Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms

Clinically relevant mutations in core metabolic genes confer antibiotic resistance

(2021) Allison J. Lopatkin et al.   SCIENCE

Metabolic and genetic basis for auxotrophies in Gram-negative species

(2020) Yara Seif et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

(2020) Reem Hassan et al.   Scientific Reports

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

(2020) Jason C. Hyun et al.   PLoS Computational Biology

A biochemically-interpretable machine learning classifier for microbial GWAS

(2020) Erol S. Kavvas et al.   Nature Communications

A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance

(2020) James K. Martin et al.   CELL

The Adaptive Response to Long-Term Nitrogen Starvation in Escherichia coli Requires the Breakdown of Allantoin

(2020) Amy Switzer et al.   JOURNAL OF BACTERIOLOGY

Beyond tug-of-war: Iron metabolism in cooperative host–microbe interactions

(2020) Grischa Y. Chen et al.   PLoS Pathogens

Machine learning-based radiomic models to predict intensity-modulated radiation therapy response, Gleason score and stage in prostate cancer

(2019) Hamid Abdollahi et al.   Radiologia Medica

Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa

(2019) Laura J. Dunphy et al.   Cell Systems

Peptidoglycan Muropeptides: Release, Perception, and Functions as Signaling Molecules

(2019) Oihane Irazoki et al.   Frontiers in Microbiology

Sequencing-based methods and resources to study antimicrobial resistance

(2019) Manish Boolchandani et al.   NATURE REVIEWS GENETICS

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Microcavity Supported Lipid Bilayers; Evaluation of Drug- Lipid Membrane Interactions by Electrochemical Impedance and Fluorescence Correlation Spectroscopy

(2019) Sivaramakrishnan Ramadurai et al.   LANGMUIR

Slow growth determines nonheritable antibiotic resistance in Salmonella enterica

(2019) Mauricio H. Pontes et al.   Science Signaling

Comparative metabolomics shows the metabolic profiles fluctuate in multi-drug resistant Escherichia coli strains

(2019) Yuexu Lin et al.   Journal of Proteomics

Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate

(2019) Allison J. Lopatkin et al.   Nature Microbiology

A machine learning-based service for estimating quality of genomes using PATRIC

(2019) Bruce Parrello et al.   BMC BIOINFORMATICS

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

(2019) Charles J Norsigian et al.   NUCLEIC ACIDS RESEARCH

The mutational landscape of quinolone resistance in Escherichia coli

(2019) Kamya Bhatnagar et al.   PLoS One

Prevalence and risk factors for multi-drug resistant Escherichia coli among poultry workers in the Federal Capital Territory, Abuja, Nigeria

(2019) Mabel Kamweli Aworh et al.   PLoS One

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

(2019) Hongzhong Lu et al.   Nature Communications

Changes in the Carbon Metabolism of Escherichia coli During the Evolution of Doxycycline Resistance

(2019) Yiwen Yang et al.   Frontiers in Microbiology

Role of Proline in Pathogen and Host Interactions

(2018) Shelbi L. Christgen et al.   ANTIOXIDANTS & REDOX SIGNALING

L‑histidine augments the oxidative damage against Gram‑negative bacteria by hydrogen peroxide

(2018) Tamiko Nagao et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them

(2018) Matthew T. Sorbara et al.   Mucosal Immunology

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates

(2018) Anna J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

(2018) Marcus Nguyen et al.   Scientific Reports

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories

(2018) João G. R. Cardoso et al.   ACS Synthetic Biology

Mobile Genetic Elements Associated with Antimicrobial Resistance

(2018) Sally R. Partridge et al.   CLINICAL MICROBIOLOGY REVIEWS

Predicting the evolution of Escherichia coli by a data-driven approach

(2018) Xiaokang Wang et al.   Nature Communications

An evaluation of multidrug-resistant Escherichia coli isolates in urinary tract infections from Aguascalientes, Mexico: cross-sectional study

(2018) Flor Y. Ramírez-Castillo et al.   Annals of Clinical Microbiology and Antimicrobials

Nitrogen Starvation Induces Persister Cell Formation in Escherichia coli

(2018) Daniel R. Brown   JOURNAL OF BACTERIOLOGY

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella

(2018) Marcus Nguyen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

(2018) Erol S. Kavvas et al.   Nature Communications

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data

(2018) Danesh Moradigaravand et al.   PLoS Computational Biology

Antibiotic resistance: a rundown of a global crisis

(2018) Bilal Aslam et al.   Infection and Drug Resistance

Regulation of the Locus of Enterocyte Effacement in Attaching and Effacing Pathogens

(2017) R. Christopher D. Furniss et al.   JOURNAL OF BACTERIOLOGY

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Oxidative stress, protein damage and repair in bacteria

(2017) Benjamin Ezraty et al.   NATURE REVIEWS MICROBIOLOGY

A New View into the Regulation of Purine Metabolism: The Purinosome

(2017) Anthony M. Pedley et al.   TRENDS IN BIOCHEMICAL SCIENCES

Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations

(2017) Mattia Zampieri et al.   Cell Reports

Oxidation Resistance of the Sulfur Amino Acids: Methionine and Cysteine

(2017) Peng Bin et al.   Biomed Research International

Purine Biosynthesis Metabolically Constrains Intracellular Survival of Uropathogenic Escherichia coli

(2016) Carrie L. Shaffer et al.   INFECTION AND IMMUNITY

Distinguishing between resistance, tolerance and persistence to antibiotic treatment

(2016) Asher Brauner et al.   NATURE REVIEWS MICROBIOLOGY

Escherichia coli β-Lactamases: What Really Matters

(2016) Priyanka Bajaj et al.   Frontiers in Microbiology

Antimicrobial Resistance Prediction in PATRIC and RAST

(2016) James J. Davis et al.   Scientific Reports

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Using Genome-scale Models to Predict Biological Capabilities

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

Boosting Bacterial Metabolism to Combat Antibiotic Resistance

(2015) Prerna Bhargava et al.   Cell Metabolism

Acetyl-CoA and the regulation of metabolism: mechanisms and consequences

(2015) Lei Shi et al.   CURRENT OPINION IN CELL BIOLOGY

Positive Effect of Carbon Sources on Natural Transformation in Escherichia coli: Role of Low-Level Cyclic AMP (cAMP)-cAMP Receptor Protein in the Derepression ofrpoS

(2015) Mengyue Guo et al.   JOURNAL OF BACTERIOLOGY

Intestinal Fucose as a Mediator of Host–Microbe Symbiosis

(2015) Joseph M. Pickard et al.   JOURNAL OF IMMUNOLOGY

Growth-dependent bacterial susceptibility to ribosome-targeting antibiotics

(2015) P. Greulich et al.   Molecular Systems Biology

Antibiotic efficacy is linked to bacterial cellular respiration

(2015) Michael A. Lobritz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From ingestion to colonization: the influence of the host environment on regulation of the LEE encoded type III secretion system in enterohaemorrhagic Escherichia coli

(2015) James P. R. Connolly et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Molecular Mechanisms Underlying Bacterial Persisters

(2014) Etienne Maisonneuve et al.   CELL

Heme uptake in bacterial pathogens

(2014) Heidi Contreras et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The fitness costs of antibiotic resistance mutations

(2014) Anita H. Melnyk et al.   Evolutionary Applications

A Cross-Disciplinary Perspective on the Innate Immune Responses to Bacterial Lipopolysaccharide

(2014) Yunhao Tan et al.   MOLECULAR CELL

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

The Alternative Role of Enterobactin as an Oxidative Stress Protector Allows Escherichia coli Colony Development

(2014) Conrado Adler et al.   PLoS One

Antibiotics induce redox-related physiological alterations as part of their lethality

(2014) D. J. Dwyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ANTIMICROBIAL DRUG RESISTANCE IN STRAINS OF Escherichia coli ISOLATED FROM FOOD SOURCES

(2014) Mohammed Uddin Rasheed et al.   REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

(2014) Jennifer R Huddleston   Infection and Drug Resistance

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks

(2013) Yang Zhao et al.   BIOINFORMATICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Iron in Infection and Immunity

(2013) James E. Cassat et al.   Cell Host & Microbe

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production

(2013) Mark P Brynildsen et al.   NATURE BIOTECHNOLOGY

Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes

(2013) Hassan Safi et al.   NATURE GENETICS

Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

(2013) Adam C. Palmer et al.   NATURE REVIEWS GENETICS

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

The human microbiome as a reservoir of antimicrobial resistance

(2013) John Penders et al.   Frontiers in Microbiology

Structural Modifications of Bacterial Lipopolysaccharide that Facilitate Gram-Negative Bacteria Evasion of Host Innate Immunity

(2013) Motohiro Matsuura   Frontiers in Immunology

The role of horizontal gene transfer in the dissemination of extended-spectrum beta-lactamase–producing Escherichia coli and Klebsiella pneumoniae isolates in an endemic setting

(2012) Yohei Doi et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Bacterial stress responses as determinants of antimicrobial resistance

(2012) K. Poole   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Pyrimidine Nucleotide Biosynthetic Pathway Modulates Production of Biofilm Determinants in Escherichia coli

(2012) Marco Garavaglia et al.   PLoS One

Iron homeostasis—Achilles’ heel of Aspergillus fumigatus?

(2011) Markus Schrettl et al.   CURRENT OPINION IN MICROBIOLOGY

Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments

(2011) Christopher J Alteri et al.   CURRENT OPINION IN MICROBIOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Polyamines reduce oxidative stress in Escherichia coli cells exposed to bactericidal antibiotics

(2011) Alexander G. Tkachenko et al.   RESEARCH IN MICROBIOLOGY

The struggle for iron - a metal at the host-pathogen interface

(2010) Manfred Nairz et al.   CELLULAR MICROBIOLOGY

Overcoming the Heme Paradox: Heme Toxicity and Tolerance in Bacterial Pathogens

(2010) L. L. Anzaldi et al.   INFECTION AND IMMUNITY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Role of Global Regulators and Nucleotide Metabolism in Antibiotic Tolerance in Escherichia coli

(2008) S. Hansen et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine

(2008) A. J. Fabich et al.   INFECTION AND IMMUNITY

Membrane lipid homeostasis in bacteria

(2008) Yong-Mei Zhang et al.   NATURE REVIEWS MICROBIOLOGY

Cell shape and cell-wall organization in Gram-negative bacteria

(2008) K. C. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA