Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems

Improvement of zero waste sustainable recovery using microbial energy generation systems: A comprehensive review

(2022) Wilgince Apollon et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

(2021) Cheewin Kittikunapong et al.   Metabolites

Electrosynthesis, modulation, and self-driven electroseparation in microbial fuel cells

(2021) Iwona Gajda et al.   iScience

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4

(2020) Hoda Nouri et al.   Scientific Reports

Insights into palladium nanoparticles produced by Shewanella oneidensis MR-1: Roles of NADH dehydrogenases and hydrogenases

(2020) Zhen-Ni Yang et al.   ENVIRONMENTAL RESEARCH

Electroactive microorganisms in bioelectrochemical systems

(2019) Bruce E. Logan et al.   NATURE REVIEWS MICROBIOLOGY

Towards development of electrogenetics using electrochemically active bacteria

(2019) Atsumi Hirose et al.   BIOTECHNOLOGY ADVANCES

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

Reversing an Extracellular Electron Transfer Pathway for Electrode-Driven Acetoin Reduction

(2019) Nicholas M. Tefft et al.   ACS Synthetic Biology

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

NADH dehydrogenases Nuo and Nqr1 contribute to extracellular electron transfer by Shewanella oneidensis MR-1 in bioelectrochemical systems

(2019) Cody S. Madsen et al.   Scientific Reports

Enzyme-Assisted Microbial Electrosynthesis of Poly(3-hydroxybutyrate) via CO2 Bioreduction by Engineered Ralstonia eutropha

(2018) Xiaoli Chen et al.   ACS Catalysis

Modular Engineering Intracellular NADH Regeneration Boosts Extracellular Electron Transfer of Shewanella oneidensis MR-1

(2018) Feng Li et al.   ACS Synthetic Biology

Engineered Shewanella oneidensis -reduced graphene oxide biohybrid with enhanced biosynthesis and transport of flavins enabled a highest bioelectricity output in microbial fuel cells

(2018) Tong Lin et al.   Nano Energy

Roles of D-Lactate Dehydrogenases in the Anaerobic Growth of Shewanella oneidensis MR-1 on Sugars

(2018) Takuya Kasai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Model-guided identification of novel gene amplification targets for improving succinate production in Escherichia coli NZN111

(2017) Xingxing Jian et al.   Integrative Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Light-Driven H2 Evolution and C═C or C═O Bond Hydrogenation by Shewanella oneidensis: A Versatile Strategy for Photocatalysis by Nonphotosynthetic Microorganisms

(2017) Sam F. Rowe et al.   ACS Catalysis

Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis

(2016) Ramanan Sekar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Improving electron trans-inner membrane movements in microbial electrocatalysts

(2016) Le Tao et al.   CHEMICAL COMMUNICATIONS

Biotransformation and biomethylation of arsenic by Shewanella oneidensis MR-1

(2016) Juan Wang et al.   CHEMOSPHERE

Extracellular electron transfer mechanisms between microorganisms and minerals

(2016) Liang Shi et al.   NATURE REVIEWS MICROBIOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions

(2015) Gen Nakagawa et al.   PLoS One

Tailoring Unique Mesopores of Hierarchically Porous Structures for Fast Direct Electrochemistry in Microbial Fuel Cells

(2015) Long Zou et al.   Advanced Energy Materials

Enhancing Bidirectional Electron Transfer of Shewanella oneidensis by a Synthetic Flavin Pathway

(2015) Yun Yang et al.   ACS Synthetic Biology

Simplifying microbial electrosynthesis reactor design

(2015) Cloelle G. S. Giddings et al.   Frontiers in Microbiology

Theoretical exploration of optimal metabolic flux distributions for extracellular electron transfer by Shewanella oneidensisMR-1

(2014) Longfei Mao et al.   Biotechnology for Biofuels

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

(2014) Wai Ong et al.   BMC Systems Biology

Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

(2014) Na-Rae Lee et al.   Microbial Cell Factories

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

(2014) Hong Yang et al.   PLoS Computational Biology

Metabolically engineered glucose-utilizing Shewanella strains under anaerobic conditions

(2013) Donggeon Choi et al.   BIORESOURCE TECHNOLOGY

Basic concepts and principles of stoichiometric modeling of metabolic networks

(2013) Timo R. Maarleveld et al.   Biotechnology Journal

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Flux variability scanning based on enforced objective flux for identifying gene amplification targets

(2012) Jong Park et al.   BMC Systems Biology

Use of cassette-electrode microbial fuel cell for wastewater treatment

(2012) Morio Miyahara et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Relative potential of biosynthetic pathways for biofuels and bio-based products

(2011) Deepak Dugar et al.   NATURE BIOTECHNOLOGY

Towards Electrosynthesis in Shewanella: Energetics of Reversing the Mtr Pathway for Reductive Metabolism

(2011) Daniel E. Ross et al.   PLoS One

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production

(2010) H. S. Choi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The octahaem SirA catalyses dissimilatory sulfite reduction in Shewanella oneidensis MR-1

(2010) Sheetal Shirodkar et al.   ENVIRONMENTAL MICROBIOLOGY

Modularity of the Mtr respiratory pathway of Shewanella oneidensis strain MR-1

(2010) Dan Coursolle et al.   MOLECULAR MICROBIOLOGY

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

(2010) Nathan E Lewis et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Microbial electrosynthesis — revisiting the electrical route for microbial production

(2010) Korneel Rabaey et al.   NATURE REVIEWS MICROBIOLOGY

Microbial Electrosynthesis: Feeding Microbes Electricity To Convert Carbon Dioxide and Water to Multicarbon Extracellular Organic Compounds

(2010) K. P. Nevin et al.   mBio

Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration

(2010) Haichun Gao et al.   Microbial Biotechnology

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

(2010) Grigoriy E. Pinchuk et al.   PLoS Computational Biology

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA

(2009) Haichun Gao et al.   ISME Journal

Mechanism and Consequences of Anaerobic Respiration of Cobalt by Shewanella oneidensis Strain MR-1

(2008) H. H. Hau et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Communities on Electron-Beam Pt-Deposited Electrodes in a Mediator-Less Microbial Fuel Cell

(2008) Ho Il Park et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY