The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale
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Title
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale
Authors
Keywords
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Journal
Microorganisms
Volume 8, Issue 12, Pages 2050
Publisher
MDPI AG
Online
2020-12-21
DOI
10.3390/microorganisms8122050
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Note: Only part of the references are listed.- Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
- (2020) Milenko Tokic et al. Biotechnology for Biofuels
- Automatic construction of metabolic models with enzyme constraints
- (2020) Pavlos Stephanos Bekiaris et al. BMC BIOINFORMATICS
- Improved protein structure prediction using potentials from deep learning
- (2020) Andrew W. Senior et al. NATURE
- MEMOTE for standardized genome-scale metabolic model testing
- (2020) Christian Lieven et al. NATURE BIOTECHNOLOGY
- K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data
- (2020) Saratram Gopalakrishnan et al. METABOLIC ENGINEERING
- A biochemically-interpretable machine learning classifier for microbial GWAS
- (2020) Erol S. Kavvas et al. Nature Communications
- Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity
- (2020) Patrick V. Phaneuf et al. BMC GENOMICS
- Revealing 29 sets of independently modulated genes inStaphylococcus aureus, their regulators, and role in key physiological response
- (2020) Saugat Poudel et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth
- (2020) Cristal Zuñiga et al. Nature Communications
- Dynamic co‐culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures
- (2020) Emrah Özcan et al. BIOTECHNOLOGY AND BIOENGINEERING
- The Bitome: digitized genomic features reveal fundamental genome organization
- (2020) Cameron R Lamoureux et al. NUCLEIC ACIDS RESEARCH
- iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning
- (2020) Kevin Rychel et al. NUCLEIC ACIDS RESEARCH
- Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
- (2020) David Heckmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
- (2020) Jan Zrimec et al. Nature Communications
- Scalable computation of intracellular metabolite concentrations
- (2020) Amir Akbari et al. COMPUTERS & CHEMICAL ENGINEERING
- DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
- (2019) Laurence Yang et al. BMC Systems Biology
- Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains
- (2019) Ilaria Massaiu et al. Microbial Cell Factories
- Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
- (2019) Joanne K. Liu et al. PLoS Computational Biology
- Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites
- (2019) Noushin Hadadi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
- (2019) Sankha Ghatak et al. NUCLEIC ACIDS RESEARCH
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
- (2019) Laurent Heirendt et al. Nature Protocols
- Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
- (2019) Vikash Pandey et al. PLoS Computational Biology
- Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates
- (2019) Charles J. Norsigian et al. Frontiers in Cellular and Infection Microbiology
- Approaches to Computational Strain Design in the Multiomics Era
- (2019) Peter C. St. John et al. Frontiers in Microbiology
- Cellular responses to reactive oxygen species are predicted from molecular mechanisms
- (2019) Laurence Yang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers
- (2019) Jae Yong Ryu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- How the avidity of polymerase binding to the –35/–10 promoter sites affects gene expression
- (2019) Tal Einav et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints
- (2019) Daan H. de Groot et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Coupled metabolic‐hydrodynamic modeling enabling rational scale‐up of industrial bioprocesses
- (2019) Guan Wang et al. BIOTECHNOLOGY AND BIOENGINEERING
- The Escherichia coli transcriptome mostly consists of independently regulated modules
- (2019) Anand V. Sastry et al. Nature Communications
- Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli
- (2019) Bin Du et al. PLoS Computational Biology
- ssbio: a Python framework for structural systems biology
- (2018) Nathan Mih et al. BIOINFORMATICS
- pyTFA and matTFA: A Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
- (2018) Pierre Salvy et al. BIOINFORMATICS
- Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method
- (2018) Bin Du et al. BIOPHYSICAL JOURNAL
- Optimization of bioprocess productivity based on metabolic-genetic network models with bilevel dynamic programming
- (2018) Banafsheh Jabarivelisdeh et al. BIOTECHNOLOGY AND BIOENGINEERING
- Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism
- (2018) Sylvain Prigent et al. BIOTECHNOLOGY AND BIOENGINEERING
- Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
- (2018) João G. R. Cardoso et al. ACS Synthetic Biology
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression
- (2018) Colton J. Lloyd et al. PLoS Computational Biology
- DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data
- (2018) Gustavo Arango-Argoty et al. Microbiome
- Synthetic gene circuits for the detection, elimination and prevention of disease
- (2018) Ferdinand Sedlmayer et al. Nature Biomedical Engineering
- PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore
- (2018) Ratul Chowdhury et al. Nature Communications
- Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
- (2018) Yara Seif et al. Nature Communications
- A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering
- (2018) Osvaldo D. Kim et al. Frontiers in Microbiology
- RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12
- (2018) Alberto Santos-Zavaleta et al. NUCLEIC ACIDS RESEARCH
- ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation
- (2018) Patrick V Phaneuf et al. NUCLEIC ACIDS RESEARCH
- Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice
- (2018) Bin Du et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
- (2018) Elizabeth Brunk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Estimating Metabolic Equilibrium Constants: Progress and Future Challenges
- (2018) Bin Du et al. TRENDS IN BIOCHEMICAL SCIENCES
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
- (2018) David Heckmann et al. Nature Communications
- Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
- (2018) Erol S. Kavvas et al. Nature Communications
- Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion
- (2017) Zachary A. King et al. METABOLIC ENGINEERING
- Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli
- (2017) Karl Kochanowski et al. Molecular Systems 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
- iML1515, a knowledgebase that computes Escherichia coli traits
- (2017) Jonathan M Monk et al. NATURE BIOTECHNOLOGY
- Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
- (2017) Ke Chen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Global transcriptional regulatory network forEscherichia colirobustly connects gene expression to transcription factor activities
- (2017) Xin Fang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metabolic Models of Protein Allocation Call for the Kinetome
- (2017) Avlant Nilsson et al. Cell Systems
- Systems biology of the structural proteome
- (2016) Elizabeth Brunk et al. BMC Systems Biology
- Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models
- (2016) Stefano Andreozzi et al. METABOLIC ENGINEERING
- iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks
- (2016) Stefano Andreozzi et al. METABOLIC ENGINEERING
- The coming of age of de novo protein design
- (2016) Po-Ssu Huang et al. NATURE
- Synchronized cycles of bacterial lysis for in vivo delivery
- (2016) M. Omar Din et al. NATURE
- Predictable tuning of protein expression in bacteria
- (2016) Mads T Bonde et al. NATURE METHODS
- Fuelling the future: microbial engineering for the production of sustainable biofuels
- (2016) James C. Liao et al. NATURE REVIEWS MICROBIOLOGY
- The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12
- (2016) Ingrid M. Keseler et al. NUCLEIC ACIDS RESEARCH
- 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
- Genetic circuit design automation
- (2016) A. A. K. Nielsen et al. SCIENCE
- Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach
- (2016) Pedro A. Saa et al. Scientific Reports
- Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
- (2016) Matthew A. Oberhardt et al. PLoS Computational Biology
- What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
- (2016) Derrick E. Fouts et al. PLoS Neglected Tropical Diseases
- Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes
- (2016) Jonathan M. Monk et al. Cell Systems
- Microbial protein: future sustainable food supply route with low environmental footprint
- (2016) Silvio Matassa et al. Microbial Biotechnology
- Antimicrobial Resistance Prediction in PATRIC and RAST
- (2016) James J. Davis et al. Scientific Reports
- Using Genome-scale Models to Predict Biological Capabilities
- (2015) Edward J. O’Brien et al. CELL
- Distributing a metabolic pathway among a microbial consortium enhances production of natural products
- (2015) Kang Zhou et al. NATURE BIOTECHNOLOGY
- Systems strategies for developing industrial microbial strains
- (2015) Sang Yup Lee et al. NATURE BIOTECHNOLOGY
- The I-TASSER Suite: protein structure and function prediction
- (2015) Jianyi Yang et al. NATURE METHODS
- The Iterative Protein Redesign and Optimization (IPRO) suite of programs
- (2014) Robert J. Pantazes et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data
- (2014) Ali Khodayari et al. METABOLIC ENGINEERING
- Optimizing genome-scale network reconstructions
- (2014) Jonathan Monk et al. NATURE BIOTECHNOLOGY
- Principles of genetic circuit design
- (2014) Jennifer A N Brophy et al. NATURE METHODS
- Constraint-based models predict metabolic and associated cellular functions
- (2014) Aarash Bordbar et al. NATURE REVIEWS GENETICS
- Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions
- (2014) Adrian Jinich et al. Scientific Reports
- Environmental Sensing of Heavy Metals Through Whole Cell Microbial Biosensors: A Synthetic Biology Approach
- (2014) Lara Tess Bereza-Malcolm et al. ACS Synthetic Biology
- Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models
- (2013) Joshua J. Hamilton et al. BIOPHYSICAL JOURNAL
- COBRApy: COnstraints-Based Reconstruction and Analysis for Python
- (2013) Ali Ebrahim et al. BMC Systems Biology
- A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects
- (2013) Elad Noor et al. FEBS LETTERS
- 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
- Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
- (2013) D. McCloskey et al. Molecular Systems Biology
- Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
- (2013) J. M. Monk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Consistent Estimation of Gibbs Energy Using Component Contributions
- (2013) Elad Noor et al. PLoS Computational Biology
- An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
- (2012) Elad Noor et al. BIOINFORMATICS
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- In silico method for modelling metabolism and gene product expression at genome scale
- (2012) Joshua A. Lerman et al. Nature Communications
- An overview of the Amber biomolecular simulation package
- (2012) Romelia Salomon-Ferrer et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
- (2012) Roi Adadi et al. PLoS Computational Biology
- eQuilibrator--the biochemical thermodynamics calculator
- (2011) A. Flamholz et al. NUCLEIC ACIDS RESEARCH
- Bacterial adaptation through distributed sensing of metabolic fluxes
- (2010) Oliver Kotte et al. Molecular Systems Biology
- A synchronized quorum of genetic clocks
- (2010) Tal Danino et al. NATURE
- Synthetic biology: applications come of age
- (2010) Ahmad S. Khalil et al. NATURE REVIEWS GENETICS
- Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis
- (2010) Sriram Chandrasekaran et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Translation efficiency is determined by both codon bias and folding energy
- (2010) Tamir Tuller et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MEME SUITE: tools for motif discovery and searching
- (2009) T. L. Bailey et al. NUCLEIC ACIDS RESEARCH
- Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
- (2008) Matthew D. Jankowski et al. BIOPHYSICAL JOURNAL
- Metabolic Control Analysis: A Tool for Designing Strategies to Manipulate Metabolic Pathways
- (2008) Rafael Moreno-Sánchez et al. JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY
- Advances in bacterial promoter recognition and its control by factors that do not bind DNA
- (2008) Shanil P. Haugen et al. NATURE REVIEWS MICROBIOLOGY
- Detailed Enzyme Kinetics in Terms of Biochemical Species: Study of Citrate Synthase
- (2008) Daniel A. Beard et al. PLoS One
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