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Reposted by Will Macnair

Ewan Birney @ewanbirney.bsky.social · 1d

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Staff Scientist

About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

embl.wd103.myworkdayjobs.com

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Reposted by Will Macnair

Rob Patro @robp.bsky.social · 2d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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#NeuroDegeneration preprints @prepub-neurodegen.bsky.social · 3d

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 · 3d

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 · 2d

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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Reposted by Will Macnair

#SingleCell preprints @prepub-singlecell.bsky.social · 2d

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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Reposted by Will Macnair

ME/CFS Science @mecfsskeptic.bsky.social · 6d

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 · 10d

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 · 9d

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 · 9d

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 · 10d

"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 · 10d

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 · 11d

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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Reposted by Will Macnair

Wolfgang Huber @wkhuber.bsky.social · 10d

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 · 14d

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 · 17d

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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Reposted by Will Macnair

Anshul Kundaje @anshulkundaje.bsky.social · 18d

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 · 19d

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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Reposted by Will Macnair

Yun S. Song @yun-s-song.bsky.social · 19d

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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Reposted by Will Macnair

Sarah Cohen @cohenlaboratory.bsky.social · 23d

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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Reposted by Will Macnair

Anshul Kundaje @anshulkundaje.bsky.social · 23d

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 · 23d

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 · 26d

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 · 25d

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 · 25d

(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 · 28d

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.