Modelling of microbial interactions in anaerobic digestion: from black to glass box

Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids

(2022) B. Conall Holohan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Review on anaerobic digestion models: Model classification & elaboration of process phenomena

(2022) Samuel Emebu et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Molecular biology and modeling analysis reveal functional roles of propionate to acetate ratios on microbial syntrophy and competition in electro-assisted anaerobic digestion

(2022) Basem S. Zakaria et al.   WATER RESEARCH

Microbial dark matter: from discovery to applications

(2022) Yuguo Zha et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

(2022) Nicola De Bernardini et al.   Microbiome

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

(2022) Feiran Li et al.   Nature Catalysis

The development of human gut microbiota fermentation capacity during the first year of life

(2022) Clarissa Schwab   Microbial Biotechnology

Development and Validation of a Dynamic First Order Kinetics Model of a Periodically Operated Well-Mixed Vessel for Anaerobic Digestion

(2021) Mauro Lafratta et al.   CHEMICAL ENGINEERING JOURNAL

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

(2021) Colton J. Lloyd et al.   PLoS Computational Biology

Considering syntrophic acetate oxidation and ionic strength improves the performance of models for food waste anaerobic digestion

(2021) Gabriel Capson-Tojo et al.   BIORESOURCE TECHNOLOGY

Mechanisms for Electron Uptake by Methanosarcina acetivorans during Direct Interspecies Electron Transfer

(2021) Dawn E. Holmes et al.   mBio

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

(2020) Stefano Campanaro et al.   Biotechnology for Biofuels

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

Altered Gut Archaea Composition and Interaction with Bacteria are Associated with Colorectal Cancer

(2020) Olabisi Oluwabukola Coker et al.   GASTROENTEROLOGY

Flux balance analysis of glucose degradation by anaerobic digestion in negative pressure

(2020) Jialong Huang et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

A Review of Landfill Microbiology and Ecology: A Call for Modernization With ‘Next Generation’ Technology

(2020) D’Arcy R. Meyer-Dombard et al.   Frontiers in Microbiology

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models

(2020) Matthew J. Scarborough et al.   mSystems

An evolving view of methane metabolism in the Archaea

(2019) Paul N. Evans et al.   NATURE REVIEWS MICROBIOLOGY

Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity

(2019) Sören Weinrich et al.   Frontiers in Microbiology

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

(2018) Pierre Salvy et al.   BIOINFORMATICS

Anaerobic digestion of food waste: A review focusing on process stability

(2018) Lei Li et al.   BIORESOURCE TECHNOLOGY

Methanogenesis

(2018) Zhe Lyu et al.   CURRENT BIOLOGY

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

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Methanogens: biochemical background and biotechnological applications

(2018) Franziska Enzmann et al.   AMB Express

A vision for a ‘microbcentric’ future

(2018) Ricardo Cavicchioli   Microbial Biotechnology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process

(2016) Sabine Koch et al.   Biotechnology for Biofuels

Using Genome-scale Models to Predict Biological Capabilities

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

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree 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

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

(2015) Joshua J. Hamilton et al.   PLoS Computational Biology

Kinetic models in industrial biotechnology – Improving cell factory performance

(2014) Joachim Almquist et al.   METABOLIC ENGINEERING

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

(2013) Matthew C. Gonnerman et al.   Biotechnology Journal

Mathematical model of anaerobic digestion in a chemostat: effects of syntrophy and inhibition

(2013) Marion Weedermann et al.   Journal of Biological Dynamics

Potential roles of anaerobic ammonium and methane oxidation in the nitrogen cycle of wetland ecosystems

(2010) Guibing Zhu et al.   APPLIED MICROBIOLOGY AND 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

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE