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/
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...
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...
link.springer.com/article/10.1...
December 9, 2025 at 9:31 AM
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...
link.springer.com/article/10.1...
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...
link.springer.com/article/10.1...
December 8, 2025 at 10:15 AM
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...
link.springer.com/article/10.1...
TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. #Microbiome #DataAugmentation #GenerativeModel #BMCbioinformatics 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 8, 2025 at 9:31 AM
TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. #Microbiome #DataAugmentation #GenerativeModel #BMCbioinformatics 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Universal noninvasive prenatal diagnosis for monogenic disorders using cell-free plasma DNA. #cfDNA #MonogenicDisorders #PrenatalDiagnosis #GenomeMedicine
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 6, 2025 at 4:00 PM
Universal noninvasive prenatal diagnosis for monogenic disorders using cell-free plasma DNA. #cfDNA #MonogenicDisorders #PrenatalDiagnosis #GenomeMedicine
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus. #StructuralVariants #Pangenomes #BrasicaNapusGenome #PlantGenomics #Bioinformatics #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 5, 2025 at 9:31 AM
Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus. #StructuralVariants #Pangenomes #BrasicaNapusGenome #PlantGenomics #Bioinformatics #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 3, 2025 at 11:30 AM
HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...
link.springer.com/article/10.1...
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...
link.springer.com/article/10.1...
December 3, 2025 at 10:15 AM
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...
link.springer.com/article/10.1...
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/article/10.1...
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…
link.springer.com
December 3, 2025 at 9:31 AM
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/article/10.1...
Xenbase: 25 years of integrating molecular and biomedical data from Xenopus. #Xenopus #MolecularData #BiomedicalData #Genetics 🧪🧬 🖥️
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...
December 2, 2025 at 7:05 PM
Xenbase: 25 years of integrating molecular and biomedical data from Xenopus. #Xenopus #MolecularData #BiomedicalData #Genetics 🧪🧬 🖥️
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...
The value of structural variants to conservation genomics in the pangenome era. #StructuralVariants #SVs #Bioinformatics #Genomics #ConservationGenomics #Pangenomes #JournalOfHeredity
academic.oup.com/jhered/advan...
academic.oup.com/jhered/advan...
December 2, 2025 at 6:05 PM
The value of structural variants to conservation genomics in the pangenome era. #StructuralVariants #SVs #Bioinformatics #Genomics #ConservationGenomics #Pangenomes #JournalOfHeredity
academic.oup.com/jhered/advan...
academic.oup.com/jhered/advan...
MeTAline: enabling reproducible and scalable metagenomic analyses. #MetagenomicAnalysis #ShotgunMetagenomics #Snakemake #Containers #HPC #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
December 2, 2025 at 5:32 PM
MeTAline: enabling reproducible and scalable metagenomic analyses. #MetagenomicAnalysis #ShotgunMetagenomics #Snakemake #Containers #HPC #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
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-...
academic.oup.com/gpb/advance-...
December 2, 2025 at 4:01 PM
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-...
academic.oup.com/gpb/advance-...
The effects of bioinformatics preprocessing on cell-free DNA fragment analysis. #cfDNA #Bioinformatics #DataProcessing #FragmentAnalysis @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
December 2, 2025 at 3:31 PM
The effects of bioinformatics preprocessing on cell-free DNA fragment analysis. #cfDNA #Bioinformatics #DataProcessing #FragmentAnalysis @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
Quantitative detection of DNA methylation from nanopore sequencing data without raw signals. #DNAmethylation #Nanopore #Sequencing #Bioinformatics @gigascience.bsky.social
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
December 2, 2025 at 2:49 PM
Quantitative detection of DNA methylation from nanopore sequencing data without raw signals. #DNAmethylation #Nanopore #Sequencing #Bioinformatics @gigascience.bsky.social
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
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/...
academic.oup.com/gigascience/...
December 2, 2025 at 12:15 PM
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/...
academic.oup.com/gigascience/...