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Computational approaches to unravel the pathways and evolution of specialized metabolism

Current opinion in plant biology, 2020-06, Vol.55, p.38-46

Mutwil, Marek

2020

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Towards revealing the functions of all genes in plants

Trends in plant science, 2014-04, Vol.19 (4), p.212-221

2014

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Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers

BMC genomics, 2021-05, Vol.22 (1), p.352-14, Article 352

2021

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Tools of the trade: studying molecular networks in plants

Current opinion in plant biology, 2016-04, Vol.30, p.143-150

2016

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Using Gene Expression to Study Specialized Metabolism-A Practical Guide

Frontiers in plant science, 2021-01, Vol.11, p.625035-625035

2021

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LSTrAP: efficiently combining RNA sequencing data into co-expression networks

BMC bioinformatics, 2017-10, Vol.18 (1), p.444-444, Article 444

2017

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Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Nature communications, 2019-02, Vol.10 (1), p.737-737, Article 737

2019

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A method for mining condition-specific co-expressed genes in Camellia sinensis based on k-means clustering

BMC plant biology, 2024-05, Vol.24 (1), p.373-373, Article 373

2024

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Removing auto-activators from yeast-two-hybrid assays by conditional negative selection

Scientific reports, 2021-03, Vol.11 (1), p.5477-5477, Article 5477

2021

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Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

Nature communications, 2023-02, Vol.14 (1), p.986-986, Article 986

2023

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Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Plant, cell and environment, 2009-12, Vol.32 (12), p.1633-1651

2009

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PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

The Plant cell, 2011-03, Vol.23 (3), p.895-910

2011

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Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

The Plant journal : for cell and molecular biology, 2017-05, Vol.90 (3), p.447-465

2017

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Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana

Frontiers in plant science, 2022-09, Vol.13, p.944992-944992

2022

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Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data

Computational and structural biotechnology journal, 2023-01, Vol.21, p.1639-1650

2023

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FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants

Plant physiology (Bethesda), 2016-03, Vol.170 (3), p.1878-1894

2016

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Volatile-Based Diagnosis for Pathogenic Wood-Rot Fungus Fulvifomes siamensis by Electronic Nose (E-Nose) and Solid-Phase Microextraction/Gas Chromatography/Mass Spectrometry

Sensors (Basel, Switzerland), 2023-05, Vol.23 (9), p.4538

2023

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Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti‐cancer metabolites

Journal of integrative plant biology, 2023-06, Vol.65 (6), p.1442-1466

2023

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Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

The New phytologist, 2017-08, Vol.215 (3), p.1009-1025

2017

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Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana

PLoS genetics, 2016-10, Vol.12 (10), p.e1006363-e1006363

2016

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Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

The New phytologist, 2018-03, Vol.217 (4), p.1521-1534

2018

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LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks

Genes, 2020-04, Vol.11 (4), p.428

2020

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Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

Nature plants, 2021-08, Vol.7 (8), p.1143-1159

2021

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Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

Plant physiology (Bethesda), 2010-01, Vol.152 (1), p.29-43

2010

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Comparative spatial proteomics of Plasmodium-infected erythrocytes

Cell reports (Cambridge), 2023-11, Vol.42 (11), p.113419-113419, Article 113419

2023

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Computational approaches to unravel the pathways and evolution of specialized metabolism

Towards revealing the functions of all genes in plants

Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers

Tools of the trade: studying molecular networks in plants

Using Gene Expression to Study Specialized Metabolism-A Practical Guide

LSTrAP: efficiently combining RNA sequencing data into co-expression networks

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

A method for mining condition-specific co-expressed genes in Camellia sinensis based on k-means clustering

Removing auto-activators from yeast-two-hybrid assays by conditional negative selection

Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana

Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants

Volatile-Based Diagnosis for Pathogenic Wood-Rot Fungus Fulvifomes siamensis by Electronic Nose (E-Nose) and Solid-Phase Microextraction/Gas Chromatography/Mass Spectrometry

Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti‐cancer metabolites

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

Comparative spatial proteomics of Plasmodium-infected erythrocytes

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