Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks

Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle

(2018) Lorenzo Caputi et al.   SCIENCE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change

(2017) Masa Tsuchiya et al.   PLoS One

Gene coexpression network analysis of oil biosynthesis in an interspecific backcross of oil palm

(2016) Chloé Guerin et al.   PLANT JOURNAL

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations

(2016) Sahra Uygun et al.   PLoS Computational Biology

Learning from Co-expression Networks: Possibilities and Challenges

(2016) Elise A. R. Serin et al.   Frontiers in Plant Science

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development: Fig. 1.

(2015) Marketa Zdarska et al.   JOURNAL OF EXPERIMENTAL BOTANY

Characterization of a spermidine hydroxycinnamoyltransferase inMalus domesticahighlights the evolutionary conservation of trihydroxycinnamoyl spermidines in pollen coat of core Eudicotyledons

(2015) Carolina Elejalde-Palmett et al.   JOURNAL OF EXPERIMENTAL BOTANY

Strigolactones spatially influence lateral root development through the cytokinin signaling network

(2015) Lingxiang Jiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Arabidopsis GERANYLGERANYL DIPHOSPHATE SYNTHASE 11 is a hub isozyme required for the production of most photosynthesis-related isoprenoids

(2015) M. Águila Ruiz-Sola et al.   NEW PHYTOLOGIST

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Gene Networks in Plant Biology: Approaches in Reconstruction and Analysis

(2015) Yupeng Li et al.   TRENDS IN PLANT SCIENCE

A review on the computational approaches for gene regulatory network construction

(2014) Lian En Chai et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

(2013) Federico M. Giorgi et al.   BIOINFORMATICS

Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

(2013) F Feltus et al.   BMC Systems Biology

A comparative study of statistical methods used to identify dependencies between gene expression signals

(2013) S. de Siqueira Santos et al.   BRIEFINGS IN BIOINFORMATICS

Supervised, semi-supervised and unsupervised inference of gene regulatory networks

(2013) S. R. Maetschke et al.   BRIEFINGS IN BIOINFORMATICS

Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

(2013) L. Lopez-Kleine et al.   Briefings in Functional Genomics

Phenolic compositions and antioxidant capacities of Chinese wild mandarin (Citrus reticulata Blanco) fruits

(2013) Yuanmei Zhang et al.   FOOD CHEMISTRY

On protocols and measures for the validation of supervised methods for the inference of biological networks

(2013) Marie Schrynemackers et al.   Frontiers in Genetics

Cytokinin Signaling Networks

(2012) Ildoo Hwang et al.   Annual Review of Plant Biology

parmigene—a parallel R package for mutual information estimation and gene network reconstruction

(2011) Gabriele Sales et al.   BIOINFORMATICS

A Multiscale Graph Theoretical Approach to Gene Regulation Networks: A Case Study in Atrial Fibrillation

(2011) F. Censi et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

(2011) Jesse Gillis et al.   PLoS One

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Reprogramming cell fates: reconciling rarity with robustness

(2009) Sui Huang   BIOESSAYS

Importing ArrayExpress datasets into R/Bioconductor

(2009) Audrey Kauffmann et al.   BIOINFORMATICS

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression

(2009) T. Obayashi et al.   DNA RESEARCH

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

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY