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James Prendergast

@jprendergast.bsky.social
33 followers 81 following 9 posts

Prof of Bioinformatics, University of Edinburgh

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James Prendergast @jprendergast.bsky.social · 13/05/2026
🚨 New preprint! How does noncoding variation drive complex traits? We built a massive atlas of cattle regulatory variants (>150k emVars!) and directly tested them in both bovine AND human cells. 🐄🧬🚶‍♂️ Read it here: www.biorxiv.org/content/10.6...
Schema of approach for mapping regulatory elements and variants in cattle and testing their cross-species activity in human cells.
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James Prendergast @jprendergast.bsky.social · 31/07/2025
🐄🔬 Bioinformatics Research Fellow @roslininstitute wanted! Build the first single-cell atlas of African cattle 🧬: scRNA-seq/eQTL pipelines, ML variant discovery, UK–Kenya collabs. full-time to Sept ’27. Apply by 18 Aug 2025 👉 tinyurl.com/wjdcfvf4 #bioinformatics #scRNAseq
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Reposted by James Prendergast
Sushmita Roy @sroyyors.bsky.social · 02/03/2025
Cross-species imputation and comparison of single-cell transcriptomic profiles genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com
Cross-species imputation and comparison of single-cell transcriptomic profiles - Genome Biology
Cross-species comparison and prediction of gene expression profiles are important to understand regulatory changes during evolution and to transfer knowledge learned from model organisms to humans. Si...
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Reposted by James Prendergast
Science Magazine @science.org · 25/01/2025
In a new Science study, researchers present CASTER, a tool that uses arrangements in DNA sequences known as site patterns to infer “species trees,” which are diagrams that depict the evolutionary relationships among species. Learn more:
scim.ag
CASTER: Direct species tree inference from whole-genome alignments
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, the...
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James Prendergast @jprendergast.bsky.social · 06/12/2024
🚀 Join our team at @roslininstitute.bsky.social looking at testing AI designed genome edits for improving cattle traits. 🧬🐄 🔍 PhD in Molecular Biology? Experience in genome editing? We need you!
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Reposted by James Prendergast
Stephen Turner @stephenturner.us · 05/12/2024
Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics www.nature.com/articles/s41467-024-… 🧬🖥️🧪 github.com/PejLab/Pantry
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Reposted by James Prendergast
bioRxiv Genetics @biorxiv-genetic.bsky.social · 30/08/2024
Credible set is sensitive to imputation quality and missing variants www.biorxiv.org/content/10.1101/202…
biorxiv.org
Credible set is sensitive to imputation quality and missing variants https://www.biorxiv.org/content/10.1101/2024.08.28.610135v1
Bayesian fine-mapping to obtain credible sets has been widely applied post GWAS to pinpoint causal v
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Reposted by James Prendergast
bioRxiv Genetics @biorxiv-genetic.bsky.social · 22/08/2024
Variant-specific priors in colocalisation analysis www.biorxiv.org/content/10.1101/202…
biorxiv.org
Variant-specific priors in colocalisation analysis https://www.biorxiv.org/content/10.1101/2024.08.21.608957v1
Linking GWAS variants to their causal gene remains an ongoing challenge. A widely used method for pe
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Reposted by James Prendergast
bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/08/2024
Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex www.biorxiv.org/content/10.1101/202…
biorxiv.org
Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex https://www.biorxiv.org/content/10.1101/2024.08.21.609075v1
Identifying cell type-specific enhancers in the brain is critical to building genetic tools for inve
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Reposted by James Prendergast
bioRxiv Genomics @biorxiv-genomic.bsky.social · 21/06/2024
Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations www.biorxiv.org/content/10.1101/202…
biorxiv.org
Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations https://www.biorxiv.org/content/10.1101/2024.06.20.599852v1
Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, sinc
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Reposted by James Prendergast
Michael Love @mikelove.bsky.social · 14/06/2024
Tidyomics, a collection of R packages that enable tidyverse-style syntax on biological datasets, is now published: rdcu.be/dKNM6 Thanks to the hard work of the authors especially @stemang.bsky.social!
rdcu.be
The tidyomics ecosystem: enhancing omic data analyses
Nature Methods - tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.
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