4.6 Review

Approaches to Computational Strain Design in the Multiomics Era

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Model-based metabolism design: constraints for kinetic and stoichiometric models

Egils Stalidzans et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2018)

Review Biochemical Research Methods

Quantitative -omic data empowers bottom-up systems biology

James T. Yurkovich et al.

CURRENT OPINION IN BIOTECHNOLOGY (2018)

Article Mathematical & Computational Biology

A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data

Zak Costello et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2018)

Editorial Material Biotechnology & Applied Microbiology

Bespoke design of whole-cell microbial machines

Claudia Vickers

MICROBIAL BIOTECHNOLOGY (2017)

Editorial Material Biotechnology & Applied Microbiology

Let's talk about flux or the importance of (intracellular) reaction rates

Lars M. Blank

MICROBIAL BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Benjamin J. Sanchez et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Review Biotechnology & Applied Microbiology

The Impact of Systems Biology on Bioprocessing

Kate Campbell et al.

TRENDS IN BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

Metabolic Models of Protein Allocation Call for the Kinetome

Avlant Nilsson et al.

CELL SYSTEMS (2017)

Review Biotechnology & Applied Microbiology

Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

Pedro A. Saa et al.

BIOTECHNOLOGY ADVANCES (2017)

Article Biophysics

Acceleration Strategies to Enhance Metabolic Ensemble Modeling Performance

Jennifer L. Greene et al.

BIOPHYSICAL JOURNAL (2017)

Article Biochemistry & Molecular Biology

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Zachary A. King et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Methods for the integration of multi-omics data: mathematical aspects

Matteo Bersanelli et al.

BMC BIOINFORMATICS (2016)

Article Mathematical & Computational Biology

Evaluation of rate law approximations in bottom-up kinetic models of metabolism

Bin Du et al.

BMC SYSTEMS BIOLOGY (2016)

Review Biochemistry & Molecular Biology

Engineering Cellular Metabolism

Jens Nielsen et al.

Review Microbiology

Current state and challenges for dynamic metabolic modeling

Eleni Vasilakou et al.

CURRENT OPINION IN MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

Minseung Kim et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach

Pedro A. Saa et al.

SCIENTIFIC REPORTS (2016)

Article Biochemistry & Molecular Biology

Characterizing Strain Variation in Engineered E.coli Using a Multi-Omics-Based Workflow

Elizabeth Brunk et al.

CELL SYSTEMS (2016)

Review Mathematical & Computational Biology

Synthetic and systems biology for microbial production of commodity chemicals

Victor Chubukov et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2016)

Article Engineering, Chemical

Facilitate Collaborations among Synthetic Biology, Metabolic Engineering and Machine Learning

Stephen Gang Wu et al.

CHEMBIOENG REVIEWS (2016)

Article Biochemistry & Molecular Biology

Using Genome-scale Models to Predict Biological Capabilities

Edward J. O'Brien et al.

Review Biochemical Research Methods

Computational methods in metabolic engineering for strain design

Matthew R. Long et al.

CURRENT OPINION IN BIOTECHNOLOGY (2015)

Review Biotechnology & Applied Microbiology

Genome scale engineering techniques for metabolic engineering

Rongming Liu et al.

METABOLIC ENGINEERING (2015)

Article Biotechnology & Applied Microbiology

13C metabolic flux analysis at a genome-scale

Saratram Gopalakrishnan et al.

METABOLIC ENGINEERING (2015)

Article Multidisciplinary Sciences

Overflow metabolism in Escherichia coli results from efficient proteome allocation

Markus Basan et al.

NATURE (2015)

Article Biochemical Research Methods

A Method to Constrain Genome-Scale Models with 13C Labeling Data

Hector Garcia Martin et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Review Biotechnology & Applied Microbiology

Analytics for metabolic engineering

Christopher J. Petzold et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2015)

Article Multidisciplinary Sciences

Stochasticity of metabolism and growth at the single-cell level

Daniel J. Kiviet et al.

NATURE (2014)

Article Biotechnology & Applied Microbiology

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

Ali Khodayari et al.

METABOLIC ENGINEERING (2014)

Article Mathematical & Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ali Ebrahim et al.

BMC SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Integrated Analysis of Transcriptomic and Proteomic Data

Saad Haider et al.

CURRENT GENOMICS (2013)

Review Biochemical Research Methods

From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals

Stephen Van Dien

CURRENT OPINION IN BIOTECHNOLOGY (2013)

Article Biochemistry & Molecular Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

Edward J. O'Brien et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Review Genetics & Heredity

Computational solutions for omics data

Bonnie Berger et al.

NATURE REVIEWS GENETICS (2013)

Article Multidisciplinary Sciences

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

Roger L. Chang et al.

SCIENCE (2013)

Article Biochemistry & Molecular Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Jonathan R. Karr et al.

Article Biochemical Research Methods

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

L. Arike et al.

JOURNAL OF PROTEOMICS (2012)

Article Multidisciplinary Sciences

In silico method for modelling metabolism and gene product expression at genome scale

Joshua A. Lerman et al.

NATURE COMMUNICATIONS (2012)

Article Biochemical Research Methods

StochKit2: software for discrete stochastic simulation of biochemical systems with events

Kevin R. Sanft et al.

BIOINFORMATICS (2011)

Review Biochemistry & Molecular Biology

Mass Spectrometry Strategies in Metabolomics

Zhentian Lei et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

Omic data from evolved E-coli are consistent with computed optimal growth from genome-scale models

Nathan E. Lewis et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

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

Christopher S. Henry et al.

NATURE BIOTECHNOLOGY (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biotechnology & Applied Microbiology

Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae

H. Wouter Wisselink et al.

METABOLIC ENGINEERING (2010)

Article Multidisciplinary Sciences

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Sriram Chandrasekaran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biotechnology & Applied Microbiology

Translating biochemical network models between different kinetic formats

Frieder Hadlich et al.

METABOLIC ENGINEERING (2009)

Article Biotechnology & Applied Microbiology

Ensemble modeling for strain development of L-lysine-producing Escherichia coli

Carolina A. Contador et al.

METABOLIC ENGINEERING (2009)

Article Biophysics

Ensemble Modeling of Metabolic Networks

Linh M. Tran et al.

BIOPHYSICAL JOURNAL (2008)

Article Biotechnology & Applied Microbiology

Network-based prediction of human tissue-specific metabolism

Tomer Shlomi et al.

NATURE BIOTECHNOLOGY (2008)

Article Engineering, Electrical & Electronic

CellDesigner 3.5: A versatile modeling tool for biochemical networks

Akira Funahashi et al.

PROCEEDINGS OF THE IEEE (2008)

Article Biochemical Research Methods

Context-specific metabolic networks are consistent with experiments

Scott A. Becker et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Multidisciplinary Sciences

Stochastic fluctuations in metabolic pathways

Erel Levine et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biophysics

Thermodynamics-based metabolic flux analysis

Christopher S. Henry et al.

BIOPHYSICAL JOURNAL (2007)

Article Biochemical Research Methods

COPASI- A COmplex PAthway SImulator

Stefan Hoops et al.

BIOINFORMATICS (2006)

Review Biochemistry & Molecular Biology

Protein identification and expression analysis using mass spectrometry

Eugene Kolker et al.

TRENDS IN MICROBIOLOGY (2006)

Review Biotechnology & Applied Microbiology

Approximative kinetic formats used in metabolic network modeling

JJ Heijnen

BIOTECHNOLOGY AND BIOENGINEERING (2005)

Article Biotechnology & Applied Microbiology

Integration of gene expression data into genome-scale metabolic models

M Åkesson et al.

METABOLIC ENGINEERING (2004)

Article Computer Science, Software Engineering

MATCONT: A MATLAB package for numerical bifurcation analysis of ODEs

A Dhooge et al.

ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE (2003)

Article Biotechnology & Applied Microbiology

Dynamic modeling of the central carbon metabolism of Escherichia coli

C Chassagnole et al.

BIOTECHNOLOGY AND BIOENGINEERING (2002)

Review Biotechnology & Applied Microbiology

13C metabolic flux analysis

W Wiechert

METABOLIC ENGINEERING (2001)