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Javier Santoyo

@jsantoyo.bsky.social
2.3K followers 2K following 970 posts

Genomics & Bioinformatics #Omics #NGS #LongReads 🧪🧬 🖥️ Opinions my own. He/Him LinkedIn: www.linkedin.com/in/javiersantoyolo…

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Javier Santoyo @jsantoyo.bsky.social · 07/03/2026
Somatic genomics as a discovery engine for biomedicine. #Genomics #CancerGenomics www.cell.com/cell/fulltex...
cell.com
Somatic genomics as a discovery engine for biomedicine
Somatic genetics uses tissue mutations to understand aging, reveal disease mechanisms, and guide new therapies.
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Reposted by Javier Santoyo
Shawn Baker @sandiegomics.bsky.social · 19/02/2026
Element reveals more information about their VITARI platform, a foray into the high-throughput sequencing market. sandiegomics.com/element-join...
sandiegomics.com
Element Joins the High-Throughput Market with the VITARI Platform
Back at JPM Element teased that they would be coming out with the VITARI, a benchtop sequencer capable of generating whole genomes for $100. This would best Illumina’s list price of $200 with the N…
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Javier Santoyo @jsantoyo.bsky.social · 23/01/2026
GPTBioInsightor—Leveraging LLMs for transparent scRAN-Seq cell type annotations. #SingleCell #scRNAseq #LLMs #AI #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...
academic.oup.com
GPTBioInsightor—Leveraging LLMs for transparent scRAN-Seq cell type annotations
Abstract. Large language models (LLMs) are rapidly becoming indispensable across the life‑sciences spectrum, from literature mining through clinical decisi
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Javier Santoyo @jsantoyo.bsky.social · 21/01/2026
Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM. #SpatialTranscriptomics #Isoforms @natbiotech.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 21/01/2026
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies. #SingleCell #scRNAseq #Benchmarking #NARgenomicsAndBioinformatics 🧪🧬 🖥️ academic.oup.com/nargab/artic...
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Javier Santoyo @jsantoyo.bsky.social · 21/01/2026
MobiCT: a UMI-based circulating tumor DNA analysis pipeline. #UMIs #cfDNA #Nextflow #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️ academic.oup.com/nargab/artic...
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Javier Santoyo @jsantoyo.bsky.social · 20/01/2026
LinkML: An Open Data Modeling Framework. #DataModel #DataSharing #FAIRdata @gigascience.bsky.social academic.oup.com/gigascience/... linkml.io
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Javier Santoyo @jsantoyo.bsky.social · 18/01/2026
An evaluation of computational methods for reconstruction of human viral DNA genomes. #ViralDNAgenomes #MethodBenchmarking @gigascience.bsky.social academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 18/01/2026
Harnessing Artificial Intelligence for Genomic Variant Prediction: Advances, Challenges, and Future Directions. #GenomicVariants #VariantInterpretation #AI @gigascience.bsky.social academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 18/01/2026
Translating short-form Python exercises to other programming languages using diverse prompting strategies. #LLMs #Programming #Bioinformatics #CodeTranslation @gigascience.bsky.social 🧪🧬 🖥️ academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 18/01/2026
A comprehensive survey of genome language models in bioinformatics. #GenomeLanguageModels #gMLs #ModelsReview #Bioinformatics #Genomics #BriefingsInBioinformatics academic.oup.com/bib/article/...
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Javier Santoyo @jsantoyo.bsky.social · 17/01/2026
REDAC: RNA-seq Expression Data Analysis Chatbot. #RNAseq #LLMss #DataAnalysis #DifferentialExpression #Sequencing #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...
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Javier Santoyo @jsantoyo.bsky.social · 17/01/2026
VST-DAVis: An R shiny Application and web-browser for Spatial Transcriptomics Data Analysis and Visualization. #SpatialTranscriptomics #DataVisualization #RNAseq #Rshiny #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...
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Javier Santoyo @jsantoyo.bsky.social · 17/01/2026
ChromoMapper: a new tool to quickly compare large genome assemblies. #GenomeAssembly #GenomeComparison #Bioinformatics #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...
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Javier Santoyo @jsantoyo.bsky.social · 17/01/2026
Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing. #SingleCell #LongRead #Sequencing #scRNAseq #Isoforms #DifferentialExpression #Bioinformaticcs #Genomics 🧪🧬 🖥️ academic.oup.com/bioinformati...
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Javier Santoyo @jsantoyo.bsky.social · 17/01/2026
ASTRO: Automated Spatial-Transcriptome whole RNA Output. #SpatialTranscriptomics #RNAseq #FFPE #Genome #Bioinformatics 🧪🧬 🖥️ academic.oup.com/bioinformati...
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Javier Santoyo @jsantoyo.bsky.social · 17/01/2026
scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️ academic.oup.com/bioinformati...
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Javier Santoyo @jsantoyo.bsky.social · 16/12/2025
CiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 16/12/2025
Search-and-remove genome editing allows selection of cells by DNA sequence. #GenomeEditing #CellSelection @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 16/12/2025
Mapping single-cell diploid chromatin fiber architectures using DAF-seq. #SingleCell #ChromatinFiberArchitecture #Sequencing #Genomics @natbiotech.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 15/12/2025
Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.#SpatialTranscriptomics #StandardizedMetrics #DataRepository #BestPractices #OpenSourceSoftware #Genomics #Bioinformatics @natbiotech.nature.com www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 15/12/2025
Whole-genome landscapes of 1,364 breast cancers. #WGS #BreastCancer #Genomics @nature.com www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 15/12/2025
Insights into natural neocentromere evolution from a cattle T2T X chromosome. #CattleGenome #T2T #HaplotypeResolvedGenome #Centromeres #Genomics @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 10/12/2025
Long-read metagenomics reveals phage dynamics in the human gut microbiome. #GutMicrobiome #Phages #LongReads #Sequencing #Genomics @nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...
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Javier Santoyo @jsantoyo.bsky.social · 09/12/2025
A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data. #RNAisoforms #GTEx #LongReads #Sequencing #Genomics #Bioinformatics #BMCgenomics link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 09/12/2025
Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 09/12/2025
Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress. #SingleCell #scRNAseq #PlateBasedAssay #10X #Genomics #BMCgenomics link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 09/12/2025
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets. #Metagenomics #AlignmentBasedSearches #Genomics #Bioinformatics #BMCbioinformatics link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 08/12/2025
MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation. #DataSimulation #CancerVariants #SequencingReads #ComputationalModelling #BMCBioinformatics 🧪🧬 🖥️ link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 08/12/2025
TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. #Microbiome #DataAugmentation #GenerativeModel #BMCbioinformatics 🧪🧬 🖥️ link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 06/12/2025
Universal noninvasive prenatal diagnosis for monogenic disorders using cell-free plasma DNA. #cfDNA #MonogenicDisorders #PrenatalDiagnosis #GenomeMedicine link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 05/12/2025
Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus. #StructuralVariants #Pangenomes #BrasicaNapusGenome #PlantGenomics #Bioinformatics #GenomeBiology 🧪🧬 🖥️ link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 03/12/2025
HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️ link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 03/12/2025
Long-read structural variant discovery and targeted short read genotyping enables population scale characterization of structural variation in rhesus macaques. #SVs #RhesusMacaqueGenomes #LonngRead #Sequencing #Genomics #Bioinformatics #GenomeBiology 🧪🧬 🖥️ link.springer.com/article/10.1...
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Javier Santoyo @jsantoyo.bsky.social · 03/12/2025
Evaluation of false positive and false negative errors in targeted next generation sequencing. #TargetNGS #Sequencing #FalsePositives #FalseNegatives #Genomics #Bioinformatics #GenomeBiology link.springer.com/article/10.1...
link.springer.com
Evaluation of false positive and false negative errors in targeted next generation sequencing - Genome Biology
Background Next-generation sequencing (NGS) has become an indispensable diagnostic tool across various diseases. However, sequencing and analysis errors remain major barriers to clinical…
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
Xenbase: 25 years of integrating molecular and biomedical data from Xenopus. #Xenopus #MolecularData #BiomedicalData #Genetics 🧪🧬 🖥️ academic.oup.com/genetics/adv...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
The value of structural variants to conservation genomics in the pangenome era. #StructuralVariants #SVs #Bioinformatics #Genomics #ConservationGenomics #Pangenomes #JournalOfHeredity academic.oup.com/jhered/advan...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
MeTAline: enabling reproducible and scalable metagenomic analyses. #MetagenomicAnalysis #ShotgunMetagenomics #Snakemake #Containers #HPC #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️ academic.oup.com/nargab/artic...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
A Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet. #HumanGenome #ReferenceGenome #ChinesePopulation #T2T #Genomics #GenomicsProteomicsAndBioinformatics 🧪🧬 🖥️ academic.oup.com/gpb/advance-...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
The effects of bioinformatics preprocessing on cell-free DNA fragment analysis. #cfDNA #Bioinformatics #DataProcessing #FragmentAnalysis @gigascience.bsky.social 🧪🧬 🖥️ academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
Quantitative detection of DNA methylation from nanopore sequencing data without raw signals. #DNAmethylation #Nanopore #Sequencing #Bioinformatics @gigascience.bsky.social academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
NApy: Efficient Statistics in Python for Large-Scale Heterogeneous Data with Enhanced Support for Missing Data. #Statistics #Python #MissingData #HeterogeneousData #Bioinformatics @gigascience.bsky.social 🧪🧬 🖥️ academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations. #RNAseq #DataAnalysis #TranscriptomicsAnalysis #Visualization #Genomics #Bioinformatics @gigascience.bsky.social 🧪🧬 🖥️ academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes. #ProkaryoticGenomes #AnnotatedGenomes #Bioinformatics #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...
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Javier Santoyo @jsantoyo.bsky.social · 02/12/2025
Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta). #LiverwortsGenome #PlantGenomics #LargeChromosomes @gigascience.bsky.social 🧪🧬 🖥️ academic.oup.com/gigascience/...
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Javier Santoyo @jsantoyo.bsky.social · 01/12/2025
RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing. #RNAmodifications #Nanopore #DirectRNAseq #Bioinformatics #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...
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Javier Santoyo @jsantoyo.bsky.social · 30/11/2025
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025. #Bioinformatics #Genomics #PublicBiomolecularData #EBI #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...
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Javier Santoyo @jsantoyo.bsky.social · 30/11/2025
The UCSC Genome Browser database: 2026 update. #GenomeBrowser #UCSC #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...
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Javier Santoyo @jsantoyo.bsky.social · 30/11/2025
Genenames.org: the HGNC and PGNC resources in 2026. #GenesNomenclature #Genomes #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...
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Javier Santoyo @jsantoyo.bsky.social · 30/11/2025
SomaMutDB 2.0: A comprehensive database for exploring somatic mutations and their functional impact in normal human tissues. #SomaticMutations #HumanTissues #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...
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