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
🐄🔬 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
Reposted by James Prendergast
Cross-species imputation and comparison of single-cell transcriptomic profiles genomebiology.biomedcentral.com/articles/10....
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...
genomebiology.biomedcentral.com
March 2, 2025 at 4:33 AM
Cross-species imputation and comparison of single-cell transcriptomic profiles genomebiology.biomedcentral.com/articles/10....
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:
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
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:
Learn more:
🚀 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!
🔍 PhD in Molecular Biology? Experience in genome editing? We need you!
December 6, 2024 at 10:35 AM
🚀 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!
🔍 PhD in Molecular Biology? Experience in genome editing? We need you!
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
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
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
Credible set is sensitive to imputation quality and missing variants https://www.biorxiv.org/content/10.1101/2024.08.28.610135v1
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
Variant-specific priors in colocalisation analysis https://www.biorxiv.org/content/10.1101/2024.08.21.608957v1
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
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
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
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
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!
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
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/dKNM6
Thanks to the hard work of the authors especially @stemang.bsky.social!