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References from Antibiotic resistance: Time of synthesis in a post-genomic age. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
2014 · External reference
Unresolved reference
2010 · External reference
Unresolved reference
2000 · External reference
Unresolved reference
1999 · External reference
10.1038/nrmicro3399
10.1038/nrmicro3399 · External reference
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms
10.1073/pnas.95.6.3140 · 1998 · External reference
10.1016/s0272-2712(18)30338-x
10.1016/s0272-2712(18)30338-x · External reference
Identification of plasmids by PCR-based replicon typing
10.1016/j.mimet.2005.03.018 · 2005 · External reference
10.1128/aac.02412-14
10.1128/aac.02412-14 · External reference
PCR typing of genetic determinants for metallo-beta-lactamases and integrases carried by gram-negative bacteria isolated in Japan, with focus on the class 3 integron
2003 · External reference
Genotyping and high flux sequencing of the bacterial pathogenic elements - integrons
10.1016/j.micpath.2017.12.073 · 2018 · External reference
10.1038/nrmicro909
10.1038/nrmicro909 · External reference
Allodemics
10.1016/s1473-3099(02)00393-6 · 2002 · External reference
10.1038/s41564-019-0503-9
10.1038/s41564-019-0503-9 · External reference
10.1016/j.ddtec.2014.02.001
10.1016/j.ddtec.2014.02.001 · External reference
10.1038/nrmicro1796
10.1038/nrmicro1796 · External reference
10.1016/j.coph.2011.07.005
10.1016/j.coph.2011.07.005 · External reference
10.1126/science.7542800
10.1126/science.7542800 · External reference
Adaptive resistance to antibiotics in bacteria: a systems biology perspective
10.1002/wsbm.1335 · 2016 · External reference
Unresolved reference
2006 · External reference
The impaired quorum sensing response of Pseudomonas aeruginosa MexAB-OprM efflux pump overexpressing mutants is not due to non-physiological efflux of 3-oxo-C12-HSL
10.1111/1462-2920.15177 · 2020 · External reference
10.1128/aac.00121-14
10.1128/aac.00121-14 · External reference
Metabolic Compensation of Fitness Costs Is a General Outcome for Antibiotic-Resistant Pseudomonas aeruginosa Mutants Overexpressing Efflux Pumps
10.1128/mbio.00500-17 · 2017 · External reference
10.1016/j.mib.2012.07.004
10.1016/j.mib.2012.07.004 · External reference
10.1073/pnas.0408966102
10.1073/pnas.0408966102 · External reference
Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens
10.3389/fcell.2020.566702 · 2020 · External reference
Using Genomics to Track Global Antimicrobial Resistance
10.3389/fpubh.2019.00242 · 2019 · External reference
10.1002/bit.20663
10.1002/bit.20663 · External reference
10.1002/cpt.1535
10.1002/cpt.1535 · External reference
10.1016/j.meegid.2017.09.022
10.1016/j.meegid.2017.09.022 · External reference
10.1016/j.chom.2016.04.015
10.1016/j.chom.2016.04.015 · External reference
10.1038/nrmicro.2017.28
10.1038/nrmicro.2017.28 · External reference
Antimicrobial resistance surveillance in the genomic age
10.1111/nyas.13289 · 2017 · External reference
10.1111/nyas.13310
10.1111/nyas.13310 · External reference
Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance
10.3389/fmicb.2019.02892 · 2019 · External reference
10.1038/nrmicro3439
10.1038/nrmicro3439 · External reference
10.1128/aac.44.7.1771-1777.2000
10.1128/aac.44.7.1771-1777.2000 · External reference
10.3390/genes2040804
10.3390/genes2040804 · External reference
10.1128/aac.47.7.2072-2081.2003
10.1128/aac.47.7.2072-2081.2003 · External reference
10.1128/aac.44.4.840-847.2000
10.1128/aac.44.4.840-847.2000 · External reference
Horizontal transfer of multiple penicillin-binding protein genes, and capsular biosynthetic genes, in natural populations of Streptococcus pneumoniae
10.1111/j.1365-2958.1991.tb02155.x · 1991 · External reference
Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism?
10.1073/pnas.96.21.11904 · 1999 · External reference
10.12688/f1000research.9685.1
10.12688/f1000research.9685.1 · External reference
Characteristics of nested living systems
10.1142/s0218339093000173 · 1993 · External reference
Current strategies for mobilome research
2014 · External reference
10.1111/nyas.13282
10.1111/nyas.13282 · External reference
The antibiotic resistance “mobilome”: searching for the link between environment and clinic
10.3389/fmicb.2013.00138 · 2013 · External reference
10.1038/nrmicro3399-c2
10.1038/nrmicro3399-c2 · External reference
10.1371/journal.ppat.1006369
10.1371/journal.ppat.1006369 · External reference
10.1038/s41576-018-0032-z
10.1038/s41576-018-0032-z · External reference
Mechanisms That Shape Microbial Pangenomes
10.1016/j.tim.2020.12.004 · 2021 · External reference
10.1016/j.gde.2005.09.006
10.1016/j.gde.2005.09.006 · External reference
10.1111/j.1574-6976.2011.00284.x
10.1111/j.1574-6976.2011.00284.x · External reference
Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance
10.1111/j.1574-6976.2011.00268.x · 2011 · External reference
10.1111/1462-2920.15238
10.1111/1462-2920.15238 · External reference
Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages
10.1128/cmr.00135-18 · 2019 · External reference
Systematic review of Group B Streptococcal capsular types, sequence types and surface proteins as potential vaccine candidates
10.1016/j.vaccine.2020.08.052 · 2020 · External reference
10.1073/pnas.1206541109
10.1073/pnas.1206541109 · External reference
Prokaryote genome fluidity: toward a system approach of the mobilome
10.1007/978-1-61779-361-5_4 · 2012 · External reference
A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings
10.1371/journal.pone.0040438 · 2012 · External reference
Unresolved reference
External reference
Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii. Diagnostics (Basel
2021 · External reference
Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013
10.1111/1469-0691.12638 · 2014 · External reference
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology
10.1371/journal.pone.0022751 · 2011 · External reference
10.1128/jcm.00262-14
10.1128/jcm.00262-14 · External reference
Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach
10.1128/jcm.00567-14 · 2014 · External reference
A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes
10.1186/1471-2164-15-1138 · 2014 · External reference
Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium
10.1128/jcm.01946-15 · 2015 · External reference
10.1038/nrmicro3093
10.1038/nrmicro3093 · External reference
Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes (“MLST+”)
10.1371/journal.pone.0123298 · 2015 · External reference
10.1111/j.1462-2920.2012.02837.x
10.1111/j.1462-2920.2012.02837.x · External reference
Ecology and Evolution of Chromosomal Gene Transfer between Environmental Microorganisms and Pathogens
10.1128/microbiolspec.mtbp-0006-2016 · 2018 · External reference
10.1128/msphere.00050-15
10.1128/msphere.00050-15 · External reference
Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance
10.3390/ijms21041363 · 2020 · External reference
Methods for correcting inference based on outcomes predicted by machine learning
10.1073/pnas.2001238117 · 2020 · External reference
Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes!
10.1093/clinchem/hvaa172 · 2020 · External reference
FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
10.1038/s41467-019-11306-6 · 2019 · External reference
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates
10.1128/aac.00483-19 · 2019 · External reference
10.1093/jac/dkaa345
10.1093/jac/dkaa345 · External reference
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens
10.1093/jac/dkx217 · 2017 · External reference
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
10.1128/aac.01310-13 · 2014 · External reference
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
2020 · External reference
10.1093/bioinformatics/bty053
10.1093/bioinformatics/bty053 · External reference
10.1186/s13073-014-0090-6
10.1186/s13073-014-0090-6 · External reference
Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data
10.1371/journal.pone.0133492 · 2015 · External reference
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
10.1099/mgen.0.000131 · 2017 · External reference
PATRIC, the bacterial bioinformatics database and analysis resource
10.1093/nar/gkt1099 · 2014 · External reference
PARGT: a software tool for predicting antimicrobial resistance in bacteria
10.1038/s41598-020-67949-9 · 2020 · External reference
10.1038/ismej.2014.106
10.1038/ismej.2014.106 · External reference
ARDB–Antibiotic Resistance Genes Database
10.1093/nar/gkn656 · 2009 · External reference
Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy
10.1093/nar/gkt1274 · 2014 · External reference
Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from <i>Staphylococcus aureus</i> Whole-Genome Sequences
10.1128/jcm.01815-17 · 2018 · External reference
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
10.1038/ncomms10063 · 2015 · External reference
Antimicrobial Resistance Prediction in PATRIC and RAST
10.1038/srep27930 · 2016 · External reference
Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat
10.1128/cmr.14.4.933-951.2001 · 2001 · External reference
10.1038/onc.2015.454
10.1038/onc.2015.454 · External reference
10.1007/s00239-015-9714-8
10.1007/s00239-015-9714-8 · External reference
Mechanism of plasmid-mediated quinolone resistance
10.1073/pnas.082092899 · 2002 · External reference
10.1016/s1473-3099(15)00424-7
10.1016/s1473-3099(15)00424-7 · External reference
MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis
10.1186/1471-2105-15-107 · 2014 · External reference
10.1038/nrmicro3033
10.1038/nrmicro3033 · External reference
The intrinsic resistome of bacterial pathogens
10.3389/fmicb.2013.00103 · 2013 · External reference
10.1371/journal.pone.0001619
10.1371/journal.pone.0001619 · External reference
Complex ciprofloxacin resistome revealed by screening a Pseudomonas aeruginosa mutant library for altered susceptibility
10.1128/aac.00222-08 · 2008 · External reference
10.1128/aac.00507-08
10.1128/aac.00507-08 · External reference
The intrinsic resistome of Pseudomonas aeruginosa to beta-lactams
10.4161/viru.2.2.15014 · 2011 · External reference
Characterization of the polymyxin B resistome of Pseudomonas aeruginosa
10.1128/aac.01583-12 · 2013 · External reference
10.1128/aac.01446-12
10.1128/aac.01446-12 · External reference
10.1128/aac.00035-09
10.1128/aac.00035-09 · External reference
10.1128/aac.00906-09
10.1128/aac.00906-09 · External reference
Transposon library screening for identification of genetic loci participating in intrinsic susceptibility and acquired resistance to antistaphylococcal agents
10.1093/jac/dks373 · 2013 · External reference
10.3389/fmicb.2016.02018
10.3389/fmicb.2016.02018 · External reference
The intrinsic resistome of Klebsiella pneumoniae
10.1016/j.ijantimicag.2018.09.012 · 2019 · External reference
10.1128/aac.00579-06
10.1128/aac.00579-06 · External reference
The intrinsic cephalosporin resistome of Listeria monocytogenes in the context of stress response, gene regulation, pathogenesis and therapeutics
10.1111/jam.12989 · 2016 · External reference
Mutational Evolution of Pseudomonas aeruginosa Resistance to Ribosome-Targeting Antibiotics
10.3389/fgene.2018.00451 · 2018 · External reference
Antimicrobial resistance: A multifaceted problem with multipronged solutions
10.1002/mbo3.945 · 2019 · External reference
Evolution of the Pseudomonas aeruginosa aminoglycoside mutational resistome in vitro and in the cystic fibrosis setting
10.1128/aac.02583-17 · 2018 · External reference
A large-scale whole-genome comparison shows that experimental evolution in response to antibiotics predicts changes in naturally evolved clinical Pseudomonas aeruginosa
10.1128/aac.01619-19 · 2019 · External reference
Evolution of the Pseudomonas aeruginosa mutational resistome in an international Cystic Fibrosis clone
10.1038/s41598-017-05621-5 · 2017 · External reference
10.1038/nrmicro2907
10.1038/nrmicro2907 · External reference
Proteomics approach to understand bacterial antibiotic resistance strategies
10.1080/14789450.2019.1681978 · 2019 · External reference
Comparative metabolomics shows the metabolic profiles fluctuate in multi-drug resistant Escherichia coli strains
10.1016/j.jprot.2019.103468 · 2019 · External reference
Metabolic mechanism of ceftazidime resistance in Vibrio alginolyticus
10.2147/idr.s179639 · 2019 · External reference
High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds
10.1126/scitranslmed.aal3973 · 2018 · External reference
Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium
10.1128/mbio.00109-21 · 2021 · External reference
The inactivation of RNase G reduces the Stenotrophomonas maltophilia susceptibility to quinolones by triggering the heat shock response
10.3389/fmicb.2015.01068 · 2015 · External reference
The Inactivation of Enzymes Belonging to the Central Carbon Metabolism Is a Novel Mechanism of Developing Antibiotic Resistance
10.1128/msystems.00282-20 · 2020 · External reference
10.1016/j.celrep.2017.07.062
10.1016/j.celrep.2017.07.062 · External reference
10.1021/acs.jproteome.8b00625
10.1021/acs.jproteome.8b00625 · External reference
10.1021/acs.jproteome.9b00687
10.1021/acs.jproteome.9b00687 · External reference
Transcriptome profiling in imipenem-selected Acinetobacter baumannii
10.1186/1471-2164-15-815 · 2014 · External reference
10.1128/aac.04037-14
10.1128/aac.04037-14 · External reference
The Role of Proteomics in Bacterial Response to Antibiotics
10.3390/ph13090214 · 2020 · External reference
Quantitative proteomics implicates YggT in streptomycin resistance in Salmonella enterica serovar Enteritidis
10.1007/s10529-021-03083-4 · 2021 · External reference
Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa
10.1128/aac.00075-16 · 2016 · External reference
Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach
10.1038/s41598-020-70581-2 · 2020 · External reference
10.1016/j.mib.2008.02.006
10.1016/j.mib.2008.02.006 · External reference
Antibiotics as intermicrobial signaling agents instead of weapons
10.1073/pnas.0608949103 · 2006 · External reference
10.1016/j.mib.2006.08.006
10.1016/j.mib.2006.08.006 · External reference
Are antibiotics naturally antibiotics?
10.1007/s10295-006-0112-5 · 2006 · External reference
Core Antibiotic-Induced Transcriptional Signatures Reflect Susceptibility to All Members of an Antibiotic Class
10.1128/aac.02296-20 · 2021 · External reference
Rapid bacterial genome sequencing: methods and applications in clinical microbiology
10.1111/1469-0691.12217 · 2013 · External reference
plasmidSPAdes: assembling plasmids from whole genome sequencing data
10.1101/048942 · 2016 · External reference
Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences
10.1371/journal.pgen.1004766 · 2014 · External reference
AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks
10.1093/bioinformatics/btw601 · 2017 · External reference
10.1101/2021.01.30.428878
10.1101/2021.01.30.428878 · External reference
10.1016/j.csbj.2020.09.012 · Admitted local publication
OMeta: an ontology-based, data-driven metadata tracking system
10.1186/s12859-018-2580-9 · 2019 · External reference
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing
10.1038/s41564-019-0656-6 · 2020 · External reference
Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions
2020 · External reference
Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics
10.15252/emmm.201910264 · 2020 · External reference
10.1016/j.arbres.2019.01.002
10.1016/j.arbres.2019.01.002 · External reference
Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?
10.1016/j.cmi.2017.10.030 · 2018 · External reference
Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis
10.1128/aac.00664-16 · 2016 · External reference
Predictable Phenotypes of Antibiotic Resistance Mutations
10.1128/mbio.00770-18 · 2018 · External reference
Resistance Sniffer: An online tool for prediction of drug resistance patterns of Mycobacterium tuberculosis isolates using next generation sequencing data
10.1016/j.ijmm.2020.151399 · 2020 · External reference
Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies
10.3390/microorganisms9010097 · 2021 · External reference
Whole genome enrichment approach for rapid detection of Mycobacterium tuberculosis and drug resistance-associated mutations from direct sputum sequencing
10.1016/j.tube.2020.101915 · 2020 · External reference
10.1111/j.1574-6976.2010.00261.x
10.1111/j.1574-6976.2010.00261.x · External reference
Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Science
2019 · External reference
One Health and Antibiotic Resistance in Agroecosystems
2018 · External reference
One Health and the Politics of Antimicrobial Resistance
10.3201/eid2304.161871 · 2017 · External reference
10.1111/1758-2229.12011
10.1111/1758-2229.12011 · External reference
10.1111/j.1574-6976.2008.00142.x
10.1111/j.1574-6976.2008.00142.x · External reference
10.1111/j.1758-2229.2009.00053.x
10.1111/j.1758-2229.2009.00053.x · External reference
10.1101/gr.5969107
10.1101/gr.5969107 · External reference
10.1126/science.1159483
10.1126/science.1159483 · External reference
Origins, acquisition and dissemination of antibiotic resistance determinants
1997 · External reference
Bottlenecks in the transferability of antibiotic resistance from natural ecosystems to human bacterial pathogens
2012 · External reference
Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health
10.3389/fmicb.2020.01914 · 2020 · External reference
10.1128/aac.00381-10
10.1128/aac.00381-10 · External reference
Pharmacodynamic model to describe the concentration-dependent selection of cefotaxime-resistant Escherichia coli
10.1128/aac.49.12.5081-5091.2005 · 2005 · External reference
The population genetics of antibiotic resistance
10.1093/clinids/24.supplement_1.s9 · 1997 · External reference
10.1111/eva.12753
10.1111/eva.12753 · External reference
10.1086/321877
10.1086/321877 · External reference
10.1038/nature17672
10.1038/nature17672 · External reference
10.1126/science.1220761
10.1126/science.1220761 · External reference
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm
10.1186/s40168-019-0735-1 · 2019 · External reference
10.1111/j.1742-7843.2005.pto960401.x
10.1111/j.1742-7843.2005.pto960401.x · External reference
10.1128/aac.45.7.2054-2059.2001
10.1128/aac.45.7.2054-2059.2001 · External reference
Surveillance of antimicrobial resistance in bacteria isolated from food animals to antimicrobial growth promoters and related therapeutic agents in Denmark
10.1111/j.1699-0463.1998.tb01391.x · 1998 · External reference
Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms
10.1038/s41467-020-15222-y · 2020 · External reference
10.1126/science.1240578
10.1126/science.1240578 · External reference
10.1128/aem.01802-16
10.1128/aem.01802-16 · External reference
Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages
10.1371/journal.pgen.1004776 · 2014 · External reference
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline
10.3389/fmicb.2018.03349 · 2019 · External reference
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates
10.1128/aac.00483-19 · 2019 · External reference
MEGARes: an antimicrobial resistance database for high throughput sequencing
10.1093/nar/gkw1009 · 2017 · External reference
A new generation of homology search tools based on probabilistic inference
2009 · External reference
A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences
10.1186/1471-2164-13-695 · 2012 · External reference
Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants
2009 · External reference
10.1126/science.1120800
10.1126/science.1120800 · External reference
Antibiotic resistance genes across a wide variety of metagenomes
10.1093/femsec/fiv168 · 2016 · External reference
Man-made microbial resistances in built environments
10.1038/s41467-019-08864-0 · 2019 · External reference
The microbiome of uncontacted Amerindians
10.1126/sciadv.1500183 · 2015 · External reference
10.1371/journal.pone.0034953
10.1371/journal.pone.0034953 · External reference
10.1038/nature10388
10.1038/nature10388 · External reference
10.1038/ismej.2008.86
10.1038/ismej.2008.86 · External reference
10.1016/j.tim.2016.11.014
10.1016/j.tim.2016.11.014 · External reference
10.1126/science.8153624
10.1126/science.8153624 · External reference
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
2014 · External reference
10.1038/nature13377
10.1038/nature13377 · External reference
Metagenomic analysis of an urban resistome before and after wastewater treatment
10.1038/s41598-020-65031-y · 2020 · External reference
10.1016/j.ijmm.2013.02.009
10.1016/j.ijmm.2013.02.009 · External reference
10.4155/fmc.12.2
10.4155/fmc.12.2 · External reference
10.1093/bioinformatics/btp105
10.1093/bioinformatics/btp105 · External reference
ACLAME: a CLAssification of Mobile genetic Elements, update 2010
10.1093/nar/gkp938 · 2010 · External reference
10.1093/nar/gkaa869
10.1093/nar/gkaa869 · External reference
Metagenomics and antibiotics
10.1111/j.1469-0691.2012.03868.x · 2012 · External reference
10.2217/fmb.13.32
10.2217/fmb.13.32 · External reference
How to discover new antibiotic resistance genes?
10.1080/14737159.2019.1592678 · 2019 · External reference
Prediction of the intestinal resistome by a three-dimensional structure-based method
10.1038/s41564-018-0292-6 · 2019 · External reference
10.1111/j.1365-2958.1995.tb02390.x
10.1111/j.1365-2958.1995.tb02390.x · External reference
10.1128/jb.173.17.5532-5538.1991
10.1128/jb.173.17.5532-5538.1991 · External reference
Mechanism of quinolone inhibition of DNA gyrase. Appearance of unique norfloxacin binding sites in enzyme-DNA complexes
10.1016/s0021-9258(19)81708-8 · 1989 · External reference
Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli
10.1128/aac.34.6.1271 · 1990 · External reference
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes
10.1186/s40168-021-01002-3 · 2021 · External reference
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
10.1038/srep25373 · 2016 · External reference
10.1016/j.gpb.2015.08.002
10.1016/j.gpb.2015.08.002 · External reference
10.1038/nbt.3423
10.1038/nbt.3423 · External reference
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
10.1093/gigascience/giaa105 · 2020 · External reference
Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater
10.1007/s10646-020-02342-w · 2021 · External reference
Freshwater monitoring by nanopore sequencing
2021 · External reference
Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey
10.1186/s40168-017-0369-0 · 2017 · External reference
10.1016/j.envint.2018.05.040
10.1016/j.envint.2018.05.040 · External reference
10.1038/nbt.2939
10.1038/nbt.2939 · External reference
10.7717/peerj.603
10.7717/peerj.603 · External reference
10.1038/nmeth.3103
10.1038/nmeth.3103 · External reference
Clustering metagenomic sequences with interpolated Markov models
10.1186/1471-2105-11-544 · 2010 · External reference
The binning of metagenomic contigs for microbial physiology of mixed cultures
10.3389/fmicb.2012.00410 · 2012 · External reference
10.7717/peerj.1165
10.7717/peerj.1165 · External reference
10.1093/bioinformatics/btv638
10.1093/bioinformatics/btv638 · External reference
10.1038/sdata.2017.203
10.1038/sdata.2017.203 · External reference
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data
10.1093/bioinformatics/bty830 · 2019 · External reference
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands
10.1099/mgen.0.000436 · 2020 · External reference
10.1038/ismej.2015.124
10.1038/ismej.2015.124 · External reference
10.7717/peerj.415
10.7717/peerj.415 · External reference
10.1186/s40168-017-0387-y
10.1186/s40168-017-0387-y · External reference
Thermodynamics and evolution
10.1006/jtbi.2000.2106 · 2000 · External reference
Natural computing and biological evolution: a new paradigm
2008 · External reference
10.1016/j.cbpa.2013.09.013
10.1016/j.cbpa.2013.09.013 · External reference
Proximate and ultimate causes of the bactericidal action of antibiotics
2020 · External reference
10.1093/acprof:oso/9780199267972.001.0001
10.1093/acprof:oso/9780199267972.001.0001 · 2006 · External reference
Unresolved reference
2014 · External reference
10.1023/a:1025449224520 · 2003 · Admitted local publication
Computing with Membranes
10.1006/jcss.1999.1693 · 2000 · External reference
10.3109/03009734.2014.901444
10.3109/03009734.2014.901444 · External reference
10.1007/978-3-030-00265-7_3
10.1007/978-3-030-00265-7_3 · 2018 · External reference
A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)
10.1186/s13062-015-0070-9 · 2015 · External reference
Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model
10.1128/aac.00593-20 · 2020 · External reference
Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model
10.1128/mbio.02460-18 · 2019 · External reference
10.1111/j.1462-2920.2012.02727.x
10.1111/j.1462-2920.2012.02727.x · External reference
10.1128/aac.00121-14
10.1128/aac.00121-14 · External reference
Role of the Multidrug Resistance Efflux Pump MexCD-OprJ in the Pseudomonas aeruginosa Quorum Sensing Response
10.3389/fmicb.2018.02752 · 2018 · External reference
10.1101/2020.03.10.986737
10.1101/2020.03.10.986737 · External reference
10.1261/rna.057257.116
10.1261/rna.057257.116 · External reference
Interventions on Metabolism: Making Antibiotic-Susceptible Bacteria
10.1128/mbio.01950-17 · 2017 · External reference
10.1371/journal.pone.0210008
10.1371/journal.pone.0210008 · External reference
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
2018 · External reference
10.1016/j.cell.2015.05.019
10.1016/j.cell.2015.05.019 · External reference
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
10.1073/pnas.1523199113 · 2016 · External reference
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
10.1038/msb.2010.115 · 2011 · External reference
10.1371/journal.pone.0147651
10.1371/journal.pone.0147651 · External reference
Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations
10.1038/srep16025 · 2015 · External reference
10.1038/nrg3643
10.1038/nrg3643 · External reference
Metabolomics Study of the Synergistic Killing of Polymyxin B in Combination with Amikacin against Polymyxin-Susceptible and -Resistant Pseudomonas aeruginosa
10.1128/aac.01587-19 · 2019 · External reference
10.1038/nprot.2009.203
10.1038/nprot.2009.203 · External reference
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
10.1038/s41596-019-0254-3 · 2020 · External reference
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
10.1371/journal.pcbi.1002980 · 2013 · External reference
Reconstructing High-Quality Large-Scale Metabolic Models with merlin
10.1007/978-1-4939-7528-0_1 · 2018 · External reference
10.1038/nbt.1672
10.1038/nbt.1672 · External reference
10.1093/bib/bbv079
10.1093/bib/bbv079 · External reference
Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species
10.1371/journal.pcbi.1003465 · 2014 · External reference
10.1093/nar/gky537
10.1093/nar/gky537 · External reference
FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
10.3389/fgene.2019.00633 · 2019 · External reference
Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation
10.1371/journal.pone.0078011 · 2013 · External reference
Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism
10.1371/journal.pcbi.1004452 · 2015 · External reference
Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
10.1038/ncomms14631 · 2017 · External reference
10.1128/jb.00900-10
10.1128/jb.00900-10 · External reference
Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance
2021 · External reference
Metabolic profiles of multidrug resistant and extensively drug resistant Mycobacterium tuberculosis unveiled by metabolomics
10.1016/j.tube.2020.102043 · 2020 · External reference
Inhibition of the ATP Synthase Eliminates the Intrinsic Resistance of Staphylococcus aureus towards Polymyxins
10.1128/mbio.01114-17 · 2017 · External reference
Na(+)-NQR Confers Aminoglycoside Resistance via the Regulation of l-Alanine Metabolism
10.1128/mbio.02086-20 · 2020 · External reference
The depressed P cycle contributes to the acquisition of ampicillin resistance in Edwardsiella piscicida
10.1016/j.jprot.2019.103562 · 2020 · External reference
Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility
10.1128/aac.01608-17 · 2018 · External reference
10.1016/j.celrep.2017.04.002
10.1016/j.celrep.2017.04.002 · External reference
10.1016/j.jprot.2018.05.006
10.1016/j.jprot.2018.05.006 · External reference
Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks
10.1016/j.ymben.2009.05.004 · 2010 · External reference
Advances in flux balance analysis
10.1016/j.copbio.2003.08.001 · 2003 · External reference
10.1128/jb.01123-08
10.1128/jb.01123-08 · External reference
10.1016/j.ymben.2003.09.002
10.1016/j.ymben.2003.09.002 · External reference
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies
10.1529/biophysj.104.043000 · 2004 · External reference
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
10.1186/1752-0509-5-163 · 2011 · External reference
10.1099/mic.0.076091-0
10.1099/mic.0.076091-0 · External reference
10.1016/j.tim.2011.12.004
10.1016/j.tim.2011.12.004 · External reference
Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies
10.1016/j.molcel.2019.04.001 · 2019 · External reference
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
10.1016/j.tibs.2004.10.001 · 2004 · External reference
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
10.1186/1752-0509-1-26 · 2007 · External reference
10.1016/j.pt.2007.06.009
10.1016/j.pt.2007.06.009 · External reference
Host-directed drug targeting of factors hijacked by pathogens
10.1126/scisignal.129re8 · 2008 · External reference
10.1038/nchembio842
10.1038/nchembio842 · External reference
10.1016/s1473-3099(20)30003-7
10.1016/s1473-3099(20)30003-7 · External reference
10.1093/trstmh/trw048
10.1093/trstmh/trw048 · External reference
Mutation-driven evolution of Pseudomonas aeruginosa in the presence of either ceftazidime or ceftazidime/avibactam
10.1128/aac.01379-18 · 2018 · External reference
Involvement of the RND efflux pump transporter SmeH in the acquisition of resistance to ceftazidime in Stenotrophomonas maltophilia
10.1038/s41598-019-41308-9 · 2019 · External reference
Mechanisms and phenotypic consequences of acquisition of tigecycline resistance by Stenotrophomonas maltophilia
10.1093/jac/dkz326 · 2019 · External reference
10.1093/nar/gkv1227
10.1093/nar/gkv1227 · External reference
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
10.1038/s41467-020-16366-7 · 2020 · External reference
Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
10.1038/s41598-021-83081-8 · 2021 · External reference
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog
2021 · External reference
10.1038/nbt.4037
10.1038/nbt.4037 · External reference