High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

(2013) W.-k. Jiang et al.   PLANT PHYSIOLOGY

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

(2013) M. G. Poolman et al.   PLANT PHYSIOLOGY

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

MetNet Online: a novel integrated resource for plant systems biology

(2012) Yves Sucaet et al.   BMC BIOINFORMATICS

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Plant B Vitamin Pathways and their Compartmentation: a Guide for the Perplexed

(2012) Svetlana Gerdes et al.   JOURNAL OF EXPERIMENTAL BOTANY

Frontiers in metabolic reconstruction and modeling of plant genomes

(2012) S. M. D. Seaver et al.   JOURNAL OF EXPERIMENTAL BOTANY

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

(2012) Kosei Tanaka et al.   NUCLEIC ACIDS RESEARCH

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

(2012) Ramy K. Aziz et al.   PLoS One

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Connecting genotype to phenotype in the era of high-throughput sequencing

(2011) Christopher S. Henry et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

(2011) Rajib Saha et al.   PLoS One

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Gramene database in 2010: updates and extensions

(2010) K. Youens-Clark et al.   NUCLEIC ACIDS RESEARCH

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants

(2010) P. Zhang et al.   PLANT PHYSIOLOGY

Biosynthesis of glucosinolates – gene discovery and beyond

(2010) Ida E. Sønderby et al.   TRENDS IN PLANT SCIENCE

A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

(2009) M. G. Poolman et al.   PLANT PHYSIOLOGY

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii

(2008) P. May et al.   GENETICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH