4.6 Article

etiBsu1209: A comprehensive multiscale metabolic model for Bacillus subtilis

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Microbiology

Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth

Jiri Vohradsky et al.

Summary: The research combines literature-mined data, gene expression kinetic modeling, and promoter sequence analysis to identify the regulon of Bacillus subtilis sigma factor SigB specifically expressed during germination and outgrowth. This computational approach provides new insights into a well-studied system and highlights the subset of the SigB regulon activated during germination and outgrowth.

MICROORGANISMS (2021)

Article Biotechnology & Applied Microbiology

Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models

Xue Yang et al.

Summary: In this paper, a novel method integrating enzymatic and thermodynamic constraints is proposed for constructing a metabolic model of E. coli, demonstrating the potential application of metabolic models with multiple constraints for accurate pathway analysis and phenotype prediction.

METABOLIC ENGINEERING (2021)

Article Multidisciplinary Sciences

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Omid Oftadeh et al.

Summary: Mathematical modeling is used to integrate multiple biological networks into a single cell model for optimizing industrial biotechnology. The yETFL model, developed for Saccharomyces cerevisiae, can predict parameters such as maximum growth rate and essential genes. This framework has the potential to be extended to a wide range of eukaryotic organisms, benefiting academic and industrial research.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

A deep learning architecture for metabolic pathway prediction

Mayank Baranwal et al.

BIOINFORMATICS (2020)

Letter Biotechnology & Applied Microbiology

MEMOTE for standardized genome-scale metabolic model testing

Christian Lieven et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemistry & Molecular Biology

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

Gregory L. Medlock et al.

CELL SYSTEMS (2020)

Article Biochemistry & Molecular Biology

Enhancement of β-Mannanase Production by Bacillus subtilis ATCC11774 through Optimization of Medium Composition

Nor Amalina Binti Mahamad Norizan et al.

MOLECULES (2020)

Review Biotechnology & Applied Microbiology

Bacillus subtilis: a universal cell factory for industry, agriculture, biomaterials and medicine

Yuan Su et al.

MICROBIAL CELL FACTORIES (2020)

Article Multidisciplinary Sciences

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

Kevin Rychel et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

Derek N. Macklin et al.

SCIENCE (2020)

Article Biochemical Research Methods

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Pierre Salvy et al.

BIOINFORMATICS (2019)

Review Biotechnology & Applied Microbiology

Current status and applications of genome-scale metabolic models

Changdai Gu et al.

GENOME BIOLOGY (2019)

Article Evolutionary Biology

Genetic Competence Drives Genome Diversity in Bacillus subtilis

Patricia H. Brito et al.

GENOME BIOLOGY AND EVOLUTION (2018)

Article Biotechnology & Applied Microbiology

Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement

Rainer Borriss et al.

MICROBIAL BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Daniel Machado et al.

NUCLEIC ACIDS RESEARCH (2018)

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)

Article Biochemistry & Molecular Biology

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

Byoung-Mo Koo et al.

CELL SYSTEMS (2017)

Article Biochemistry & Molecular Biology

BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases

Oveis Jamialahmadi et al.

MOLECULAR BIOSYSTEMS (2016)

Article Biochemical Research Methods

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Elad Noor et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Using Genome-scale Models to Predict Biological Capabilities

Edward J. O'Brien et al.

Article Biochemistry & Molecular Biology

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Mario L. Arrieta-Ortiz et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Article Microbiology

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

Semen A. Leyn et al.

JOURNAL OF BACTERIOLOGY (2013)

Article Microbiology

An updated metabolic view of the Bacillus subtilis 168 genome

Eugeni Belda et al.

MICROBIOLOGY-SGM (2013)

Article Biotechnology & Applied Microbiology

Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of 13C metabolic flux analysis

Martin Ruehl et al.

BIOTECHNOLOGY AND BIOENGINEERING (2012)

Article Biochemistry & Molecular Biology

13C-flux Analysis Reveals NADPH-balancing Transhydrogenation Cycles in Stationary Phase of Nitrogen-starving Bacillus subtilis

Martin Ruehl et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Biotechnology & Applied Microbiology

Dynamic Flux Responses in Riboflavin Overproducing Bacillus subtilis to Increasing Glucose Limitation in Fed-Batch Culture

Martin Ruehl et al.

BIOTECHNOLOGY AND BIOENGINEERING (2010)

Article Biochemistry & Molecular Biology

Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis

Roelco J. Kleijn et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemical Research Methods

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

Ines Thiele et al.

NATURE PROTOCOLS (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

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Christopher S. Henry et al.

GENOME BIOLOGY (2009)

Article Biophysics

Thermodynamics-based metabolic flux analysis

Christopher S. Henry et al.

BIOPHYSICAL JOURNAL (2007)

Article Biotechnology & Applied Microbiology

OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

AP Burgard et al.

BIOTECHNOLOGY AND BIOENGINEERING (2003)