Bioinformatics group leader at the Roslin Institute, University of Edinburgh
Joined June 2016
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🚨New Preprint! How does noncoding variation shape complex traits? We built a high-resolution atlas of cattle regulatory variants (>150k) and directly tested their cross-species activity in matched human cells! Read it here: biorxiv.org/content/10.64898… 1\n
But it’s not a perfect 1:1. Species-specific effects were enriched at evolutionarily young sequences and certain motifs, showing the limits of cross-species extrapolation. We also trained a deep-learning model to predict promoter activity from sequence 🤖🧠
Huge thanks to the incredible team at @RoslinInstitute and our collaborators. This resource provides a key resource for prioritising 🐄causal variants and transferring functional models across species. Check out the full paper here: biorxiv.org/content/10.64898…
🐄🔬 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
James Prendergast retweeted
Our @CommsBio #bovineTB #eQTL #TWAS #OneHealth paper on #WorldTBDay. Excellent #ComputationalGenomics work by @jf_grady & collaborators @roslininstitute, @ETH_en. Support @agriculture_ie, @Researchirel, @UCD_OneHealth, @UCD_Conway, @ucdagfood, @ucdvetmed
nature.com/articles/s42003-0…
James Prendergast retweeted
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs academic.oup.com/bioinformat…
James Prendergast retweeted
How do SVs, satellite DNA & gene content shape avian genome evolution? We analyzed 45 HiFi genomes across 3 Scrub-Jay species with distinct population sizes. Grateful to be on this incredible team led by @ScottVEdwards1! "Comparative population pangenomes" biorxiv.org/content/10.1101/…
James Prendergast retweeted
New online! Diversity and consequences of structural variation in the human genome bit.ly/4g1ZQSQ
James Prendergast retweeted
New publication:
Human ACE2 transgenic pigs are susceptible to SARS-CoV-2 and develop COVID-19-like disease
@kennethbaillie @roslininstitute @TheDickVet @EdinUni_CIR
Read more here: nature.com/articles/s41467-0…
James Prendergast retweeted
Gfa2bin enables graph-based GWAS by converting genome graphs to pan-genomic genotypes biorxiv.org/content/10.1101/…
🚀 Join our team at @roslininstitute looking at validating AI designed genome edits for improving cattle traits. 🧬🐄
🔍 PhD in Molecular Biology? Experience in genome editing? We need you!
elxw.fa.em3.oraclecloud.com/…
James Prendergast retweeted
An integrative approach to prioritize candidate causal genes for complex traits in cattle biorxiv.org/cgi/content/shor… #biorxiv_genomic
James Prendergast retweeted
Great to see @GillianMcHugo's new #Cattle #PopulationGenomics paper out😀Support @Researchirel, @ucdvetmed, @UCD_Conway, @UCD_Research, @UCD_OneHealth
#admixture #LocalAncestry #OneHealth
Collaboration: @LrFrantz, @emmelinehill, @mststats, @kmeade11
doi.org/10.1038/s41437-024-0…
Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes nature.com/articles/s41564-0…
James Prendergast retweeted
Ever wondered what this compelling selection signature means for adaptation? We combined selection in African cattle with gene expression data from @ex_farm to identify potential traits under selection! Thanks to co-authors @LingzhaoF @JGDPrendergast 💪🏻 link.springer.com/10.1186/s1…
James Prendergast retweeted
Artificial-intelligence tools offer a variety of approaches to help scientists to sift through the literature. @Nature spoke to developers of these tools and researchers who use them to garner tips on how to apply them and pitfalls to watch out for. go.nature.com/4dE5325
SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies biorxiv.org/content/10.1101/…
