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Minimap2: pairwise alignment for nucleotide sequences

Bioinformatics, 2018-09, Vol.34 (18), p.3094-3100

2018

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DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays

Bioinformatics (Oxford, England), 2019-09, Vol.35 (17), p.3055-3062

2019

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STREME: accurate and versatile sequence motif discovery

Bioinformatics (Oxford, England), 2021-09, Vol.37 (18), p.2834-2840

2021

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Genome Detective: an automated system for virus identification from high-throughput sequencing data

Bioinformatics, 2019-03, Vol.35 (5), p.871-873

2019

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BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

Bioinformatics (Oxford, England), 2019-07, Vol.35 (13), p.2193-2198

2019

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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

Bioinformatics, 2019-11, Vol.35 (22), p.4754-4756

2019

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SVIM: structural variant identification using mapped long reads

Bioinformatics (Oxford, England), 2019-09, Vol.35 (17), p.2907-2915

2019

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M3Drop: dropout-based feature selection for scRNASeq

Bioinformatics (Oxford, England), 2019-08, Vol.35 (16), p.2865-2867

2019

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BCFtools/csq: haplotype-aware variant consequences

Bioinformatics (Oxford, England), 2017-07, Vol.33 (13), p.2037-2039

2017

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Hive plots—rational approach to visualizing networks

Briefings in bioinformatics, 2012-09, Vol.13 (5), p.627-644

2012

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CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization

Bioinformatics (Oxford, England), 2017-10, Vol.33 (19), p.3131-3133

2017

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WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

Bioinformatics (Oxford, England), 2017-10, Vol.33 (19), p.3113-3114

2017

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NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data

Bioinformatics (Oxford, England), 2021-07, Vol.37 (11), p.1600-1601

2021

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Network-based integration of multi-omics data for prioritizing cancer genes

Bioinformatics, 2018-07, Vol.34 (14), p.2441-2448

2018

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Flexbar 3.0 - SIMD and multicore parallelization

Bioinformatics (Oxford, England), 2017-09, Vol.33 (18), p.2941-2942

2017

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LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning

Bioinformatics, 2018-11, Vol.34 (22), p.3825-3834

2018

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Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning

Bioinformatics, 2022-01, Vol.38 (2), p.325-334

2022

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Shouji: a fast and efficient pre-alignment filter for sequence alignment

Bioinformatics, 2019-11, Vol.35 (21), p.4255-4263

2019

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CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data

Bioinformatics, 2018-02, Vol.34 (3), p.381-387

2018

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findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies

Bioinformatics, 2018-02, Vol.34 (4), p.550-557

2018

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SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data

Bioinformatics, 2019-04, Vol.35 (8), p.1269-1277

2019

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Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona

Bioinformatics, 2021-12, Vol.38 (1), p.211-219

2021

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Spectral clustering based on learning similarity matrix

Bioinformatics, 2018-06, Vol.34 (12), p.2069-2076

2018

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StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

Bioinformatics, 2022-03, Vol.38 (7), p.2049-2051

2022

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Combining multiple tools outperforms individual methods in gene set enrichment analyses

Bioinformatics (Oxford, England), 2017-02, Vol.33 (3), p.414-424

2017

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Minimap2: pairwise alignment for nucleotide sequences

DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays

STREME: accurate and versatile sequence motif discovery

Genome Detective: an automated system for virus identification from high-throughput sequencing data

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

SVIM: structural variant identification using mapped long reads

M3Drop: dropout-based feature selection for scRNASeq

BCFtools/csq: haplotype-aware variant consequences

Hive plots—rational approach to visualizing networks

CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data

Network-based integration of multi-omics data for prioritizing cancer genes

Flexbar 3.0 - SIMD and multicore parallelization

LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning

Shouji: a fast and efficient pre-alignment filter for sequence alignment

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data

findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies

SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data

Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona

Spectral clustering based on learning similarity matrix

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

Combining multiple tools outperforms individual methods in gene set enrichment analyses

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