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Javier Santoyo@jsantoyo
17 Oct 2025
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic. #SomaticVariants #ShortReads #LongReads #VariantCalling #Genomics #Bioinformatics #ToolsBenchmarking #ReferenceDatasets @NatureBiotech nature.com/articles/s41587-0…
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Javier Santoyo@jsantoyo
7 Jul 2025
A comparison of long-read single-cell transcriptomic approaches. #LongRead #SingleCell #Transcriptomics #ToolsBenchmarking #Genomics #Bioinformatics @biorxiv_bioinfo @AnitaScoonesPhd biorxiv.org/content/10.1101/…
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Javier Santoyo@jsantoyo
7 Jul 2025
An optimised computational approach for the identification of somatic structural variants in cancer. #SomaticStructuralVariants #CancerGenetics #Genomics #Bioinformatics #ToolsBenchmarking @biorxiv_bioinfo biorxiv.org/content/10.1101/…
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Javier Santoyo@jsantoyo
30 Jul 2024
Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data. #StructuralVariantPipelines #TGS #LongReads #ToolsBenchmarking @GenomeBiology genomebiology.biomedcentral.…

Comprehensive and deep evaluation of structural variation detection pipelines with third-generation...

Genome Biology - Structural variation (SV) detection methods using third-generation sequencing data are widely employed, yet accurately detecting SVs remains challenging. Different methods often...

link.springer.com
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Javier Santoyo@jsantoyo
30 May 2024
Benchmarking of bioinformatics tools for the hybrid de novo assembly of human whole-genome sequencing data. #WGS #GenomeAssembly #ToolsBenchmarking @LabCflores @biorxivpreprint biorxiv.org/content/10.1101/…

Benchmarking of bioinformatics tools for the hybrid de novo assembly of human whole-genome sequen...

Accurate and complete de novo assembled genomes sustain variant identification and catalyze the discovery of new genomic features and biological functions. However, accurate and precise de novo...

biorxiv.org
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Javier Santoyo@jsantoyo
29 Oct 2023
Benchmarking single-cell hashtag oligo demultiplexing methods. #SingleCell #scRNAseq #HastagOligo #HTO #DemultiplexingTools #ToolsBenchmarking #NARgenomicsAndBioinformatics academic.oup.com/nargab/arti…
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Javier Santoyo@jsantoyo
3 Oct 2023
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. #RNAseq #LongReads #Sequencing #RNAdataAnalysis #ToolsBenchmarking #Bioinformatics @naturemethods nature.com/articles/s41592-0…

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures

Nature Methods - This analysis leverages experimentally sequenced data and in silico mixtures to simulate transcript expression differences, which enables a performance assessment of long-read...

nature.com
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Javier Santoyo@jsantoyo
19 Sep 2023
A systematic comparison of human mitochondrial genome assembly tools. #HumanMitochondrialGenome #GenomeAssembly #ToolsBenchmarking @BMCBioinfo bmcbioinformatics.biomedcent…

A systematic comparison of human mitochondrial genome assembly tools

BMC Bioinformatics - Mitochondria are the cell organelles that produce most of the chemical energy required to power the cell's biochemical reactions. Despite being a part of a eukaryotic host...

link.springer.com
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Javier Santoyo@jsantoyo
16 Sep 2023
Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data. #YchrClassifiers #Haplogroups #WGS #WES #ToolsBenchmarking @LabCflores #ComputationalStructuralBiotechnologyJournal sciencedirect.com/science/ar…
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Javier Santoyo@jsantoyo
4 Sep 2023
Benchmarking single-cell hashtag oligo demultiplexing methods. #SingleCell #scRNAse #HastagOligo #HTO #DemultiplexingTools #ToolsBenchmarking @biorxivpreprint biorxiv.org/content/10.1101/…

Benchmarking single-cell hashtag oligo demultiplexing methods

Sample multiplexing is often used to reduce cost and limit batch effects in single-cell RNA sequencing (scRNA-seq) experiments. A commonly used multiplexing technique involves tagging cells prior to...

biorxiv.org
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Javier Santoyo@jsantoyo
29 Apr 2023
Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. #LongReads #RNAseq #VariantCalling #ToolsBenchmarking #Bioinformatics @GenomeBiology genomebiology.biomedcentral.…
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Javier Santoyo@jsantoyo
8 Jan 2023
Systematic benchmarking of statistical methods to assess differential expression of circular RNAs. #DifferentialExpression #CircularRNA #ToolsBenchmarking #Bioinformatics @BriefingBioinfo academic.oup.com/bib/advance…

Systematic benchmarking of statistical methods to assess differential expression of circular RNAs

Abstract. Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA

academic.oup.com
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Javier Santoyo@jsantoyo
17 Dec 2022
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. #ShotgunMetagenomics #TaxonomicClassification #LongReads #Sequencing #ToolsBenchmarking #Bioinformatics @BMCBioinfo @DPortik bmcbioinformatics.biomedcent…
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Javier Santoyo@jsantoyo
16 Dec 2022
Benchmarking and integration of methods for deconvoluting spatial transcriptomic data. #SpatialTransciprtomics #ToolsBenchmarking #Bioinformatics academic.oup.com/bioinformat…
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Javier Santoyo@jsantoyo
26 Nov 2022
Accuracy and completeness of long read metagenomic assemblies. #MetagenomicsAssembly #ToolsBenchmarking #Bioinformatics @biorxiv_bioinfo biorxiv.org/content/10.1101/…
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Javier Santoyo@jsantoyo
21 Oct 2022
Graph construction method impacts variation representation and analyses in a bovine super-pangenome. #BovinePangenomes #ToolsBenchmarking @biorxivpreprint biorxiv.org/content/10.1101/…
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Javier Santoyo@jsantoyo
10 Oct 2022
Benchmarking Automated Cell Type Annotation Tools for Single-cell ATAC-seq Data. #scATACseq #SingleCellAnnotation #ToolsBenchmarking @biorxivpreprint biorxiv.org/content/10.1101/…

Benchmarking Automated Cell Type Annotation Tools for Single-cell ATAC-seq Data

As single-cell chromatin accessibility profiling methods advance, scATAC-seq has become ever more important in the study of candidate regulatory genomic regions and their roles underlying developme...

biorxiv.org
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Javier Santoyo@jsantoyo
17 Sep 2022
Comparison of scRNA-seq data analysis method combinations. #scRNAseq #DataAnalysis #ToolsBenchmarking #Bioinformatics #BriefingsInFunctionalGenomics academic.oup.com/bfg/advance…

Comparison of scRNA-seq data analysis method combinations

Abstract. Single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data analysis refers to the use of appropriate methods to analyze the dataset generated

academic.oup.com
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Javier Santoyo@jsantoyo
20 Aug 2022
Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework. #ExomeSplicingVariants #ToolsBenchmarking #MachineLearning #Bioinformatics @BriefingBioinfo academic.oup.com/bib/advance…
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Javier Santoyo@jsantoyo
16 Aug 2022
Complex genome assembly based on long-read sequencing' #GenomeAssembly #LongReads #ToolsBenchmarking @BriefingBioinfo #Bioinformatics academic.oup.com/bib/advance…

Complex genome assembly based on long-read sequencing

Abstract. High-quality genome chromosome-scale sequences provide an important basis for genomics downstream analysis, especially the construction of haplot

academic.oup.com
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