Javier Santoyo
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jsantoyo.bsky.social
Javier Santoyo
@jsantoyo.bsky.social
2.2K followers 2K following 910 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
SeqManager: A Web-Based Tool for Efficient Sequencing Data Storage Management and Duplicate Detection. #SequencingData #DataStorage #DuplicateDetection #Genomics #Bioinformatics @bioinfoadv.bsky.social
academic.oup.com/bioinformati...
SeqManager: A Web-Based Tool for Efficient Sequencing Data Storage Management and Duplicate Detection
AbstractMotivation. Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storag
academic.oup.com
November 20, 2025 at 9:31 AM
jsantoyo.bsky.social
GREGoR: accelerating genomics for rare diseases. #ShortRead #LongRead #Sequencing #LRS #NGS #MultiOmics #Genomics #DataSets #RareDiseases @nature.com
www.nature.com/articles/s41... 🧪🧬 🖥️
November 19, 2025 at 4:41 PM
jsantoyo.bsky.social
FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT). #Kmers #MaskedBWT #Genomics #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...
November 18, 2025 at 11:30 AM
jsantoyo.bsky.social
Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2. #MicrobialCommunities #Metagenomics #MicrobesProfiling #Microbiome
microbiomejournal.biomedcentral.com/articles/10....
November 18, 2025 at 10:15 AM
jsantoyo.bsky.social
Y-chromosome alteration and its impact on cancer progression and metastasis. #YChr #Cancer #Metastasis #CellularMolecularBiologyLetters 🧪🧬
cmbl.biomedcentral.com/articles/10....
November 18, 2025 at 9:31 AM
jsantoyo.bsky.social
ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing. #CNV #WGS #ShallowSequencing #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 4:01 PM
jsantoyo.bsky.social
Synteny plot quality control with SyntenyQC. #SyntenyPlots #Grnomivd #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 11:49 AM
jsantoyo.bsky.social
Target and Biomarker Exploration Portal for Drug Discovery. #BiomarkerExploration #DrugDiscovery #NetworkAnalysis #LLMs #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 10:15 AM
jsantoyo.bsky.social
Spider: a flexible and unified framework for simulating spatial transcriptomics data. #SpatialTranscriptomics #DataSimulation #Genomics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 9:31 AM
jsantoyo.bsky.social
OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. #StructuralVariants #SVs #SVcomparison #SVidentification #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 8:32 AM
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