Javier Santoyo
@jsantoyo.bsky.social
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/
Opinions my own. He/Him
Lab: https://genomics.ed.ac.uk/
LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/
ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing. #CNV #WGS #ShallowSequencing #Bioinformatics 🧬 🖥️
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November 15, 2025 at 4:01 PM
ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing. #CNV #WGS #ShallowSequencing #Bioinformatics 🧬 🖥️
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Synteny plot quality control with SyntenyQC. #SyntenyPlots #Grnomivd #Bioinformatics 🧬 🖥️
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November 15, 2025 at 11:49 AM
Synteny plot quality control with SyntenyQC. #SyntenyPlots #Grnomivd #Bioinformatics 🧬 🖥️
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Target and Biomarker Exploration Portal for Drug Discovery. #BiomarkerExploration #DrugDiscovery #NetworkAnalysis #LLMs #Bioinformatics 🧬 🖥️
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November 15, 2025 at 10:15 AM
Target and Biomarker Exploration Portal for Drug Discovery. #BiomarkerExploration #DrugDiscovery #NetworkAnalysis #LLMs #Bioinformatics 🧬 🖥️
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Spider: a flexible and unified framework for simulating spatial transcriptomics data. #SpatialTranscriptomics #DataSimulation #Genomics #Bioinformatics 🧬 🖥️
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November 15, 2025 at 9:31 AM
Spider: a flexible and unified framework for simulating spatial transcriptomics data. #SpatialTranscriptomics #DataSimulation #Genomics #Bioinformatics 🧬 🖥️
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OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. #StructuralVariants #SVs #SVcomparison #SVidentification #Bioinformatics 🧪🧬 🖥️
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November 15, 2025 at 8:32 AM
OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. #StructuralVariants #SVs #SVcomparison #SVidentification #Bioinformatics 🧪🧬 🖥️
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insilicoSV: a flexible grammar-based framework for structural variant simulation and placement. #StructuralVariants #SVs #SVsimulation #SimulatedData #Genomics #Bioinformatics 🧪🧬 🖥️
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November 9, 2025 at 8:05 PM
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement. #StructuralVariants #SVs #SVsimulation #SimulatedData #Genomics #Bioinformatics 🧪🧬 🖥️
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Genome size estimation from long read overlaps. #GenomeSize #LongRead #Sequencing #Genomics #Bioinformatics 🧪🧬 🖥️
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November 9, 2025 at 7:05 PM
Genome size estimation from long read overlaps. #GenomeSize #LongRead #Sequencing #Genomics #Bioinformatics 🧪🧬 🖥️
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HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements. #EndogenousViralElements #EukaryoticHostGenomes #Genomics #Bioinformatics 🧪🧬 🖥️
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November 9, 2025 at 6:05 PM
HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements. #EndogenousViralElements #EukaryoticHostGenomes #Genomics #Bioinformatics 🧪🧬 🖥️
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PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification. #PathogenSurveillance #Nextflow #Bioinformatics #WGS #PathogenIdentification @biorxivpreprint.bsky.social
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November 9, 2025 at 5:49 PM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification. #PathogenSurveillance #Nextflow #Bioinformatics #WGS #PathogenIdentification @biorxivpreprint.bsky.social
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igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review. #IGV #InteractiveVisualizationss #GeneticVariants #VariantReview @biorxivpreprint.bsky.social
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November 9, 2025 at 4:00 PM
igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review. #IGV #InteractiveVisualizationss #GeneticVariants #VariantReview @biorxivpreprint.bsky.social
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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 🧪🧬
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November 9, 2025 at 10:15 AM
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 🧪🧬
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November 9, 2025 at 9:31 AM
Assembling unmapped reads reveals hidden variation in South Asian genomes. #GenomeVariation #UnmappedReads #SouthAsianPopulation @biorxivpreprint.bsky.social
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November 9, 2025 at 8:32 AM
Assembling unmapped reads reveals hidden variation in South Asian genomes. #GenomeVariation #UnmappedReads #SouthAsianPopulation @biorxivpreprint.bsky.social
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Site-specific DNA insertion into the human genome with engineered recombinases. #GenomeEditing #DNAinsertion #LargeSerineRecombinases @natbiotech.nature.com
www.nature.com/articles/s41...
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November 8, 2025 at 8:05 PM
Site-specific DNA insertion into the human genome with engineered recombinases. #GenomeEditing #DNAinsertion #LargeSerineRecombinases @natbiotech.nature.com
www.nature.com/articles/s41...
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Curating 16S rRNA databases enhances taxonomic accuracy and computational efficiency in microbial profiling. #Metabarcoding #16S #rRNA #BacterialGenomes #SequenceDatabases #DatabaseCuration #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
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November 8, 2025 at 7:05 PM
Curating 16S rRNA databases enhances taxonomic accuracy and computational efficiency in microbial profiling. #Metabarcoding #16S #rRNA #BacterialGenomes #SequenceDatabases #DatabaseCuration #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
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Beyond reference bias: Making pangenomes accessible with PangyPlot. #GenomeBrowser #PangenomeGraphs #GeneAnnotations #Visualization #Genomics #Bioinformatics @biorxivpreprint.bsky.social
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November 8, 2025 at 5:31 PM
Beyond reference bias: Making pangenomes accessible with PangyPlot. #GenomeBrowser #PangenomeGraphs #GeneAnnotations #Visualization #Genomics #Bioinformatics @biorxivpreprint.bsky.social
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RNA stability enhancers for durable base-modified mRNA therapeutics. #RNAstability #mRNAtherapeutics @natbiotech.nature.com
www.nature.com/articles/s41...
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November 8, 2025 at 4:01 PM
RNA stability enhancers for durable base-modified mRNA therapeutics. #RNAstability #mRNAtherapeutics @natbiotech.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A comprehensive view of somatic mosaicism by single-cell DNA analysis. #SingleCell #scDNAseq #SomaticMosaicism @biorxivpreprint.bsky.social 🧪🧬 🖥️
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November 8, 2025 at 3:25 PM
A comprehensive view of somatic mosaicism by single-cell DNA analysis. #SingleCell #scDNAseq #SomaticMosaicism @biorxivpreprint.bsky.social 🧪🧬 🖥️
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Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence. #MycobacteriumTuberculosis #Pangenome #ReferenceSequence @biorxivpreprint.bsky.social 🧪
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November 8, 2025 at 11:49 AM
Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence. #MycobacteriumTuberculosis #Pangenome #ReferenceSequence @biorxivpreprint.bsky.social 🧪
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Generating long deletions across the genome with pooled paired prime editing screens. #GenomeDeletions #LongDeletions #PairedPrimeEditing #Genomics @biorxivpreprint.bsky.social 🧪🧬
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November 8, 2025 at 10:15 AM
Generating long deletions across the genome with pooled paired prime editing screens. #GenomeDeletions #LongDeletions #PairedPrimeEditing #Genomics @biorxivpreprint.bsky.social 🧪🧬
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Svirlpool: structural variant detection from long read sequencing by local assembly. #LongRead #Sequencing #LRS #StructuralVariants #SVs @biorxivpreprint.bsky.social
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November 8, 2025 at 9:31 AM
Svirlpool: structural variant detection from long read sequencing by local assembly. #LongRead #Sequencing #LRS #StructuralVariants #SVs @biorxivpreprint.bsky.social
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A multi-tissue atlas of genetic regulatory effects in sheep. #SheepGenome #GeneticRegulation #GeneticVariants #Genomics #FarmGTEX #SheepGTEX @biorxivpreprint.bsky.social
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November 8, 2025 at 8:32 AM
A multi-tissue atlas of genetic regulatory effects in sheep. #SheepGenome #GeneticRegulation #GeneticVariants #Genomics #FarmGTEX #SheepGTEX @biorxivpreprint.bsky.social
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PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases. #BacterialDatabase #BacterialGenomes #SequeceIndexing #Kmers #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
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November 7, 2025 at 8:05 PM
PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases. #BacterialDatabase #BacterialGenomes #SequeceIndexing #Kmers #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
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A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons. #CanineGenomes #Retrotransposon #LINE1 #SINE #GenomeAssembly #GenomeEvolution #Genomics @biorxivpreprint.bsky.social 🧪🧬 🖥️
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November 7, 2025 at 7:05 PM
A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons. #CanineGenomes #Retrotransposon #LINE1 #SINE #GenomeAssembly #GenomeEvolution #Genomics @biorxivpreprint.bsky.social 🧪🧬 🖥️
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Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing. #DirectRNAseq #RNAsequencing #RNAmodifications #m6A #Genomics #Bioinformatics @nanoporetech.com 🧪🧬 🖥️
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November 7, 2025 at 6:05 PM
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...
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