association studies for Alzheimer's disease and related dementia #NeuroDegeneration 🧪🧠
http://medrxiv.org/cgi/content/short/2025.10.20.25338060v1
http://medrxiv.org/cgi/content/short/2025.10.20.25338060v1
October 24, 2025 at 7:02 AM
Consensus meta-analysis of genome-wide association studies for Alzheimer's disease and related dementia #NeuroDegeneration 🧪🧠
http://medrxiv.org/cgi/content/short/2025.10.20.25338060v1
http://medrxiv.org/cgi/content/short/2025.10.20.25338060v1
Reposted by Will Macnair
APOE3 astrocytes can rescue lipid abnormalities and dystrophic neurites of APOE4 human neurons #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.10.24.684364v1
https://www.biorxiv.org/content/10.1101/2025.10.24.684364v1
October 25, 2025 at 4:02 PM
APOE3 astrocytes can rescue lipid abnormalities and dystrophic neurites of APOE4 human neurons #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.10.24.684364v1
https://www.biorxiv.org/content/10.1101/2025.10.24.684364v1
Reposted by Will Macnair
Furthermore I am more convinced that the real AI breakthrough is the attention concept (attention being all you need from the famous paper) - the ability to do data-driven model discovery. LLMs are just one place where this attention scheme is powerful. There are many more.
October 26, 2025 at 7:48 AM
Furthermore I am more convinced that the real AI breakthrough is the attention concept (attention being all you need from the famous paper) - the ability to do data-driven model discovery. LLMs are just one place where this attention scheme is powerful. There are many more.