Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence

Systematic review and meta-analysis of mortality of patients infected with carbapenem-resistant Klebsiella pneumoniae

(2017) Liangfei Xu et al.   Annals of Clinical Microbiology and Antimicrobials

Weighted mutual information analysis substantially improves domain-based functional network models

(2016) Jung Eun Shim et al.   BIOINFORMATICS

Spectrum of excess mortality due to carbapenem-resistant Klebsiella pneumoniae infections

(2016) C. Hauck et al.   CLINICAL MICROBIOLOGY AND INFECTION

Temporal flux in β-lactam resistance among Klebsiella pneumoniae in Western Australia

(2016) Jarrad M. Hall et al.   JOURNAL OF MEDICAL MICROBIOLOGY

COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

(2016) Sunmo Yang et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Coupling the CRISPR/Cas9 System with Lambda Red Recombineering Enables Simplified Chromosomal Gene Replacement in Escherichia coli

(2015) Michael E. Pyne et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ribosomal RNA methyltransferases contribute toStaphylococcus aureusvirulence

(2015) Tatsuhiko Kyuma et al.   FEBS Journal

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

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Genome-Wide Identification of Klebsiella pneumoniae Fitness Genes during Lung Infection

(2015) Michael A. Bachman et al.   mBio

EcoliNet: a database of cofunctional gene network for Escherichia coli

(2015) Hanhae Kim et al.   Database-The Journal of Biological Databases and Curation

Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans

(2015) Hanhae Kim et al.   Scientific Reports

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

(2015) Junha Shin et al.   PLoS One

Genomic and Transcriptomic Analyses of Colistin-Resistant Clinical Isolates of Klebsiella pneumoniae Reveal Multiple Pathways of Resistance

(2014) Meredith S. Wright et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

(2014) Jeffrey E Barrick et al.   BMC GENOMICS

Molecular mechanisms of β-lactam resistance in carbapenemase-producing Klebsiella pneumoniae from Sri Lanka

(2014) Jarrad M. Hall et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction

(2013) Junha Shin et al.   Molecular BioSystems

YeastNet v3: a public database of data-specific and integrated functional gene networks forSaccharomyces cerevisiae

(2013) Hanhae Kim et al.   NUCLEIC ACIDS RESEARCH

JiffyNet: a web-based instant protein network modeler for newly sequenced species

(2013) Eiru Kim et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Adaptive and Mutational Resistance: Role of Porins and Efflux Pumps in Drug Resistance

(2012) L. Fernandez et al.   CLINICAL MICROBIOLOGY REVIEWS

Porin alterations present in non-carbapenemase-producing Enterobacteriaceae with high and intermediate levels of carbapenem resistance in Chile

(2012) A. Wozniak et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Contribution of Resistance-Nodulation-Division Efflux Pump OperonsmeU1-V-W-U2-Xto Multidrug Resistance of Stenotrophomonas maltophilia

(2011) Chao-Hsien Chen et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Klebsiella pneumoniaeOuter Membrane Porins OmpK35 and OmpK36 Play Roles in both Antimicrobial Resistance and Virulence

(2011) Yu-Kuo Tsai et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Carbapenems: Past, Present, and Future

(2011) Krisztina M. Papp-Wallace et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Antibiotic resistance and its cost: is it possible to reverse resistance?

(2010) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Outer membrane permeability and antibiotic resistance

(2008) Anne H. Delcour   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS