Lightnews — Scholar-powered news

Javier Santoyo

@jsantoyo.bsky.social

2.2K followers 2K following 770 posts

Genomics & Bioinformatics Scientist at the University of Edinburgh | Head of Edinburgh Genomics | #Omics #NGS #LongReads 🧬 🖥️ Opinions my own. He/Him Lab: https://genomics.ed.ac.uk/ LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/

genomics.ed.ac.uk

Posts Media Videos Starter Packs

Javier Santoyo @jsantoyo.bsky.social · 5h

SMART v10: three decades of the protein domain annotation resource. #ProteinDomain #ProteinAnnotation @narjournal.bsky.social
academic.oup.com/nar/advance-...

Javier Santoyo @jsantoyo.bsky.social · 6h

An Overview of Computational Methods for Gene Prediction in Eukaryotes: Strengths, Limitations, and Future Directions. #GenePrediction #Review @BioinfoAdv
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 7h

Advances and challenges in understanding evolution through genome comparison. #Evolution #GenomeComparison #Genomics #Bioinformatics @bioinfoadv.bsky.social 🧬 🖥️
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 8h

KinMethyl: Robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration. #DNAmethylation #ProkaryoticDNA #HiFi #Sequencing #KineticSignal @bioinfoadv.bsky.social 🧬 🖥️
academic.oup.com/bioinformati...

1 1 1

Javier Santoyo @jsantoyo.bsky.social · 9h

Nextpie: A web-based reporting tool and database for reproducible Nextflow pipelines. #Nextlow #WebReportingTool #Bioinformatics @bioinfoadv.bsky.social 🧬 🖥️
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 9h

FastGA: Fast Genome Alignment. #GenomeAlignment #Genomics #Bioinformatics @bioinfoadv.bsky.social 🧬 🖥️
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 13h

Framework for Monitoring Urban Microbiomes and Diagnosing Pathogen Risk. #Metagenomics #UrbanMicrobiome #Genomics #MAGs #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 15h

Full-length isoform constructor (FLIC) – a tool for isoform discovery based on long reads. #RNAisoforms #FullLengthIsoforms #IsoformDiscovery #LongRead #Sequencing #Genomics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 16h

scBSP: A fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data. #SpatialOmics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

Javier Santoyo @jsantoyo.bsky.social · 16h

Comprehensive benchmarking with guidelines for analyzing transposable element-derived RNA expression. #TransposableElements #Benchmarking #RNAexpression @biorxivpreprint.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

2 7

Javier Santoyo @jsantoyo.bsky.social · 5d

Nanopore sequencing and haplotyping of mitochondrial DNA hypervariable regions and its application on mixed stain. #MitochondrialDNA #HypervariableRegions #Nanopore #Sequencing #ForensicDNA #ForensicScienceInternational_Genetics
www.sciencedirect.com/science/arti...

1 1

Javier Santoyo @jsantoyo.bsky.social · 5d

Long-read nucleosome mapping of single chromatin fibers using DNA methylation and Nanopore sequencing. #LongRead #Nanopore #Sequencing #Chromatin #DNAmethylation @biophysj.bsky.social 🧪 🧬
www.sciencedirect.com/science/arti...

1 4

Javier Santoyo @jsantoyo.bsky.social · 5d

The Great Genotyper: a graph-based method for population genotyping of small and structural variants. #GeneticVariants #StructuralVariants #GenomeGraphs #PopulationGenomics #Genotyping @gigascience.bsky.social 🧪 🧬 🖥️
academic.oup.com/gigascience/...

Javier Santoyo @jsantoyo.bsky.social · 5d

Potential impact of long-read sequencing on complement-mediated diseases. #LongRead #Sequencing #Genomics #ComplementGenes #Immunology @cp-trendsimmuno.bsky.social 🧪 🧬 🖥️
www.sciencedirect.com/science/arti...

www.sciencedirect.com

Javier Santoyo @jsantoyo.bsky.social · 8d

A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures.#SomaticVariantDetection #HapMap #Pangenomics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

Javier Santoyo @jsantoyo.bsky.social · 8d

A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection. #ShortRead #Sequencing #TwoColorSequencing #SomaticVariants @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

1 2

Javier Santoyo @jsantoyo.bsky.social · 8d

Analytical Validation of a Pan-Cancer NGS Assay for In-House Liquid Biopsy Testing: An International Multicenter Study. #PanCancerNGS #LiquidBiopsy @jmdiagn.bsky.social
www.jmdjournal.org/article/S152...

Javier Santoyo @jsantoyo.bsky.social · 8d

Evaluation of long-read genome sequencing for genomic profiling of myeloid cancers. #LongReads #Sequencing #GenomicProfiling #MyeloidCancers @jmdiagn.bsky.social
www.jmdjournal.org/article/S152...

Javier Santoyo @jsantoyo.bsky.social · 8d

A closed-loop method for precise genome size estimation using HiFi reads. #GenomeSize #HiFi #LongReads #Genomics #Bioinformatics #BMCgenomics 🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

2 3

Javier Santoyo @jsantoyo.bsky.social · 8d

The complete genome assembly of Astragalus membranaceus: enabling more accurate genetic research. #MongolianMilkvetchGenome #T2T @gigascience.bsky.social 🧬 🖥️
academic.oup.com/gigascience/...

Javier Santoyo @jsantoyo.bsky.social · 8d

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information. #Ychromosome #EvolutionaryInformation #GeneticVariants #HumanGenome @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/article/...

1 3

Javier Santoyo @jsantoyo.bsky.social · 8d

JG2: an updated version of the Japanese population-specific reference genome. #HumanGenome #ReferenceGenome #HaploidAssemblies #JapanesePopulation #HumanGenomeVariation 🧬 🖥️
www.nature.com/articles/s41...

Javier Santoyo @jsantoyo.bsky.social · 8d

T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population. #HumanGenome #ReferenceGenome #T2t_CHM13 #SwedishPopulation #GeneticVariation @genomeresearch.bsky.social 🧬 🖥️
genome.cshlp.org/content/earl...

Javier Santoyo @jsantoyo.bsky.social · 9d

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. #Pangenome #ReadMapping #PangenomeGraphs @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

Javier Santoyo @jsantoyo.bsky.social · 9d

The Emirati T2T-Level Pangenome: A Graph of 58 Complete Genomes. #ReferenceGenome #HumanGenome #T2T #PangenomeGraph #PopulationGenomics #EmiratiGenomeProgram #Genomics @biorxivpreprint.bsky.social 🖥️
www.biorxiv.org/content/10.1...