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Javier Santoyo@jsantoyo
18 Oct 2025
Multitask benchmarking of single-cell multimodal omics integration methods. #SingleCell #MultiOmics #MethodsBenchmarking @naturemethods nature.com/articles/s41592-0…
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Javier Santoyo@jsantoyo
24 Sep 2025
Systematic benchmarking of computational methods to identify spatially variable genes. #SpatialTranscriptomics #MethodsBenchmarking @GenomeBiology genomebiology.biomedcentral.…
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Javier Santoyo@jsantoyo
29 Jun 2025
A Benchmark of Modern Statistical Phasing Methods. #DNAphasing #MethodsBenchmarking #Genomics #Bioinformatics @biorxiv_genomic biorxiv.org/content/10.1101/…
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1,202
Javier Santoyo@jsantoyo
10 Aug 2024
Benchmarking clustering, alignment, and integration methods for spatial transcriptomic. #SpatialTranscriptomics #MethodsBenchmarking @GenomeBiology genomebiology.biomedcentral.…

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

Genome Biology - Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions...

link.springer.com
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Javier Santoyo@jsantoyo
14 Jun 2024
Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data. #RNAseq #MethodsBenchmarking #Bioinformatics biorxiv.org/content/10.1101/…

Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data

In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods used...

biorxiv.org
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1,151
Javier Santoyo@jsantoyo
7 Jun 2024
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. #LongRead #Sequencing #RNAseq #MethodsBenchmarking #TranscriptomieAnalysis @naturemethods nature.com/articles/s41592-0…

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Nature Methods - This Registered Report presents the results of the Long-read RNA-Seq Genome Annotation Assessment Project, which is a community effort for benchmarking long-read methods for...

nature.com
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Javier Santoyo@jsantoyo
15 Apr 2024
A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes. #DNAmethylation #LongReads #MethodsBenchmarking @GenomeBiology genomebiology.biomedcentral.…
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Javier Santoyo@jsantoyo
15 Oct 2023
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods. #SpatiallyVariableGenes #SpatialTranscriptomics #MethodsBenchmarking @GenomeBiology genomebiology.biomedcentral.…

Disparities in spatially variable gene calling highlight the need for benchmarking spatial transc...

Genome Biology - Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic...

link.springer.com
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Javier Santoyo@jsantoyo
7 Aug 2023
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. #LongReads #RNAseq #TranscriptomeAnalysis #GenomeAnnotationAssessment #LRGASP #MethodsBenchmarking @biorxivpreprint biorxiv.org/content/10.1101/…
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Javier Santoyo@jsantoyo
14 Mar 2023
Benchmarking genome assembly methods on metagenomic sequencing data. #Metagenomics #GenomeAssembly #MethodsBenchmarking #Bioinformatics @BriefingBioinfo academic.oup.com/bib/advance…

Benchmarking genome assembly methods on metagenomic sequencing data

Abstract. Metagenome assembly is an efficient approach to reconstruct microbial genomes from metagenomic sequencing data. Although short-read sequencing ha

academic.oup.com
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Javier Santoyo@jsantoyo
19 Jun 2022
Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis. #RNAmodifications #BisulfiteSequencing #MethodsBenchmarking #Sequencing #Bioinformatics academic.oup.com/nargab/arti… #NARgenomicsAndBioinformatics

Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis

Abstract. The presence of 5-methylcytosine (m5C) in RNA molecules has been known for decades and its importance in regulating RNA metabolism has gradually

academic.oup.com
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Javier Santoyo@jsantoyo
16 Feb 2022
Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data. #circRNA #RNAseq #MethodsBenchmarking bmcgenomics.biomedcentral.co… #BMCgenomics
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Javier Santoyo@jsantoyo
18 Jan 2022
Microbiome differential abundance methods produce different results across 38 datasets. #Microbiome #DifferentiallyAbundantMicrobes #ResultsBias #MethodsBenchmarking nature.com/articles/s41467-0… @NatureComms

Microbiome differential abundance methods produce different results across 38 datasets

Nature Communications - Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential...

nature.com
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Javier Santoyo@jsantoyo
11 Jan 2022
A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq. #SingleCell #scRNAseq #CellTypeIdentification #MethodsBenchmarking #Bioinformatics academic.oup.com/bib/advance… @BriefingBioinfo
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Javier Santoyo@jsantoyo
14 Jul 2021
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. #HighMolecularWeight #DNApreservation #LongReads #Sequencing #MethodsBenchmarking biorxiv.org/content/10.1101/…

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range...

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to...

biorxiv.org
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