Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling

Epidemiology and outcomes of bloodstream infections in 177 severe burn patients from an industrial disaster: a multicentre retrospective study

(2018) C.Q. Tang et al.   CLINICAL MICROBIOLOGY AND INFECTION

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

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Novel Polymyxin Combination With Antineoplastic Mitotane Improved the Bacterial Killing Against Polymyxin-Resistant Multidrug-Resistant Gram-Negative Pathogens

(2018) Thien B. Tran et al.   Frontiers in Microbiology

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

(2018) Charles J. Norsigian et al.   Frontiers in Genetics

Metabolic constraints on the evolution of antibiotic resistance

(2017) Mattia Zampieri et al.   Molecular Systems Biology

Variable spontaneous mutation rate in clinical strains of multidrug-resistant Acinetobacter baumannii and differentially expressed proteins in a hypermutator strain

(2017) Morteza Karami-Zarandi et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Untargeted metabolomics analysis reveals key pathways responsible for the synergistic killing of colistin and doripenem combination against Acinetobacter baumannii

(2017) Mohd Hafidz Mahamad Maifiah et al.   Scientific Reports

Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections

(2017) Luana Presta et al.   Scientific Reports

Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations

(2017) Mattia Zampieri et al.   Cell Reports

Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach

(2017) Xiaoting Hua et al.   Frontiers in Cellular and Infection Microbiology

Risk Factors, Clinical Presentation, and Outcome of Acinetobacter baumannii Bacteremia

(2017) Tala Ballouz et al.   Frontiers in Cellular and Infection Microbiology

Acinetobacter baumannii strains isolated from patients in intensive care units in Goiânia, Brazil: Molecular and drug susceptibility profiles

(2017) Suellen Rocha Araújo Castilho et al.   PLoS One

ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks

(2016) Pedro A. Saa et al.   BIOINFORMATICS

The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets

(2016) Pablo Ivan Pereira Ramos et al.   BMC GENOMICS

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A penicillin-binding protein inhibits selection of colistin-resistant, lipooligosaccharide-deficientAcinetobacter baumannii

(2016) Joseph M. Boll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The induction and identification of novel Colistin resistance mutations in Acinetobacter baumannii and their implications

(2016) Nguyen Thi Khanh Nhu et al.   Scientific Reports

Polymyxin Resistance in Acinetobacter baumannii: Genetic Mutations and Transcriptomic Changes in Response to Clinically Relevant Dosage Regimens

(2016) Soon-Ee Cheah et al.   Scientific Reports

Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii

(2016) Mohd Hafidz Mahamad Maifiah et al.   Scientific Reports

Simple Method for Markerless Gene Deletion in Multidrug-Resistant Acinetobacter baumannii

(2015) Man Hwan Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Using Genome-scale Models to Predict Biological Capabilities

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

Antimicrobial interactions: mechanisms and implications for drug discovery and resistance evolution

(2015) Tobias Bollenbach   CURRENT OPINION IN MICROBIOLOGY

The transcriptomic response ofAcinetobacter baumanniito colistin and doripenem alone and in combination in anin vitropharmacokinetics/pharmacodynamics model

(2015) Rebekah Henry et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

(2015) Larry A. Gallagher et al.   JOURNAL OF BACTERIOLOGY

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification of Acinetobacter baumannii Genes Necessary for Persistence in the Lung

(2014) N. Wang et al.   mBio

Prediction of antibiotic resistance by gene expression profiles

(2014) Shingo Suzuki et al.   Nature Communications

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Biological Cost of Different Mechanisms of Colistin Resistance and Their Impact on Virulence in Acinetobacter baumannii

(2013) Alejandro Beceiro et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis

(2013) Fei He et al.   BMC Systems Biology

Pharmacology of polymyxins: new insights into an ‘old’ class of antibiotics

(2013) Tony Velkov et al.   Future Microbiology

A secondary mode of action of polymyxins against Gram-negative bacteria involves the inhibition of NADH-quinone oxidoreductase activity

(2013) Zakuan Z Deris et al.   JOURNAL OF ANTIBIOTICS

Fortifying the barrier: the impact of lipid A remodelling on bacterial pathogenesis

(2013) Brittany D. Needham et al.   NATURE REVIEWS MICROBIOLOGY

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii

(2013) Daniel N. Farrugia et al.   PLoS One

Rapid Killing of Acinetobacter baumannii by Polymyxins Is Mediated by a Hydroxyl Radical Death Pathway

(2012) Timothy R. Sampson et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

VANTED v2: a framework for systems biology applications

(2012) Hendrik Rohn et al.   BMC Systems Biology

Carbapenem-associated multidrug-resistant Acinetobacter baumannii are sensitised by aztreonam in combination with polyamines

(2012) Louis Malone et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

(2012) Arvind K. Chavali et al.   TRENDS IN MICROBIOLOGY

Colistin-Resistant, Lipopolysaccharide-Deficient Acinetobacter baumannii Responds to Lipopolysaccharide Loss through Increased Expression of Genes Involved in the Synthesis and Transport of Lipoproteins, Phospholipids, and Poly-β-1,6-N-Acetylglucosamine

(2011) Rebekah Henry et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Colistin Resistance in Acinetobacter baumannii Is Mediated by Complete Loss of Lipopolysaccharide Production

(2010) J. H. Moffatt et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

fAUC/MIC is the most predictive pharmacokinetic/pharmacodynamic index of colistin against Acinetobacter baumannii in murine thigh and lung infection models

(2010) R. V. Dudhani et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

Resistance to Colistin in Acinetobacter baumannii Associated with Mutations in the PmrAB Two-Component System

(2009) M. D. Adams et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

(2009) Bevan Chung et al.   BMC Systems Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

(2009) Hyun Uk Kim et al.   Molecular BioSystems

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

(2008) Maxime Durot et al.   BMC Systems Biology

ATPase genes of diverse multidrug-resistant Acinetobacter baumannii isolates frequently harbour integrated DNA

(2008) F. Shaikh et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY