Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data

JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

(2019) Xuan Zhang et al.   BMC GENOMICS

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

(2018) Wen Chen et al.   BMC GENOMICS

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system

(2018) Nisha Govender et al.   Scientific Reports

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

(2015) S. Ballouz et al.   BIOINFORMATICS

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

Border Control--A Membrane-Linked Interactome of Arabidopsis

(2014) A. M. Jones et al.   SCIENCE

Yield performance of half-sib families of physic nut (Jatropha curcas L.)

(2014) Victor Mousinho Spinelli et al.   Crop Breeding and Applied Biotechnology

Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.)

(2014) Ying-Hai Liang et al.   Horticulture Research

Jatropha curcas, a biofuel crop: Functional genomics for understanding metabolic pathways and genetic improvement

(2013) Fatemeh Maghuly et al.   Biotechnology Journal

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

Efficient key pathway mining: combining networks and OMICS data

(2012) Nicolas Alcaraz et al.   Integrative Biology

Medicinal property, phytochemistry and pharmacology of several Jatropha species (Euphorbiaceae): A review

(2012) Carla W. Sabandar et al.   PHYTOCHEMISTRY

Global Analysis of Gene Expression Profiles in Developing Physic Nut (Jatropha curcas L.) Seeds

(2012) Huawu Jiang et al.   PLoS One

Clustering gene expression data with a penalized graph-based metric

(2011) Ariel E Bayá et al.   BMC BIOINFORMATICS

De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

(2011) Purushothaman Natarajan et al.   BMC GENOMICS

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Mining metabolic pathways through gene expression

(2010) Timothy Hancock et al.   BIOINFORMATICS

Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

(2010) Yongjin Li et al.   BIOINFORMATICS

AtPIN: Arabidopsis thaliana Protein Interaction Network

(2010) Marcelo M Brandão et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis

(2010) P. Li et al.   NUCLEIC ACIDS RESEARCH

PAIR: the predicted Arabidopsis interactome resource

(2010) Mingzhi Lin et al.   NUCLEIC ACIDS RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS