Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Genome wide analysis of protein production load in Trichoderma reesei

(2016) Tiina M. Pakula et al.   Biotechnology for Biofuels

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production

(2014) Justyna Nocon et al.   METABOLIC ENGINEERING

Updates in Rhea—a manually curated resource of biochemical reactions

(2014) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

sybil – Efficient constraint-based modelling in R

(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

(2012) Elad Noor et al.   BIOINFORMATICS

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

(2012) Luis Caspeta et al.   BMC Systems Biology

Dynamic flux balance analysis of the metabolism ofSaccharomyces cerevisiaeduring the shift from fully respirative or respirofermentative metabolic states to anaerobiosis

(2012) Paula Jouhten et al.   FEBS Journal

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

(2012) Balaji Balagurunathan et al.   Microbial Cell Factories

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803

(2011) Katsunori Yoshikawa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Correlation of gene expression and protein production rate - a system wide study

(2011) Mikko Arvas et al.   BMC GENOMICS

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism

(2011) Markus Heinonen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

YMDB: the Yeast Metabolome Database

(2011) T. Jewison et al.   NUCLEIC ACIDS RESEARCH

The biomass objective function

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

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Genome sequence of the recombinant protein production host Pichia pastoris

(2009) Kristof De Schutter et al.   NATURE BIOTECHNOLOGY

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

(2009) Z. Xu et al.   NUCLEIC ACIDS RESEARCH

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

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

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

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

(2008) Wanwipa Vongsangnak et al.   BMC GENOMICS

Analysis of Aspergillus nidulans metabolism at the genome-scale

(2008) Helga David et al.   BMC GENOMICS

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

(2008) Mikael Rørdam Andersen et al.   Molecular Systems Biology

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Impact of systems biology on metabolic engineering ofSaccharomyces cerevisiae

(2007) Jens Nielsen et al.   FEMS YEAST RESEARCH