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 have a serious question for the bioinformatics community - it is now very trendy to assign genes to modules or groups and then annotate those groups using various strategies. When I read the methods for papers it is unclear to me how one comes up with the strategy they use - see below:
January 22, 2026 at 9:18 AM
I have a serious question for the bioinformatics community - it is now very trendy to assign genes to modules or groups and then annotate those groups using various strategies. When I read the methods for papers it is unclear to me how one comes up with the strategy they use - see below:
Reposted by Will Macnair
Small Molecule Agonists of TREM2 Reprogram Microglia and Protect Synapses in Human Alzheimer's Models #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.01.19.700278v1
https://www.biorxiv.org/content/10.64898/2026.01.19.700278v1
January 22, 2026 at 8:02 AM
Small Molecule Agonists of TREM2 Reprogram Microglia and Protect Synapses in Human Alzheimer's Models #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.01.19.700278v1
https://www.biorxiv.org/content/10.64898/2026.01.19.700278v1
Reposted by Will Macnair
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
Reposted by Will Macnair
The spectrum of inflammatory responses - doi.org/10.1126/scie...
The spectrum of inflammatory responses
doi.org
January 19, 2026 at 6:39 AM
The spectrum of inflammatory responses - doi.org/10.1126/scie...
Reposted by Will Macnair
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
January 15, 2026 at 11:57 AM
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
Reposted by Will Macnair
Benchmarking computational decontamination of ambient RNA #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.01.13.699237v1
https://www.biorxiv.org/content/10.64898/2026.01.13.699237v1
January 15, 2026 at 5:00 PM
Benchmarking computational decontamination of ambient RNA #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.01.13.699237v1
https://www.biorxiv.org/content/10.64898/2026.01.13.699237v1
Reposted by Will Macnair
New preprint from the lab and wonderful work by Seppe de Winter:
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 15, 2026 at 8:31 AM
New preprint from the lab and wonderful work by Seppe de Winter:
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
Reposted by Will Macnair
Most iPSC lines come from European donors. Now, two teams in Africa are studying neurodevelopment and neurodegeneration using iPSCs and organoids from African donors.
By Lauren Schenkman
www.thetransmitter.org/cellular-neu...
By Lauren Schenkman
www.thetransmitter.org/cellular-neu...
Bringing African ancestry into cellular neuroscience
Two independent teams in Africa are developing stem cell lines and organoids from local populations to explore neurodevelopmental and neurodegenerative conditions.
www.thetransmitter.org
January 14, 2026 at 4:38 PM
Most iPSC lines come from European donors. Now, two teams in Africa are studying neurodevelopment and neurodegeneration using iPSCs and organoids from African donors.
By Lauren Schenkman
www.thetransmitter.org/cellular-neu...
By Lauren Schenkman
www.thetransmitter.org/cellular-neu...
Reposted by Will Macnair
How can a common virus contribute to a rare disease?
A new @cp-immunity.bsky.social study from @biomedizin.unibas.ch links EBV to early MS-like lesion formation by showing how B cells can act at the very start of the disease process.
🔗 doi.org/10.1016/j.ce...
@unibas.ch #EBV #MultipleSclerosis
A new @cp-immunity.bsky.social study from @biomedizin.unibas.ch links EBV to early MS-like lesion formation by showing how B cells can act at the very start of the disease process.
🔗 doi.org/10.1016/j.ce...
@unibas.ch #EBV #MultipleSclerosis
January 14, 2026 at 7:33 AM
How can a common virus contribute to a rare disease?
A new @cp-immunity.bsky.social study from @biomedizin.unibas.ch links EBV to early MS-like lesion formation by showing how B cells can act at the very start of the disease process.
🔗 doi.org/10.1016/j.ce...
@unibas.ch #EBV #MultipleSclerosis
A new @cp-immunity.bsky.social study from @biomedizin.unibas.ch links EBV to early MS-like lesion formation by showing how B cells can act at the very start of the disease process.
🔗 doi.org/10.1016/j.ce...
@unibas.ch #EBV #MultipleSclerosis
This is my experience too. Too many compbio papers choose quantity over insight. Typically the insight is harder to get to, but it's so much more valuable...
I partially blame computational packages in my field - they pump out so many (often very visually appealing) dense figures and authors just dump it all into the papers - sometimes I don’t think they even bother to try and understand what the figure is actually representing
January 13, 2026 at 11:56 AM
This is my experience too. Too many compbio papers choose quantity over insight. Typically the insight is harder to get to, but it's so much more valuable...
Reposted by Will Macnair
The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.01.10.694705v1
https://www.biorxiv.org/content/10.64898/2026.01.10.694705v1
January 11, 2026 at 5:01 PM
The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.01.10.694705v1
https://www.biorxiv.org/content/10.64898/2026.01.10.694705v1
Reposted by Will Macnair
Factorization of Alzheimer's disease genetic risk influences allow patient stratification, predicting disease onset, cognitive decline, and cell-type specific responses https://www.biorxiv.org/content/10.64898/2026.01.02.697432v1
January 8, 2026 at 11:31 AM
Factorization of Alzheimer's disease genetic risk influences allow patient stratification, predicting disease onset, cognitive decline, and cell-type specific responses https://www.biorxiv.org/content/10.64898/2026.01.02.697432v1
Reposted by Will Macnair
Mitochondrial transfer from glia to neurons protects against peripheral neuropathy @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 7, 2026 at 6:54 PM
Mitochondrial transfer from glia to neurons protects against peripheral neuropathy @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Will Macnair
Motor System Oligodendroglia Atlas Reveals Activation States Associated with Region-Specific Vulnerability in ALS #NeuroDegeneration 🧪🧠
https://www.researchsquare.com/article/rs-8351425/latest
https://www.researchsquare.com/article/rs-8351425/latest
January 7, 2026 at 5:02 PM
Motor System Oligodendroglia Atlas Reveals Activation States Associated with Region-Specific Vulnerability in ALS #NeuroDegeneration 🧪🧠
https://www.researchsquare.com/article/rs-8351425/latest
https://www.researchsquare.com/article/rs-8351425/latest
Reposted by Will Macnair
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 7:27 PM
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Reposted by Will Macnair
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 6:42 PM
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Reposted by Will Macnair
Extremely excited & proud to share our new preprint - we provide for the first time a single cell map of the mouse brain across sex, the estrous cycle, and peripartum! Data are 🔥 👇
"Single-cell map of the female brain across reproductive transitions"
www.biorxiv.org/content/10.6...
"Single-cell map of the female brain across reproductive transitions"
www.biorxiv.org/content/10.6...
January 4, 2026 at 8:45 PM
Extremely excited & proud to share our new preprint - we provide for the first time a single cell map of the mouse brain across sex, the estrous cycle, and peripartum! Data are 🔥 👇
"Single-cell map of the female brain across reproductive transitions"
www.biorxiv.org/content/10.6...
"Single-cell map of the female brain across reproductive transitions"
www.biorxiv.org/content/10.6...
Reposted by Will Macnair
While we've been somewhat successful in spurring adoption of alevin-fry/simpleaf for scRNAseq processing, an impediment Dongze brought to our attention (now working directly w/ many experimentalists) was the need for a nice QC report for it's output; hence QCatch www.biorxiv.org/content/10.1... 1/x
QCatch: A framework for quality control assessment and analysis of single-cell sequencing data
Motivation: Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (...
www.biorxiv.org
January 3, 2026 at 6:18 PM
While we've been somewhat successful in spurring adoption of alevin-fry/simpleaf for scRNAseq processing, an impediment Dongze brought to our attention (now working directly w/ many experimentalists) was the need for a nice QC report for it's output; hence QCatch www.biorxiv.org/content/10.1... 1/x
Reposted by Will Macnair
One thing I wrote about here is how technology has made buses *way* more convenient while techno-futurists were obsessed with flying taxis and self-driving cars.
January 2, 2026 at 2:17 PM
One thing I wrote about here is how technology has made buses *way* more convenient while techno-futurists were obsessed with flying taxis and self-driving cars.
Reposted by Will Macnair
Genome-wide association studies identify genetic determinants of synucleinopathy biomarkers. #NeuroDegeneration 🧪🧠
https://www.medrxiv.org/content/10.64898/2025.12.29.25343142v1
https://www.medrxiv.org/content/10.64898/2025.12.29.25343142v1
December 31, 2025 at 8:01 AM
Genome-wide association studies identify genetic determinants of synucleinopathy biomarkers. #NeuroDegeneration 🧪🧠
https://www.medrxiv.org/content/10.64898/2025.12.29.25343142v1
https://www.medrxiv.org/content/10.64898/2025.12.29.25343142v1
Reposted by Will Macnair
We have two PI positions open at Helmholtz Munich. Exciting opportunities for early-career scientists!
jobs.helmholtz-muenchen.de/jobposting/8...
jobs.helmholtz-muenchen.de/jobposting/8...
Principal Investigators (f/m/x) for (i) AI in Biomedicine and (ii) AI Foundations
jobs.helmholtz-muenchen.de
December 19, 2025 at 5:35 PM
We have two PI positions open at Helmholtz Munich. Exciting opportunities for early-career scientists!
jobs.helmholtz-muenchen.de/jobposting/8...
jobs.helmholtz-muenchen.de/jobposting/8...
Reposted by Will Macnair
December 16, 2025 at 8:50 PM
Reposted by Will Macnair
T follicular helper cells adopt alter egos and localize to diverse niches - what gene expression programs distinguish Tfh in the germinal center? After dissociating tissue samples into single-cell suspension, can we infer which Tfh were positioned in GCs? Check out our new preprint! bit.ly/3XVsrCI
Multimodal analysis defines GNG4 as a distinguishing feature of germinal center-positioned CD4 T follicular helper cells in humans
CD4 T follicular helper (Tfh) cells coordinate humoral immune responses within germinal centers (GC) of lymphoid tissue. Despite their critical roles in vaccination and autoimmunity, the gene expressi...
bit.ly
December 15, 2025 at 5:03 PM
T follicular helper cells adopt alter egos and localize to diverse niches - what gene expression programs distinguish Tfh in the germinal center? After dissociating tissue samples into single-cell suspension, can we infer which Tfh were positioned in GCs? Check out our new preprint! bit.ly/3XVsrCI
Reposted by Will Macnair
Conserved phenotype and function of human brain border-associated macrophages in iPSC-derived models #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2025.12.11.693582v1
https://www.biorxiv.org/content/10.64898/2025.12.11.693582v1
December 14, 2025 at 5:00 PM
Conserved phenotype and function of human brain border-associated macrophages in iPSC-derived models #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2025.12.11.693582v1
https://www.biorxiv.org/content/10.64898/2025.12.11.693582v1
Reposted by Will Macnair
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵: