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Reposted by Will Macnair

#NeuroDegeneration preprints @prepub-neurodegen.bsky.social · 1d

Beyond amyloid and tau: synaptic and neurodegenerative biomarkers shape MCI progression #NeuroDegeneration 🧪🧠
http://medrxiv.org/cgi/content/short/2025.10.06.25337445v1

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Reposted by Will Macnair

#NeuroDegeneration preprints @prepub-neurodegen.bsky.social · 1d

Aquaporin-4 polymorphisms modify the penetrance of Parkinson's disease in leucine-rich repeat kinase 2 carriers #NeuroDegeneration 🧪🧠
http://medrxiv.org/cgi/content/short/2025.10.04.25337325v1

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Reposted by Will Macnair

#SingleCell preprints @prepub-singlecell.bsky.social · 6h

Optimal Gene Panel Selection for Targeted Spatial Transcriptomics Experiments #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.10.08.681071v1

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#SingleCell preprints @prepub-singlecell.bsky.social · 6h

Finding the perfect promoter: Correlating single-cell transcriptome data with gene drive performance #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.10.08.681126v1

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ME/CFS Science @mecfsskeptic.bsky.social · 5d

1) We’ve written an article about the DecodeME results: what the study measured, what the results show, and why its findings are important.

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Reposted by Will Macnair

#NeuroDegeneration preprints @prepub-neurodegen.bsky.social · 8d

Integrative multiomic analysis links TDP-43-driven splicing defects to cascading proteomic disruption of ALS/FTD pathways #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.09.29.679403v1

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Will Macnair @willmacnair.bsky.social · 7d

The only issue with them is that there are far too many to keep up with, but that’s mainly science’s fault rather than mine :D

Will Macnair @willmacnair.bsky.social · 7d

Good opportunity to promote my two pet preprint bots 😃

- @prepub-singlecell.bsky.social for #singlecell papers
- @prepub-neurodegen.bsky.social for #neurodegeneration papers

Richard Sever @richardsever.bsky.social · 9d

"One of the simplest and most reliable ways to stay current is through journal table of contents (ToC) alerts"

Discuss...

My 2c: For many fields, this is an inefficient strategy for primary research - most papers simply won't be relevant. But... 1/n

www.nature.com/articles/d41...

How to find the papers you need to read — and avoid the ones you don’t

With thousands of papers being published everyday, it can be a task working out which matter. Here are some tips to help you decide.

www.nature.com

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Will Macnair @willmacnair.bsky.social · 9d

Experimental design is the most important step in any experiment! Everything is downstream of it, so a mistake there can irretrievably mess up your experiment.

I also think its challenges are under appreciated. It’s simple but subtle, and you have to think hard and clearly about your question.

Wolfgang Huber @wkhuber.bsky.social · 9d

Am contributing to a collaborative dry-wet project proposal and everyone incl. myself thinks I should be writing about fancy algorithms. Instead, I spend all time on experimental design,power, what do we know or not, what do we aim to show? And on 2nd thought, that's probably OK for a statistician.

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Wolfgang Huber @wkhuber.bsky.social · 9d

Skymind: I'm learning about 'spatially aware clustering' in spatial omics and wondering how it is different from 'segmentation'? (in essence, not by way of marketing)

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Will Macnair @willmacnair.bsky.social · 13d

I made this not that posts #SingleCell preprints: bsky.app/profile/prep...

It’s pretty sensitive but not at all specific 😅 There is really interesting stuff in there, but there’s a LOT

bsky.app

Reposted by Will Macnair

#NeuroDegeneration preprints @prepub-neurodegen.bsky.social · 15d

Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.09.23.678110v1

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Anshul Kundaje @anshulkundaje.bsky.social · 17d

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Yun S. Song @yun-s-song.bsky.social · 17d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

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Yun S. Song @yun-s-song.bsky.social · 17d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

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Sarah Cohen @cohenlaboratory.bsky.social · 21d

Wonderful to see our paper on the #organelle signatures of #neurons and #astrocytes out in final form - congratulations, Shannon Rhoads and team!🎉 t.co/BPxKlbU6Ou

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Anshul Kundaje @anshulkundaje.bsky.social · 21d

New faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT

Polly Fordyce @pollyfordyce.bsky.social · 21d

Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...

Faculty Recruitment

chemh.stanford.edu

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David Weiskopf believes in you @dave.bzky.team · 24d

The thing about an ebike is i bought one and now i am biking like 30 miles a week instead of zero miles a week on the regular bike i love but don't think about using every day.

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Reposted by Will Macnair

Nature Neuroscience @natneuro.nature.com · 23d

Augmenting AMPA receptor signaling after spinal cord injury increases ependymal-derived neural stem/progenitor cell migration and promotes functional recovery

www.nature.com/articles/s41...

Augmenting AMPA receptor signaling after spinal cord injury increases ependymal-derived neural stem/progenitor cell migration and promotes functional recovery - Nature Neuroscience

Hachem et al. show that AMPAR signaling drives the acute activation of ependymal-derived neural stem/progenitor cells after spinal cord injury and that this mechanism can be targeted therapeutically to harness the endogenous regenerative potential of the spinal cord.

www.nature.com

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Reposted by Will Macnair

Prashanthi Ravichandran @prashanthi-ravi.bsky.social · 23d

(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium

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Reposted by Will Macnair

Haky Im @hakyim.bsky.social · 26d

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

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Reposted by Will Macnair

Will Macnair @willmacnair.bsky.social · Sep 7

I want to do some NMF/topic modelling type analysis of single cell data. Does anyone have recommendations?

Essential:
- still maintained
- can handle big datasets (e.g. 500k cells)
- not a hassle to actually install...

Optional:
- handles batch effects
- recapitulates biology :D

Thanks!

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Will Macnair @willmacnair.bsky.social · Sep 7

Oh nice, that looks like it has its own implementation of cNMF, which I wanted to try but installation was annoying. Thanks!

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Will Macnair @willmacnair.bsky.social · Sep 7

It's just single cell/nuclei expression data, although multi-modal methods could be interesting too.

Will Macnair @willmacnair.bsky.social · Sep 7

I want to do some NMF/topic modelling type analysis of single cell data. Does anyone have recommendations?

Essential:
- still maintained
- can handle big datasets (e.g. 500k cells)
- not a hassle to actually install...

Optional:
- handles batch effects
- recapitulates biology :D

Thanks!

2 1 1

Reposted by Will Macnair

Nature @nature.com · Sep 7

Nature research paper: Single-cell transcriptomic and genomic changes in the ageing human brain

go.nature.com/4mRVCl0

Single-cell transcriptomic and genomic changes in the ageing human brain - Nature

Sequencing analyses of human prefrontal cortex from donors ranging in age from 0.4 to 104 years show that ageing correlates with an accumulation of somatic mutations in short housekeeping genes and a reduction in the expression of these genes.

go.nature.com

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