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
LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/
Opinions my own. He/Him
LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/
GPTBioInsightor—Leveraging LLMs for transparent scRAN-Seq cell type annotations. #SingleCell #scRNAseq #LLMs #AI #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...
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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
academic.oup.com
January 23, 2026 at 9:31 AM
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/bioinformati...
Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM. #SpatialTranscriptomics #Isoforms @natbiotech.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 21, 2026 at 11:30 AM
Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM. #SpatialTranscriptomics #Isoforms @natbiotech.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies. #SingleCell #scRNAseq #Benchmarking #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
January 21, 2026 at 10:15 AM
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies. #SingleCell #scRNAseq #Benchmarking #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
MobiCT: a UMI-based circulating tumor DNA analysis pipeline. #UMIs #cfDNA #Nextflow #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
January 21, 2026 at 9:31 AM
MobiCT: a UMI-based circulating tumor DNA analysis pipeline. #UMIs #cfDNA #Nextflow #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
LinkML: An Open Data Modeling Framework. #DataModel #DataSharing #FAIRdata @gigascience.bsky.social
academic.oup.com/gigascience/...
linkml.io
academic.oup.com/gigascience/...
linkml.io
January 20, 2026 at 2:49 PM
LinkML: An Open Data Modeling Framework. #DataModel #DataSharing #FAIRdata @gigascience.bsky.social
academic.oup.com/gigascience/...
linkml.io
academic.oup.com/gigascience/...
linkml.io
An evaluation of computational methods for reconstruction of human viral DNA genomes. #ViralDNAgenomes #MethodBenchmarking @gigascience.bsky.social
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
January 18, 2026 at 11:31 AM
An evaluation of computational methods for reconstruction of human viral DNA genomes. #ViralDNAgenomes #MethodBenchmarking @gigascience.bsky.social
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
Harnessing Artificial Intelligence for Genomic Variant Prediction: Advances, Challenges, and Future Directions. #GenomicVariants #VariantInterpretation #AI @gigascience.bsky.social
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
January 18, 2026 at 10:15 AM
Harnessing Artificial Intelligence for Genomic Variant Prediction: Advances, Challenges, and Future Directions. #GenomicVariants #VariantInterpretation #AI @gigascience.bsky.social
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
Translating short-form Python exercises to other programming languages using diverse prompting strategies. #LLMs #Programming #Bioinformatics #CodeTranslation @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
January 18, 2026 at 9:31 AM
Translating short-form Python exercises to other programming languages using diverse prompting strategies. #LLMs #Programming #Bioinformatics #CodeTranslation @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
A comprehensive survey of genome language models in bioinformatics. #GenomeLanguageModels #gMLs #ModelsReview #Bioinformatics #Genomics #BriefingsInBioinformatics
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January 18, 2026 at 8:32 AM
A comprehensive survey of genome language models in bioinformatics. #GenomeLanguageModels #gMLs #ModelsReview #Bioinformatics #Genomics #BriefingsInBioinformatics
academic.oup.com/bib/article/...
academic.oup.com/bib/article/...
REDAC: RNA-seq Expression Data Analysis Chatbot. #RNAseq #LLMss #DataAnalysis #DifferentialExpression #Sequencing #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
January 17, 2026 at 5:31 PM
REDAC: RNA-seq Expression Data Analysis Chatbot. #RNAseq #LLMss #DataAnalysis #DifferentialExpression #Sequencing #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
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...
academic.oup.com/bioinformati...
January 17, 2026 at 4:00 PM
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...
academic.oup.com/bioinformati...
ChromoMapper: a new tool to quickly compare large genome assemblies. #GenomeAssembly #GenomeComparison #Bioinformatics #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
January 17, 2026 at 11:49 AM
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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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...
academic.oup.com/bioinformati...
January 17, 2026 at 10:15 AM
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...
academic.oup.com/bioinformati...
ASTRO: Automated Spatial-Transcriptome whole RNA Output. #SpatialTranscriptomics #RNAseq #FFPE #Genome #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
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January 17, 2026 at 9:31 AM
ASTRO: Automated Spatial-Transcriptome whole RNA Output. #SpatialTranscriptomics #RNAseq #FFPE #Genome #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
January 17, 2026 at 8:32 AM
scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
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CiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 16, 2025 at 11:30 AM
CiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Search-and-remove genome editing allows selection of cells by DNA sequence. #GenomeEditing #CellSelection @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 16, 2025 at 10:15 AM
Search-and-remove genome editing allows selection of cells by DNA sequence. #GenomeEditing #CellSelection @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Mapping single-cell diploid chromatin fiber architectures using DAF-seq. #SingleCell #ChromatinFiberArchitecture #Sequencing #Genomics @natbiotech.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 16, 2025 at 9:31 AM
Mapping single-cell diploid chromatin fiber architectures using DAF-seq. #SingleCell #ChromatinFiberArchitecture #Sequencing #Genomics @natbiotech.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com/articles/s41...
December 15, 2025 at 11:30 AM
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...
www.nature.com/articles/s41...
Whole-genome landscapes of 1,364 breast cancers. #WGS #BreastCancer #Genomics @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 15, 2025 at 10:15 AM
Whole-genome landscapes of 1,364 breast cancers. #WGS #BreastCancer #Genomics @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Insights into natural neocentromere evolution from a cattle T2T X chromosome. #CattleGenome #T2T #HaplotypeResolvedGenome #Centromeres #Genomics @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 15, 2025 at 9:31 AM
Insights into natural neocentromere evolution from a cattle T2T X chromosome. #CattleGenome #T2T #HaplotypeResolvedGenome #Centromeres #Genomics @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome. #GutMicrobiome #Phages #LongReads #Sequencing #Genomics @nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 10, 2025 at 9:31 AM
Long-read metagenomics reveals phage dynamics in the human gut microbiome. #GutMicrobiome #Phages #LongReads #Sequencing #Genomics @nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
link.springer.com/article/10.1...
December 9, 2025 at 12:15 PM
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...
link.springer.com/article/10.1...
Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 9, 2025 at 11:30 AM
Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics
link.springer.com/article/10.1...
link.springer.com/article/10.1...
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...
link.springer.com/article/10.1...
December 9, 2025 at 10:15 AM
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...
link.springer.com/article/10.1...