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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

Bioinformatics (Oxford, England), 2016-09, Vol.32 (18), p.2847-2849

2016

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Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites

Briefings in bioinformatics, 2018-09, Vol.19 (5), p.1022-1034

2018

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Empirical comparison of structure-based pathway methods

Briefings in bioinformatics, 2016-03, Vol.17 (2), p.336-345

2016

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Enteropathway: the metabolic pathway database for the human gut microbiota

Briefings in bioinformatics, 2024-07, Vol.25 (5)

2024

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Network-constrained regularization and variable selection for analysis of genomic data

Bioinformatics, 2008-05, Vol.24 (9), p.1175-1182

2008

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GSEA-InContext: identifying novel and common patterns in expression experiments

Bioinformatics, 2018-07, Vol.34 (13), p.i555-i564

2018

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A review of network-based approaches to drug repositioning

Briefings in bioinformatics, 2018-09, Vol.19 (5), p.878-892

2018

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Reactome diagram viewer: data structures and strategies to boost performance

Bioinformatics, 2018-04, Vol.34 (7), p.1208-1214

2018

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MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome‐metabolome data

Bioinformatics, 2022-03, Vol.38 (6), p.1615-1623

2022

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MetPA: a web-based metabolomics tool for pathway analysis and visualization

Bioinformatics, 2010-09, Vol.26 (18), p.2342-2344

2010

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CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models

Bioinformatics (Oxford, England), 2017-06, Vol.33 (11), p.1741-1743

2017

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DyNet: visualization and analysis of dynamic molecular interaction networks

Bioinformatics (Oxford, England), 2016-09, Vol.32 (17), p.2713-2715

2016

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Exploring the structure and function of temporal networks with dynamic graphlets

Bioinformatics (Oxford, England), 2015-06, Vol.31 (12), p.i171-i180

2015

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Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

Bioinformatics, 2012-02, Vol.28 (3), p.373-380

2012

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Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

Bioinformatics (Oxford, England), 2016-09, Vol.32 (17), p.i455-i463

2016

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Differential network analysis for the identification of condition-specific pathway activity and regulation

Bioinformatics, 2013-07, Vol.29 (14), p.1776-1785

2013

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FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction

Bioinformatics, 2016-02, Vol.32 (3), p.398-408

2016

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SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds

Bioinformatics (Oxford, England), 2015-06, Vol.31 (12), p.2046-2048

2015

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Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data

Bioinformatics, 2022-07, Vol.38 (14), p.3662-3664

2022

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PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas

Bioinformatics (Oxford, England), 2023-11, Vol.39 (11)

2023

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ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts

Bioinformatics, 2016-05, Vol.32 (10), p.1536-1543

2016

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PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data

Bioinformatics (Oxford, England), 2017-07, Vol.33 (14), p.2238-2240

2017

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sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome

Bioinformatics (Oxford, England), 2023-03, Vol.39 (3)

2023

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Hierarchical modelling of microbial communities

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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ReconMap: an interactive visualization of human metabolism

Bioinformatics (Oxford, England), 2017-02, Vol.33 (4), p.605-607

2017

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites

Empirical comparison of structure-based pathway methods

Enteropathway: the metabolic pathway database for the human gut microbiota

Network-constrained regularization and variable selection for analysis of genomic data

GSEA-InContext: identifying novel and common patterns in expression experiments

A review of network-based approaches to drug repositioning

Reactome diagram viewer: data structures and strategies to boost performance

MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome‐metabolome data

MetPA: a web-based metabolomics tool for pathway analysis and visualization

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models

DyNet: visualization and analysis of dynamic molecular interaction networks

Exploring the structure and function of temporal networks with dynamic graphlets

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

Differential network analysis for the identification of condition-specific pathway activity and regulation

FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction

SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds

Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data

PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas

ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data

sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome

Hierarchical modelling of microbial communities

ReconMap: an interactive visualization of human metabolism

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