A Genome-Scale Metabolic Reconstruction of Phytophthora infestans With the Integration of Transcriptional Data Reveals the Key Metabolic Patterns Involved in the Interaction of Its Host

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

(2015) Semidán Robaina Estévez et al.   PLoS One

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Modeling the Differences in Biochemical Capabilities ofPseudomonasSpecies by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

(2014) Parizad Babaei et al.   TheScientificWorldJOURNAL

A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology

(2013) Michael F Seidl et al.   BMC GENOMICS

De novo pyrimidine biosynthesis in the oomycete plant pathogen Phytophthora infestans

(2013) Leonor García-Bayona et al.   GENE

Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii

(2013) C. Song et al.   Molecular Systems Biology

Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen Septoria tritici during Two Phases of the Compatible Interaction

(2013) Fen Yang et al.   PLoS One

Growth in rice cells requires de novo purine biosynthesis by the blast fungus Magnaporthe oryzae

(2013) Jessie Fernandez et al.   Scientific Reports

Software applications for flux balance analysis

(2012) M. Lakshmanan et al.   BRIEFINGS IN BIOINFORMATICS

Insights into metabolic efficiency from flux analysis

(2012) Xuewen Chen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen

(2012) David E. L. Cooke et al.   PLoS Pathogens

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

(2011) Paul A Jensen et al.   BMC Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Computational methods for metabolic reconstruction

(2010) Esa Pitkänen et al.   CURRENT OPINION IN BIOTECHNOLOGY

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

A secreted effector protein (SNE1) from Phytophthora infestans is a broadly acting suppressor of programmed cell death

(2010) Brendan S. Kelley et al.   PLANT JOURNAL

Metabolic adaptation ofPhytophthora infestansduring growth on leaves, tubers and artificial media

(2009) HOWARD S. JUDELSON et al.   MOLECULAR PLANT PATHOLOGY

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

In silico genome-scale reconstruction and validation of theCorynebacterium glutamicummetabolic network

(2008) Kjeld Raunkjaer Kjeldsen et al.   BIOTECHNOLOGY AND BIOENGINEERING

Phytophthora infestans: the plant (and R gene) destroyer

(2008) WILLIAM FRY   MOLECULAR PLANT PATHOLOGY

Is maximization of molar yield in metabolic networks favoured by evolution?

(2007) Stefan Schuster et al.   JOURNAL OF THEORETICAL BIOLOGY