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

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

(2017) Colin Ruprecht et al.   PLANT JOURNAL

Beyond Genomics: Studying Evolution with Gene Coexpression Networks

(2017) Colin Ruprecht et al.   TRENDS IN PLANT SCIENCE

Tools of the trade: studying molecular networks in plants

(2016) Sebastian Proost et al.   CURRENT OPINION IN PLANT BIOLOGY

An essential role of caffeoyl shikimate esterase in monolignol biosynthesis inMedicago truncatula

(2016) Chan Man Ha et al.   PLANT JOURNAL

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

(2016) Oren Tzfadia et al.   Frontiers in Plant Science

Learning from Co-expression Networks: Possibilities and Challenges

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

Monolignol ferulate conjugates are naturally incorporated into plant lignins

(2016) S. D. Karlen et al.   Science Advances

Amino Acid Export in Developing Arabidopsis Seeds Depends on UmamiT Facilitators

(2015) Benedikt Müller et al.   CURRENT BIOLOGY

Effects ofPHENYLALANINE AMMONIA LYASE(PAL) knockdown on cell wall composition, biomass digestibility, and biotic and abiotic stress responses inBrachypodium

(2015) Cynthia L. Cass et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Plant Genome Integrative Explorer Resource: PlantGenIE.org

(2015) David Sundell et al.   NEW PHYTOLOGIST

Roles of cell wall peroxidases in plant development

(2015) Edith Francoz et al.   PHYTOCHEMISTRY

LACCASE5 Is Required for Lignification of theBrachypodium distachyonCulm

(2015) Yin Wang et al.   PLANT PHYSIOLOGY

NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants

(2015) Yoshimi Nakano et al.   Frontiers in Plant Science

The Cell Biology of Cellulose Synthesis

(2014) Heather E. McFarlane et al.   Annual Review of Plant Biology

Impact of the Brown-Midrib bm5 Mutation on Maize Lignins

(2014) Valérie Méchin et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Rescue of syringyl lignin and sinapate ester biosynthesis in Arabidopsis thaliana by a coniferaldehyde 5-hydroxylase from Eucalyptus globulus

(2014) José Renán García et al.   PLANT CELL REPORTS

The Cellulase KORRIGAN Is Part of the Cellulose Synthase Complex

(2014) T. Vain et al.   PLANT PHYSIOLOGY

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress

(2014) Henry D. Priest et al.   PLoS One

Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

(2014) Peyman Zarrineh et al.   PLoS One

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

p-Coumaroyl-CoA:monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway inBrachypodium distachyon

(2013) Deborah L. Petrik et al.   PLANT JOURNAL

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

(2013) M. Itkin et al.   SCIENCE

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

(2013) Christopher Y. Park et al.   PLoS Computational Biology

Plant cell wall lignification and monolignol metabolism

(2013) Yin Wang et al.   Frontiers in Plant Science

AtABCG29 Is a Monolignol Transporter Involved in Lignin Biosynthesis

(2012) Santiago Alejandro et al.   CURRENT BIOLOGY

Identification of Grass-specific Enzyme That Acylates Monolignols withp-Coumarate

(2012) Saunia Withers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations

(2012) Stefanie De Bodt et al.   NEW PHYTOLOGIST

Metabolic engineering of novel lignin in biomass crops

(2012) Ruben Vanholme et al.   NEW PHYTOLOGIST

The MORPH Algorithm: Ranking Candidate Genes for Membership in Arabidopsis and Tomato Pathways

(2012) O. Tzfadia et al.   PLANT CELL

CHITINASE-LIKE1/POM-POM1 and Its Homolog CTL2 Are Glucan-Interacting Proteins Important for Cellulose Biosynthesis in Arabidopsis

(2012) C. Sanchez-Rodriguez et al.   PLANT CELL

POM-POM2/CELLULOSE SYNTHASE INTERACTING1 Is Essential for the Functional Association of Cellulose Synthase and Microtubules in Arabidopsis

(2012) M. Bringmann et al.   PLANT CELL

The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program

(2012) M. Fasoli et al.   PLANT CELL

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

(2012) Rohan V. Patel et al.   PLANT JOURNAL

Disrupting thecinnamyl alcohol dehydrogenase 1gene (BdCAD1) leads to altered lignification and improved saccharification inBrachypodium distachyon

(2012) Madeleine Bouvier d'Yvoire et al.   PLANT JOURNAL

Arabinogalactan-proteins and the research challenges for these enigmatic plant cell surface proteoglycans

(2012) Li Tan et al.   Frontiers in Plant Science

Lignocellulose: A chewy problem

(2011) Katharine Sanderson   NATURE

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

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

(2011) M. Mutwil et al.   PLANT CELL

Disruption of LACCASE4 and 17 Results in Tissue-Specific Alterations to Lignification of Arabidopsis thaliana Stems

(2011) S. Berthet et al.   PLANT CELL

Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579-containing proteins that are essential for normal xylan deposition in the secondary cell wall

(2011) David Brown et al.   PLANT JOURNAL

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Brachypodium as a Model for the Grasses: Today and the Future

(2011) Jelena Brkljacic et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A structural phylogenetic map for chloroplast photosynthesis

(2011) John F. Allen et al.   TRENDS IN PLANT SCIENCE

Large-Scale Co-Expression Approach to Dissect Secondary Cell Wall Formation Across Plant Species

(2011) Colin Ruprecht et al.   Frontiers in Plant Science

TiSGeD: a database for tissue-specific genes

(2010) S. J. Xiao et al.   BIOINFORMATICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the LycophyteSelaginellaand Flowering Plants

(2010) Jing-Ke Weng et al.   PLANT CELL

Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis

(2010) José M. Jiménez-Gómez et al.   PLoS Genetics

An Enantiocomplementary Dirigent Protein for the Enantioselective Laccase-Catalyzed Oxidative Coupling of Phenols

(2009) Benjamin Pickel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hydroxycinnamates in lignification

(2009) John Ralph   PHYTOCHEMISTRY REVIEWS

MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis

(2009) J. Zhou et al.   PLANT CELL

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

(2009) S. Proost et al.   PLANT CELL

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

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

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

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

The Effects on Lignin Structure of Overexpression of Ferulate 5-Hydroxylase in Hybrid Poplar1

(2009) J. J. Stewart et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR

(2008) Shin-Young Hong et al.   BMC PLANT BIOLOGY

The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1

(2008) Naoki Takahashi et al.   EMBO JOURNAL

Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches

(2008) Atsushi Takabayashi et al.   PLANT JOURNAL