allydunham.bsky.social @allydunham.bsky.social · 27/03/2026Great to present our work on MAVEs as part of www.ebi.ac.uk/perturbation... at #VariantEffect26 - always a very enjoyable meeting!ebi.ac.ukPerturbation Catalogue 052
Reposted by @allydunham.bsky.socialLeopold Parts @leopoldparts.bsky.social · 05/11/2025New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome. 🔗 biorxiv.org/content/10.1... A short thread (by Juliane Weller)👇biorxiv.orgGenerating long deletions across the genome with pooled paired prime editing screensEngineered 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... 34520
allydunham.bsky.social @allydunham.bsky.social · 13/10/2025Accompanied by a less polished nextflow pipeline to handle multiple samples and pre-processing - github.com/allydunham/d.... Configurably downsample, merge and trim reads before quantification plus FastQC, SeqKit Stats and a quanitification QC plot. Inspired by the github.com/cancerit/QUA....github.comGitHub - allydunham/dnacomb_pipeline: Versatile Nextflow pipeline processing sequence reads into count tables using DNACombVersatile Nextflow pipeline processing sequence reads into count tables using DNAComb - allydunham/dnacomb_pipeline 000
allydunham.bsky.social @allydunham.bsky.social · 13/10/2025I have more features planned to support my work, for instance multiple constructs in one library, combinations of sub-libraries and a region type expecting variants to a base sequence, but issues and pull-requests with other bugs and suggestions are very welcome too. 100
allydunham.bsky.social @allydunham.bsky.social · 13/10/2025Simulated tests and benchmarks and our datasets suggest the tool is generally accurate and robust as well as pretty quick. Feels like a state that could be useful more widely so a good time to share, although I do expect more bugs to come out with wider usage! 100
allydunham.bsky.social @allydunham.bsky.social · 13/10/2025Currently position in reads, flanking patterns and full alignment can be used to extract regions and extact matching, hamming distance and (bounded) Levenshtein used to compare to your library. This lets you nicely balance match accuracy with speed for your design. 120
allydunham.bsky.social @allydunham.bsky.social · 13/10/2025It takes in (paired) fastq/a files, a JSON expected read structure, an optional expected combinations TSV and a strategy for extracting and matching variable regions and outputs count tables against your library. 100
allydunham.bsky.social @allydunham.bsky.social · 13/10/2025We'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....github.comGitHub - allydunham/dnacomb: CLI tool for flexibly parsing structured sequence reads into count tables and comparing them to expected librariesCLI tool for flexibly parsing structured sequence reads into count tables and comparing them to expected libraries - allydunham/dnacomb 163
Reposted by @allydunham.bsky.socialNadav Ahituv @nadavahituv.bsky.social · 22/04/2025MPRAbase (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...genome.cshlp.orgMPRAbase 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 02910
Reposted by @allydunham.bsky.socialLeopold Parts @leopoldparts.bsky.social · 10/02/2025We're hiring to expand on the work to understand the human genome by engineering it! lnkd.in/da-gitNclnkd.inWellcome Sanger Institute hiring Postdoctoral Fellow | Generative and Synthetic Genomics in Hinxton, England, United Kingdom | LinkedInPosted 2:51:51 PM. Do you want to help us improve human health and understand life on Earth? Make your mark by shaping…See this and similar jobs on LinkedIn. 0128
Reposted by @allydunham.bsky.socialLeopold Parts @leopoldparts.bsky.social · 15/01/2025We 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 🧵 www.biorxiv.org/content/10.1... 318376
Reposted by @allydunham.bsky.socialLeopold Parts @leopoldparts.bsky.social · 02/12/2024Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 25824
