@allydunham.bsky.social
π€ 36
π₯ 62
π 6
reposted by
Leopold Parts
3 months ago
New π§¬βοΈ pre-print! We show that paired prime editing can efficiently generate large deletions β even >1 Mb β with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome. π
biorxiv.org/content/10.1...
A short thread (by Juliane Weller)π
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Generating long deletions across the genome with pooled paired prime editing screens
Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has...
https://biorxiv.org/content/10.1101/2025.11.03.686307v1
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We've been screening across many DNA construct structures with variable number/size of interesting regions - e.g. spacer, extension and barcode for prime editing. There wasn't a widely used tool to process these complex structured reads so I ended up developing
github.com/allydunham/d...
.
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GitHub - allydunham/dnacomb: CLI tool for flexibly parsing structured sequence reads into count tables and comparing them to expected libraries
CLI tool for flexibly parsing structured sequence reads into count tables and comparing them to expected libraries - allydunham/dnacomb
https://github.com/allydunham/dnacomb
4 months ago
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reposted by
Nadav Ahituv
10 months ago
MPRAbase (
mprabase.ucsf.edu
) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos,
@vagar.bsky.social
, ilias Georgakopoulos-Soares & others.
genome.cshlp.org/content/earl...
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MPRAbase a Massively Parallel Reporter Assay database
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
https://genome.cshlp.org/content/early/2025/04/22/gr.280387.124.abstract?papetoc
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reposted by
Leopold Parts
about 1 year ago
We're hiring to expand on the work to understand the human genome by engineering it!
lnkd.in/da-gitNc
add a skeleton here at some point
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reposted by
Leopold Parts
about 1 year ago
We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels π§΅
www.biorxiv.org/content/10.1...
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reposted by
Leopold Parts
about 1 year ago
Does my mutation have the same impact as yours? Population genetics π€ π₯Έ π€ π€‘ meets single cell CRISPRi β‘ !
www.biorxiv.org/content/10.1...
Led by Claudia Feng, Oliver Stegle, Britta Velten,
@sangerinstitute.bsky.social
.
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LinkedIn
This link will take you to a page thatβs not on LinkedIn
https://lnkd.in/dq9fmJiW
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