James Prendergast

🐄🔬 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

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/s4200…

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs academic.oup.com/bioinformatics…

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/10.110…

New online! Diversity and consequences of structural variation in the human genome bit.ly/4g1ZQSQ

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/s4146…

Gfa2bin enables graph-based GWAS by converting genome graphs to pan-genomic genotypes biorxiv.org/content/10.110…

🚀 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/hcmUI/Candidat…

An integrative approach to prioritize candidate causal genes for complex traits in cattle biorxiv.org/cgi/content/sh… #biorxiv_genomic

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…

Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes nature.com/articles/s4156…

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/s12864…

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

@ROwen_93 @roslininstitute Best of luck Rachel!

After a wonderful almost 3 years in the @JGDPrendergast lab at @roslininstitute, I have sadly moved on to pastures new! I will miss all of my colleagues and friends but I am excited to start a new adventure!

Apparently I will be out of a job soon on.ft.com/4eOZSx7 via @FT

SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies biorxiv.org/content/10.110…

VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing nature.com/articles/s4146…

Join us in the Computational Biology team at Beautiful Melbourne, a leading research unit in statistical genetics and genomics using big data to improve productivity and welfare of agricultural species. Apply if interested in analyses of super big datasets!

Rongrong has released relevant datasets and workflows, including phyloP and phastCons scores for cattle and entire #Nextflow workflow so users can annotate their variants with same set of features for training their own AI models 6\6

Models we already have though will be effective at improving breeding values and for fine-mapping GWAS peaks. 5\6

Our new paper on using AI models to predict functional regulatory variants in cattle (and humans) is now online. A thread of the key findings... 1\n biorxiv.org/content/10.110…