James Prendergast
James Prendergast
@jprendergast.bsky.social
Prof of Bioinformatics, University of Edinburgh
🐄🔬 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
July 31, 2025 at 10:55 AM
Reposted by James Prendergast
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:
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...
scim.ag
January 25, 2025 at 3:07 PM
🚀 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!
December 6, 2024 at 10:35 AM
Reposted by James Prendergast
Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics https://www.nature.com/articles/s41467-024-54840-8 🧬🖥️🧪 https://github.com/PejLab/Pantry
December 5, 2024 at 7:30 PM
Reposted by James Prendergast
Credible set is sensitive to imputation quality and missing variants https://www.biorxiv.org/content/10.1101/2024.08.28.610135v1
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
www.biorxiv.org
August 30, 2024 at 12:32 AM
Reposted by James Prendergast
Variant-specific priors in colocalisation analysis https://www.biorxiv.org/content/10.1101/2024.08.21.608957v1
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
www.biorxiv.org
August 22, 2024 at 5:32 PM
Reposted by James Prendergast
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
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
www.biorxiv.org
August 22, 2024 at 7:33 AM
Reposted by James Prendergast
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
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
www.biorxiv.org
June 21, 2024 at 7:33 AM
Reposted by James Prendergast
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!
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.
rdcu.be
June 14, 2024 at 12:08 PM