The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Authors
Keywords
-
Journal
Nature Communications
Volume 11, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-01-14
DOI
10.1038/s41467-019-13818-7
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- pyTFA and matTFA: A Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
- (2018) Pierre Salvy et al. BIOINFORMATICS
- KBase: The United States Department of Energy Systems Biology Knowledgebase
- (2018) Adam P Arkin et al. NATURE BIOTECHNOLOGY
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression
- (2018) Colton J. Lloyd et al. PLoS Computational Biology
- Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
- (2017) Benjamín J Sánchez et al. Molecular Systems Biology
- SteadyCom: Predicting microbial abundances while ensuring community stability
- (2017) Siu Hung Joshua Chan et al. PLoS Computational Biology
- Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
- (2017) Ding Ma et al. Scientific Reports
- solveME: fast and reliable solution of nonlinear ME models
- (2016) Laurence Yang et al. BMC BIOINFORMATICS
- Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
- (2016) Stefanía Magnúsdóttir et al. NATURE BIOTECHNOLOGY
- Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements
- (2016) Dan Davidi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
- (2015) Zachary A. King et al. PLoS Computational Biology
- optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks
- (2014) Wout Megchelenbrink et al. PLoS One
- Visual account of protein investment in cellular functions
- (2014) W. Liebermeister et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism inE. coliK-12 MG1655 that is biochemically and thermodynamically consistent
- (2013) Douglas McCloskey et al. BIOTECHNOLOGY AND BIOENGINEERING
- COBRApy: COnstraints-Based Reconstruction and Analysis for Python
- (2013) Ali Ebrahim et al. BMC Systems Biology
- Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
- (2013) E. J. O{middle dot}Brien et al. Molecular Systems Biology
- Groups: knowledge spreadsheets for symbolic biocomputing
- (2013) Michael Travers et al. Database-The Journal of Biological Databases and Curation
- Sizing up metatranscriptomics
- (2012) Mary Ann Moran et al. ISME Journal
- In silico method for modelling metabolism and gene product expression at genome scale
- (2012) Joshua A. Lerman et al. Nature Communications
- A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011
- (2011) J. D. Orth et al. Molecular Systems Biology
- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
- (2011) Jan Schellenberger et al. Nature Protocols
- SABIO-RK--database for biochemical reaction kinetics
- (2011) U. Wittig et al. NUCLEIC ACIDS RESEARCH
- iMAT: an integrative metabolic analysis tool
- (2010) Hadas Zur et al. BIOINFORMATICS
- Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis
- (2010) Andreas Otto et al. Nature Communications
- Flux balance analysis accounting for metabolite dilution
- (2010) Tomer Benyamini et al. GENOME BIOLOGY
- Biopython: freely available Python tools for computational molecular biology and bioinformatics
- (2009) P. J. A. Cock et al. BIOINFORMATICS
- BioNumbers—the database of key numbers in molecular and cell biology
- (2009) Ron Milo et al. NUCLEIC ACIDS RESEARCH
- Physical biology of the cell, by Rob Phillips, Jane Kondev and Julie Theriot
- (2009) Robert Gilbert Crystallography Reviews
- Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
- (2008) Matthew D. Jankowski et al. BIOPHYSICAL JOURNAL
- Use of Randomized Sampling for Analysis of Metabolic Networks
- (2008) Jan Schellenberger et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Context-Specific Metabolic Networks Are Consistent with Experiments
- (2008) Scott A. Becker et al. PLoS Computational Biology
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started