Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

Phosphorylation is an on/off switch for 5-hydroxyconiferaldehydeO-methyltransferase activity in poplar monolignol biosynthesis

(2015) Jack P. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cyni framework for network inference in Cytoscape

(2014) O. Guitart-Pla et al.   BIOINFORMATICS

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

(2014) Sergiu Netotea et al.   BMC GENOMICS

An Arabidopsis gene regulatory network for secondary cell wall synthesis

(2014) M. Taylor-Teeples et al.   NATURE

Systems Biology of Lignin Biosynthesis inPopulus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling

(2014) Hsi-Chuan Chen et al.   PLANT CELL

Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin inPopulus trichocarpa

(2014) Jack P. Wang et al.   PLANT CELL

Complexity of the transcriptional network controlling secondary wall biosynthesis

(2014) Ruiqin Zhong et al.   PLANT SCIENCE

Systematic Identification of Cell-Wall Related Genes in Populus Based on Analysis of Functional Modules in Co-Expression Network

(2014) Bin Cai et al.   PLoS One

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Comparative studies of differential gene calling using RNA-Seq data

(2013) Ximeng Zheng et al.   BMC BIOINFORMATICS

Modeling transcriptional networks regulating secondary growth and wood formation in forest trees

(2013) Lijun Liu et al.   PHYSIOLOGIA PLANTARUM

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

(2013) Y.-C. Lin et al.   PLANT CELL

Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa

(2013) Rui Shi et al.   PLANTA

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

(2013) S. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis

(2013) R. Vanholme et al.   SCIENCE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa

(2012) Q. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation

(2011) Nathaniel Street et al.   BMC PLANT BIOLOGY

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics

(2011) Xiaohan Yang et al.   PLANT SCIENCE

Down-regulation of glycosyltransferase 8D genes in Populus trichocarpa caused reduced mechanical strength and xylan content in wood

(2011) Q. Li et al.   TREE PHYSIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Update on Mechanisms of Plant Cell Wall Biosynthesis: How Plants Make Cellulose and Other (1->4)- -D-Glycans

(2010) N. C. Carpita   PLANT PHYSIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

(2009) Rui Shi et al.   PLANT AND CELL PHYSIOLOGY

An update on the nomenclature for the cellulose synthase genes in Populus

(2009) Manoj Kumar et al.   TRENDS IN PLANT SCIENCE