Javier Santoyo's Avatar

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/

2,238 Followers  |  1,985 Following  |  948 Posts  |  Joined: 06.11.2023  |  1.983

Latest posts by jsantoyo.bsky.social on Bluesky

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Long-read metagenomics reveals phage dynamics in the human gut microbiome. #GutMicrobiome #Phages #LongReads #Sequencing #Genomics @nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...

10.12.2025 09:31 — 👍 1    🔁 0    💬 0    📌 0
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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...

09.12.2025 12:15 — 👍 1    🔁 1    💬 0    📌 0
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Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics
link.springer.com/article/10.1...

09.12.2025 11:30 — 👍 1    🔁 0    💬 0    📌 0
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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...

09.12.2025 10:15 — 👍 0    🔁 0    💬 0    📌 0

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...

09.12.2025 09:31 — 👍 0    🔁 0    💬 0    📌 0
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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...

08.12.2025 10:15 — 👍 0    🔁 0    💬 0    📌 0
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TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. #Microbiome #DataAugmentation #GenerativeModel #BMCbioinformatics 🧪🧬 🖥️
link.springer.com/article/10.1...

08.12.2025 09:31 — 👍 2    🔁 0    💬 0    📌 0
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Universal noninvasive prenatal diagnosis for monogenic disorders using cell-free plasma DNA. #cfDNA #MonogenicDisorders #PrenatalDiagnosis #GenomeMedicine
link.springer.com/article/10.1...

06.12.2025 16:00 — 👍 0    🔁 0    💬 0    📌 0
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Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus. #StructuralVariants #Pangenomes #BrasicaNapusGenome #PlantGenomics #Bioinformatics #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...

05.12.2025 09:31 — 👍 2    🔁 0    💬 0    📌 0
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HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️
link.springer.com/article/10.1...

03.12.2025 11:30 — 👍 2    🔁 2    💬 0    📌 0
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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...

03.12.2025 10:15 — 👍 2    🔁 0    💬 0    📌 0
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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…

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...

03.12.2025 09:31 — 👍 0    🔁 0    💬 0    📌 0
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Xenbase: 25 years of integrating molecular and biomedical data from Xenopus. #Xenopus #MolecularData #BiomedicalData #Genetics 🧪🧬 🖥️
academic.oup.com/genetics/adv...

02.12.2025 19:05 — 👍 1    🔁 0    💬 0    📌 0
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The value of structural variants to conservation genomics in the pangenome era. #StructuralVariants #SVs #Bioinformatics #Genomics #ConservationGenomics #Pangenomes #JournalOfHeredity
academic.oup.com/jhered/advan...

02.12.2025 18:05 — 👍 2    🔁 0    💬 0    📌 0
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MeTAline: enabling reproducible and scalable metagenomic analyses. #MetagenomicAnalysis #ShotgunMetagenomics #Snakemake #Containers #HPC #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️
academic.oup.com/nargab/artic...

02.12.2025 17:32 — 👍 2    🔁 0    💬 0    📌 0
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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-...

02.12.2025 16:01 — 👍 0    🔁 0    💬 0    📌 0
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The effects of bioinformatics preprocessing on cell-free DNA fragment analysis. #cfDNA #Bioinformatics #DataProcessing #FragmentAnalysis @gigascience.bsky.social 🧪🧬 🖥️
academic.oup.com/gigascience/...

02.12.2025 15:31 — 👍 0    🔁 0    💬 0    📌 0
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Quantitative detection of DNA methylation from nanopore sequencing data without raw signals. #DNAmethylation #Nanopore #Sequencing #Bioinformatics @gigascience.bsky.social
academic.oup.com/gigascience/...

02.12.2025 14:49 — 👍 0    🔁 0    💬 0    📌 0
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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/...

02.12.2025 12:15 — 👍 0    🔁 0    💬 0    📌 0
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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/...

02.12.2025 11:30 — 👍 3    🔁 0    💬 0    📌 0
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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-...

02.12.2025 10:15 — 👍 2    🔁 3    💬 1    📌 0
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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/...

02.12.2025 09:31 — 👍 5    🔁 2    💬 0    📌 0
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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-...

01.12.2025 09:31 — 👍 1    🔁 1    💬 0    📌 0
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EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025. #Bioinformatics #Genomics #PublicBiomolecularData #EBI #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

30.11.2025 20:05 — 👍 3    🔁 0    💬 0    📌 0
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The UCSC Genome Browser database: 2026 update. #GenomeBrowser #UCSC #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

30.11.2025 19:05 — 👍 8    🔁 0    💬 0    📌 0
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Genenames.org: the HGNC and PGNC resources in 2026. #GenesNomenclature #Genomes #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

30.11.2025 18:05 — 👍 1    🔁 0    💬 0    📌 0
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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-...

30.11.2025 17:49 — 👍 3    🔁 0    💬 0    📌 0
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TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution Abstract. Transposable elements (TEs) are repetitive DNA sequences typically silenced in normal tissues. Their dysregulation in cancer can significantly im

TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution. #TransposableElements #TE #HumanCancer #SingleCells #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

30.11.2025 16:01 — 👍 1    🔁 0    💬 0    📌 0
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Ensembl 2026. #Genomes# Annotation #Genomics #Bioinformatics #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

30.11.2025 11:31 — 👍 2    🔁 0    💬 0    📌 0
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JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes Abstract. The Joint Open Genome and Omics Platform 1.0 (JoGo) is a global, long-read-based human haplotype database covering 19 194 MANE-standardized prote

JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes.#GeneticStandard #GeneHaplotypes #Bioinformatics #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

30.11.2025 10:15 — 👍 2    🔁 0    💬 0    📌 0

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