Javier Santoyo
@jsantoyo
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Genomics & Bioinformatics Scientist at @EdinburghUni. Head of @edgenome | #Omics #NGS #LongReads | Views my own | Also @ https://t.co/TCJKasgyMt
Edinburgh
Joined May 2011
RT @CellGenomics: LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early bra….
cell.com
Adami et al. demonstrate that evolutionarily young L1s are expressed in human pluripotent stem cells and are dynamically regulated throughout neural differentiation. The study examines the role of...
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RT @TrendsGenetics: 3D genome sequencing technology in its mid-teens: past, present, and future .
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RT @biorxiv_bioinfo: FAVABEAN and FALAPhyl: Open-Source Pipelines for Scalable 16s rRNA Microbiome Data Processing and Visualization https:….
biorxiv.org
Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between...
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RT @biorxiv_bioinfo: Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution #biorx….
biorxiv.org
Bulk RNA-seq deconvolution typically uses single-cell RNA-sequencing (scRNA-seq) references, but some cell types are only detectable through single-nucleus RNA sequencing (snRNA-seq). Because...
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RT @NatureRevGenet: New online! Imaging-based multimodal profiling of single cells with STAMP .
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RT @acarroll_ATG: I'll be speaking in this webinar ( on September 10, where I'll share our benchmarks and observati….
event.on24.com
Wednesday, September 10, 2025 at 12:00 PM Eastern Daylight Time.
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Pangenome-guided sequence assembly via binary optimisation. #GenomeAssembly #PangenomeGuiedeAssembly @biorxiv_genomic .
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Clinical metagenomics for diagnosis and surveillance of viral pathogens. #ClinicalMetagenomics #Diagnosis #Surveillance #Genomics @NatureRevMicro .
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Prompt-based bioinformatics: a new interface for multi-omics analysis. #Bioinformatics #LLMss #PromptBasedBioinformatics #OmicsDataAnalysis @NatureRevGenet #Comment .
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VN1K: a genome graph-based and function-driven multi-omics and phenomics resource for the Vietnamese population. #HumanGenome #ReferenceGenome #VietnamesePopulation @biorxiv_genomic .
biorxiv.org
Vietnam, the 16th most populated nation, remains profoundly underrepresented in global genomic databases. Here, we present VN1K, a first-ever comprehensive and well-curated resource of multi-omics...
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A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias. #RhesusMacaque #ReferenceGenome #T2T #Genomics @biorxiv_genomic .
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Uncovering Functional Sequence Gaps in Human Reference Genomes using African Pan Genome Contig Sequences. #T2T #HumanGenome #ReferenceGenome #AfricanPangenome @biorxivpreprint.
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Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @NatureComms .
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Beyond polyA: scalable single-cell total RNA-seq unifies coding and non-coding transcriptomics. #SingleCellTotalRNA #scRNAseq #scNoncodingRNA @biorxiv_genomic .
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Synteny and linkage decay in bacteriophage pangenomes. #Bacteriophages #Pangenomes @biorxiv_genomic .
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Heterogeneity of Genetic Sequence within Quasi-species of Influenza Virus Revealed by Single-Molecule Sequencing. #VirusQuasiSpecies #SingleMoleculeSequencing #sUMIs #Genomics @biorxiv_genomic .
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SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses. #WGS #Pipeline #Bioinformatics @biorxiv_genomic .
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SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale. #SingleCell #scRNAseq #Rust #Bioinformatics @biorxiv_bioinfo .
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Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis. #HiC #SingleCell #ChromatinContactMaps @biorxiv_bioinfo .
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