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Alex Pollen

@brainevodevo.bsky.social
1.3K followers 146 following 46 posts

Studying specializations and vulnerabilities of human brain development

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Alex Pollen @brainevodevo.bsky.social · 07/11/2025
We begin by performing cross-species analysis of developing initial classes of both striatal and cortical inhibitory neuron populations by integrating single cell sequencing data from 8 mammals, spanning from primates to marsupials.
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Our analysis revealed that human and bonobo mitochondria typically outcompete those from chimpanzee, but we also identified a fraction of cells where chimpanzee mitochondria win and cells where both mitochondria survive.
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
We put CellBouncer to the test with a challenging demultiplexing problem of assigning 24 hominid tetraploid composite cell lines generated by Bryan Pavlovic to both individuals-of-origin and identifying the mitochondrial haplotypes present. www.biorxiv.org/content/10.1...
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
CellBouncer tools were crucial for our study of dopaminergic evolution that included ventral midbrain organoids with up to 17 individuals from 4 species, led by Sara Nolbrant, @jenellewallace.bsky.social, and Jingwen Ding: www.biorxiv.org/content/10.1...
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Finally, CellBouncer harmonizes independent metrics for doublet identification to produce a global doublet rate
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
CellBouncer assigns sgRNAs and other perturbation tags to cell-of-origin, accounting for low coverage and increased tag background
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
CellBouncer also provides independent validation methods for statistical confidence in assignments, including a tool for determining individual proportion in bulk (and pseudobulk) RNA-seq data
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Importantly, CellBouncer uses sequence variation as an external ground-truth for ambient RNA determination, improving individual-of-origin assignments and enabling cell level corrections, while providing insights into the nature and sources of ambient RNA.
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Genotype-free assignments for an unknown number of individuals by discovery of mitochondrial haplotypes
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Individual-of-origin assignments for cells that account for deep population structure, scale across large SNP sets, and are robust to ambient RNA
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Alignment-free rapid species assignments with an underlying statistical model
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Alex Pollen @brainevodevo.bsky.social · 24/03/2025
Introducing CellBouncer, a unified demultiplexing toolkit built by nkschaefer.bsky.social to check IDs and keep the riff raff out of single cell genomics datasets, including by using genetic variation as an external ground-truth for ambient RNA removal: www.biorxiv.org/content/10.1...
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Alex Pollen @brainevodevo.bsky.social · 12/11/2024
@jenellewallace.bsky.social led a preview of two outstanding papers from the labs of Cecile Charrier, Pierre Vanderhaeghen, and @franckp.bsky.social that connect regulation of the tempo of synaptogenesis by the human-specific gene SRGAP2C to ASD-linked genes: authors.elsevier.com/a/1k3583BtfH...
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Alex Pollen @brainevodevo.bsky.social · 29/12/2023
Building on our recent review, Tyler Fair performed CRISPRi-based genetic screens to assign human-specific deletions to molecular and cellular phenotypes: www.biorxiv.org/content/10.1...
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