Javier Santoyo
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jsantoyo.bsky.social
Javier Santoyo
@jsantoyo.bsky.social
2.2K followers 2K following 900 posts
Genomics & Bioinformatics Scientist at the University of Edinburgh | Head of Edinburgh Genomics | #Omics #NGS #LongReads 🧪🧬 🖥️
Opinions my own. He/Him

Lab: https://genomics.ed.ac.uk/
LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/
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jsantoyo.bsky.social
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement. #StructuralVariants #SVs #SVsimulation #SimulatedData #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
November 9, 2025 at 8:05 PM
jsantoyo.bsky.social
Genome size estimation from long read overlaps. #GenomeSize #LongRead #Sequencing #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
November 9, 2025 at 7:05 PM
jsantoyo.bsky.social
HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements. #EndogenousViralElements #EukaryoticHostGenomes #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
November 9, 2025 at 6:05 PM
jsantoyo.bsky.social
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification. #PathogenSurveillance #Nextflow #Bioinformatics #WGS #PathogenIdentification @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 9, 2025 at 5:49 PM
jsantoyo.bsky.social
igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review. #IGV #InteractiveVisualizationss #GeneticVariants #VariantReview @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 9, 2025 at 4:00 PM
jsantoyo.bsky.social
Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
Orchestrating Microbiome Analysis with Bioconductor
The expansion of microbiome research has led to the accumulation of interlinked datasets encompassing versatile taxonomic and functional assays. The analysis of increasingly large and heterogeneous…
www.biorxiv.org
November 9, 2025 at 11:31 AM
jsantoyo.bsky.social
Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes. #NonCanonicalDNA #NonB_DNA #GenomeRegulation @biorxivpreprint.bsky.social 🧪🧬
www.biorxiv.org/content/10.1...
November 9, 2025 at 10:15 AM
jsantoyo.bsky.social
The Clinical Genomic Variation Landscape. #GenomicVariants
www.medrxiv.org/content/10.1...
November 9, 2025 at 9:31 AM
jsantoyo.bsky.social
Assembling unmapped reads reveals hidden variation in South Asian genomes. #GenomeVariation #UnmappedReads #SouthAsianPopulation @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 9, 2025 at 8:32 AM
jsantoyo.bsky.social
Site-specific DNA insertion into the human genome with engineered recombinases. #GenomeEditing #DNAinsertion #LargeSerineRecombinases @natbiotech.nature.com
www.nature.com/articles/s41...
November 8, 2025 at 8:05 PM
jsantoyo.bsky.social
Curating 16S rRNA databases enhances taxonomic accuracy and computational efficiency in microbial profiling. #Metabarcoding #16S #rRNA #BacterialGenomes #SequenceDatabases #DatabaseCuration #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
November 8, 2025 at 7:05 PM
jsantoyo.bsky.social
DESpace2: detection of differential spatial patterns in spatial omics data. #SpatialOmics #DifferentialSpatialPatterns #scRNAseq #Genomics #Bioinformatics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
DESpace2: detection of differential spatial patterns in spatial omics data
Spatially resolved transcriptomics (SRT) enables the investigation of mRNA expression in a spatial context. While several SRT analysis frameworks have been developed, the vast majority of them focus…
www.biorxiv.org
November 8, 2025 at 6:05 PM
jsantoyo.bsky.social
Beyond reference bias: Making pangenomes accessible with PangyPlot. #GenomeBrowser #PangenomeGraphs #GeneAnnotations #Visualization #Genomics #Bioinformatics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 8, 2025 at 5:31 PM
jsantoyo.bsky.social
RNA stability enhancers for durable base-modified mRNA therapeutics. #RNAstability #mRNAtherapeutics @natbiotech.nature.com
www.nature.com/articles/s41...
November 8, 2025 at 4:01 PM
jsantoyo.bsky.social
A comprehensive view of somatic mosaicism by single-cell DNA analysis. #SingleCell #scDNAseq #SomaticMosaicism @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
November 8, 2025 at 3:25 PM
jsantoyo.bsky.social
Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence. #MycobacteriumTuberculosis #Pangenome #ReferenceSequence @biorxivpreprint.bsky.social 🧪
www.biorxiv.org/content/10.1...
November 8, 2025 at 11:49 AM
jsantoyo.bsky.social
Generating long deletions across the genome with pooled paired prime editing screens. #GenomeDeletions #LongDeletions #PairedPrimeEditing #Genomics @biorxivpreprint.bsky.social 🧪🧬
www.biorxiv.org/content/10.1...
November 8, 2025 at 10:15 AM
jsantoyo.bsky.social
Svirlpool: structural variant detection from long read sequencing by local assembly. #LongRead #Sequencing #LRS #StructuralVariants #SVs @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 8, 2025 at 9:31 AM
jsantoyo.bsky.social
A multi-tissue atlas of genetic regulatory effects in sheep. #SheepGenome #GeneticRegulation #GeneticVariants #Genomics #FarmGTEX #SheepGTEX @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 8, 2025 at 8:32 AM
jsantoyo.bsky.social
PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases. #BacterialDatabase #BacterialGenomes #SequeceIndexing #Kmers #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
November 7, 2025 at 8:05 PM
jsantoyo.bsky.social
A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons. #CanineGenomes #Retrotransposon #LINE1 #SINE #GenomeAssembly #GenomeEvolution #Genomics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
November 7, 2025 at 7:05 PM
jsantoyo.bsky.social
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing. #DirectRNAseq #RNAsequencing #RNAmodifications #m6A #Genomics #Bioinformatics @nanoporetech.com 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
November 7, 2025 at 6:05 PM
jsantoyo.bsky.social
Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding. #Metabarcoding #Metagenomics #Yeast #FoodFermentation @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 7, 2025 at 5:32 PM
jsantoyo.bsky.social
mRNA 3′ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth. #miRNA #miRNAdegratdation #3UTR @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
November 7, 2025 at 2:49 PM
jsantoyo.bsky.social
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing. #DirectRNAseq #Sequencing #RNAmodifications @nanoporetech.com
www.biorxiv.org/content/10.1...
November 6, 2025 at 11:30 AM