Software applications toward quantitative metabolic flux analysis and modeling

FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

(2012) Hendrik Rohn et al.   BMC Systems Biology

Creating views on integrated multidomain data

(2011) H. Rohn et al.   BIOINFORMATICS

Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation

(2011) Gaby Wangorsch et al.   BMC Systems Biology

Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification

(2011) Sven Nahnsen et al.   JOURNAL OF PROTEOME RESEARCH

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Relative potential of biosynthetic pathways for biofuels and bio-based products

(2011) Deepak Dugar et al.   NATURE BIOTECHNOLOGY

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

(2011) Jan Schellenberger et al.   Nature Protocols

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

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

Staphylococcus aureus physiological growth limitations: Insights from flux calculations built on proteomics and external metabolite data

(2011) Chunguang Liang et al.   PROTEOMICS

Path finding methods accounting for stoichiometry in metabolic networks

(2011) Jon Pey et al.   GENOME BIOLOGY

A parallel algorithm to compute chemical organizations in biological networks

(2010) F. Centler et al.   BIOINFORMATICS

Exploring metabolic pathways in genome-scale networks via generating flux modes

(2010) A. Rezola et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Isotopologue Profiling ofLegionella pneumophila

(2010) Eva Eylert et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Carbon metabolism of intracellular bacterial pathogens and possible links to virulence

(2010) Wolfgang Eisenreich et al.   NATURE REVIEWS MICROBIOLOGY

Computing the shortest elementary flux modes in genome-scale metabolic networks

(2009) Luis F. de Figueiredo et al.   BIOINFORMATICS

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database

(2009) Konstantinos Moutselos et al.   BMC BIOINFORMATICS

Decomposing complex reaction networks using random sampling, principal component analysis, and basis rotation

(2009) Christian L Barrett et al.   BMC Systems Biology

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

(2009) C. Kaleta et al.   GENOME RESEARCH

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

(2009) Lake-Ee Quek et al.   Microbial Cell Factories

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

TinkerCell: modular CAD tool for synthetic biology

(2009) Deepak Chandran et al.   Journal of Biological Engineering

Large-scale computation of elementary flux modes with bit pattern trees

(2008) Marco Terzer et al.   BIOINFORMATICS

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Comparative Pathway Analyzer—a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms

(2008) Sebastian Oehm et al.   NUCLEIC ACIDS RESEARCH