Constraint-based modeling in microbial food biotechnology

MARSI: metabolite analogues for rational strain improvement

(2018) João G R Cardoso et al.   BIOINFORMATICS

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries

(2018) Shu Pan et al.   CURRENT OPINION IN BIOTECHNOLOGY

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Model-based quantification of metabolic interactions from dynamic microbial-community data

(2017) Mark Hanemaaijer et al.   PLoS One

Lactic Acid Bacteria as Cell Factories for the Generation of Bioactive Peptides

(2017) Lucia Brown et al.   PROTEIN AND PEPTIDE LETTERS

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

(2017) Lokanand Koduru et al.   Scientific Reports

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

(2017) Sebastián N. Mendoza et al.   Frontiers in Microbiology

Metabolic Models of Protein Allocation Call for the Kinetome

(2017) Avlant Nilsson et al.   Cell Systems

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

(2017) Olga Ponomarova et al.   Cell Systems

Perspectives and Challenges in Microbial Communities Metabolic Modeling

(2017) Emanuele Bosi et al.   Frontiers in Genetics

Next-generation probiotics: the spectrum from probiotics to live biotherapeutics

(2017) Paul W. O’Toole et al.   Nature Microbiology

Elucidation of complexity and prediction of interactions in microbial communities

(2017) Cristal Zuñiga et al.   Microbial Biotechnology

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

Public goods and metabolic strategies

(2016) Herwig Bachmann et al.   CURRENT OPINION IN MICROBIOLOGY

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Genome-scale metabolic models as platforms for strain design and biological discovery

(2016) Bashir Sajo Mienda   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Constraint-based stoichiometric modelling from single organisms to microbial communities

(2016) Willi Gottstein et al.   Journal of the Royal Society Interface

Metabolic assessment of E. coli as a Biofactory for commercial products

(2016) Xiaolin Zhang et al.   METABOLIC ENGINEERING

Predicting microbial interactions through computational approaches

(2016) Chenhao Li et al.   METHODS

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

Genome-Editing Technologies: Principles and Applications

(2016) Thomas Gaj et al.   Cold Spring Harbor Perspectives in Biology

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

(2016) Minseung Kim et al.   Nature Communications

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

(2016) Daniel A. Cuevas et al.   Frontiers in Microbiology

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

(2016) Elizabeth Brunk et al.   Cell Systems

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic interactions in microbial communities: untangling the Gordian knot

(2015) Olga Ponomarova et al.   CURRENT OPINION IN MICROBIOLOGY

Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks

(2015) Elias W. Krumholz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unraveling interactions in microbial communities - from co-cultures to microbiomes

(2015) Justin Tan et al.   JOURNAL OF MICROBIOLOGY

Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production

(2015) Kai H. Zhuang et al.   METABOLIC ENGINEERING

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

(2015) Paulo Maia et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias et al.   NUCLEIC ACIDS RESEARCH

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic network modeling of microbial communities

(2015) Matthew B. Biggs et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

(2015) Mark Hanemaaijer et al.   Frontiers in Microbiology

Lactic acid bacteria as a cell factory for riboflavin production

(2015) Kiran Thakur et al.   Microbial Biotechnology

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

(2014) Ibrahim E El-Semman et al.   BMC Systems Biology

Prediction of intracellular metabolic states from extracellular metabolomic data

(2014) Maike K. Aurich et al.   Metabolomics

The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology

(2014) Patrick MF Derkx et al.   Microbial Cell Factories

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Genome –Scale Reconstruction of Metabolic Networks of Lactobacillus casei ATCC 334 and 12A

(2014) Elena Vinay-Lara et al.   PLoS One

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

(2014) J. H. van Heerden et al.   SCIENCE

Production of Aroma Compounds in Lactic Fermentations

(2014) E.J. Smid et al.   Annual Review of Food Science and Technology

Elucidating the interactions between the human gut microbiota and its host through metabolic modeling

(2014) Saeed Shoaie et al.   Frontiers in Genetics

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation

(2013) Nicolas A. L. Flahaut et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial heterogeneity affects bioprocess robustness: Dynamic single-cell analysis contributes to understanding of microbial populations

(2013) Frank Delvigne et al.   Biotechnology Journal

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Lactic Acid Bacteria as a Cell Factory for the Delivery of Functional Biomolecules and Ingredients in Cereal-Based Beverages: A Review

(2013) Deborah M. Waters et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Software platforms to facilitate reconstructing genome-scale metabolic networks

(2013) Joshua J. Hamilton et al.   ENVIRONMENTAL MICROBIOLOGY

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

(2013) Swagatika Sahoo et al.   HUMAN MOLECULAR GENETICS

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Software applications toward quantitative metabolic flux analysis and modeling

(2012) T. Dandekar et al.   BRIEFINGS IN BIOINFORMATICS

Predicting Drug Targets and Biomarkers of Cancer via Genome-Scale Metabolic Modeling

(2012) L. Jerby et al.   CLINICAL CANCER RESEARCH

Towards metagenome-scale models for industrial applications—the case of Lactic Acid Bacteria

(2012) Filipe Branco dos Santos et al.   CURRENT OPINION IN BIOTECHNOLOGY

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Earliest evidence for cheese making in the sixth millennium bc in northern Europe

(2012) Mélanie Salque et al.   NATURE

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Transcriptomes Reveal Genetic Signatures Underlying Physiological Variations Imposed by Different Fermentation Conditions in Lactobacillus plantarum

(2012) Peter A. Bron et al.   PLoS One

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

(2011) A. Bordbar et al.   JOURNAL OF INTERNAL MEDICINE

Systems biology of lactic acid bacteria: a critical review

(2011) Bas Teusink et al.   Microbial Cell Factories

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis

(2011) Filipe Santos et al.   Microbial Cell Factories

Systems solutions by lactic acid bacteria: from paradigms to practice

(2011) Willem M de Vos   Microbial Cell Factories

An integrated approach to characterize genetic interaction networks in yeast metabolism

(2011) Balázs Szappanos et al.   NATURE GENETICS

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Use of genome-scale metabolic models for understanding microbial physiology

(2010) Liming Liu et al.   FEBS LETTERS

Understanding the physiology of Lactobacillus plantarum at zero growth

(2010) Philippe Goffin et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Mathematical models of cell factories: moving towards the core of industrial biotechnology

(2010) Marija Cvijovic et al.   Microbial Biotechnology

Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid Bacteria

(2009) M. I. Pastink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

(2009) Caroline B. Milne et al.   Biotechnology Journal

A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression

(2009) Gian M. Oddone et al.   METABOLIC ENGINEERING

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

(2009) Bas Teusink et al.   PLoS Computational Biology

Postgenomic Analysis of Streptococcus thermophilus Cocultivated in Milk with Lactobacillus delbrueckii subsp. bulgaricus: Involvement of Nitrogen, Purine, and Iron Metabolism

(2008) L. Herve-Jimenez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence

(2008) Hyohak Song et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

The lactic acid bacterium as a cell factory for food ingredient production

(2007) Jeroen Hugenholtz   INTERNATIONAL DAIRY JOURNAL

Effects of Various Sugars Added to Growth and Drying Media upon Thermotolerance and Survival throughout Storage of Freeze-Dried lactobacillus delbrueckii ssp. bulgaricus

(2004) Ana S. Carvalho et al.   BIOTECHNOLOGY PROGRESS