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Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9780471729259.mc01e03s19openalex-snapshot

Genome‐Wide Fitness and Genetic Interactions Determined by Tn‐seq, a High‐Throughput Massively Parallel Sequencing Method for Microorganisms

inferredcites →https://doi.org/10.1007/978-1-4613-1161-4openalex-snapshot

The Regulation of Cellular Systems

inferredcites →https://doi.org/10.1016/j.chom.2009.08.003openalex-snapshot

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

inferredcites →https://doi.org/10.1016/j.gde.2005.09.006openalex-snapshot

The microbial pan-genome

inferredcites →https://doi.org/10.1016/s0882-4010(95)90125-6openalex-snapshot

Virulence of Streptococcus pneumoniae in mice: a standardized method for preparation and frozen storage of the experimental bacterial inoculum

inferredcites →https://doi.org/10.1021/cr030112jopenalex-snapshot

RifamycinMode of Action, Resistance, and Biosynthesis

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First Proteomic Study of S-Glutathionylation in Cyanobacteria

inferredcites →https://doi.org/10.1021/pr500859aopenalex-snapshot

First Succinyl-Proteome Profiling of Extensively Drug-Resistant Mycobacterium tuberculosis Revealed Involvement of Succinylation in Cellular Physiology

inferredcites →https://doi.org/10.1038/msb.2013.32openalex-snapshot

Efficient translation initiation dictates codon usage at gene start

inferredcites →https://doi.org/10.1038/nature00935openalex-snapshot

Functional profiling of the Saccharomyces cerevisiae genome

inferredcites →https://doi.org/10.1038/nmeth.1377openalex-snapshot

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

inferredcites →https://doi.org/10.1038/nmeth.3313openalex-snapshot

Simultaneous generation of many RNA-seq libraries in a single reaction

inferredcites →https://doi.org/10.1038/nrg2085openalex-snapshot

Exploring genetic interactions and networks with yeast

inferredcites →https://doi.org/10.1038/nrmicro1901openalex-snapshot

Microbiology in the post-genomic era

inferredcites →https://doi.org/10.1038/nrmicro2298openalex-snapshot

The population genetics of commensal Escherichia coli

inferredcites →https://doi.org/10.1038/nrmicro3033openalex-snapshot

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

inferredcites →https://doi.org/10.1038/srep12620openalex-snapshot

Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine

inferredcites →https://doi.org/10.1039/c3ib40120kopenalex-snapshot

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria

inferredcites →https://doi.org/10.1073/pnas.0906627106openalex-snapshot

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

inferredcites →https://doi.org/10.1073/pnas.1201031109openalex-snapshot

Inhibitor of streptokinase gene expression improves survival after group A streptococcus infection in mice

inferredcites →https://doi.org/10.1074/jbc.m111.304311openalex-snapshot

Characterization of Central Carbon Metabolism of Streptococcus pneumoniae by Isotopologue Profiling

inferredcites →https://doi.org/10.1093/nar/gkr988openalex-snapshot

KEGG for integration and interpretation of large-scale molecular data sets

inferredcites →https://doi.org/10.1093/nar/gku126openalex-snapshot

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

inferredcites →https://doi.org/10.1099/mic.0.055467-0openalex-snapshot

Genome-wide transcriptional profiling of the cell envelope stress response and the role of LisRK and CesRK in Listeria monocytogenes

inferredcites →https://doi.org/10.1101/cshperspect.a010215openalex-snapshot

The Pneumococcus: Epidemiology, Microbiology, and Pathogenesis

inferredcites →https://doi.org/10.1101/gr.097097.109openalex-snapshot

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

inferredcites →https://doi.org/10.1101/gr.137430.112openalex-snapshot

A fine scale phenotype–genotype virulence map of a bacterial pathogen

inferredcites →https://doi.org/10.1111/j.1420-9101.2005.00921.xopenalex-snapshot

The biological limitations of transcriptomics in elucidating stress and stress responses

inferredcites →https://doi.org/10.1111/j.1574-6976.2011.00302.xopenalex-snapshot

Pathogenesis in tuberculosis: transcriptomic approaches to unraveling virulence mechanisms and finding new drug targets

inferredcites →https://doi.org/10.1126/science.1059581openalex-snapshot

Loss of Huntingtin-Mediated BDNF Gene Transcription in Huntington's Disease

inferredcites →https://doi.org/10.1128/aac.01617-06openalex-snapshot

Quinolone-Mediated Bacterial Death

inferredcites →https://doi.org/10.1128/cmr.16.3.430-450.2003openalex-snapshot

Versatility of Aminoglycosides and Prospects for Their Future

inferredcites →https://doi.org/10.1128/ec.5.4.638-649.2006openalex-snapshot

Conserved Fungal Genes as Potential Targets for Broad-Spectrum Antifungal Drug Discovery

inferredcites →https://doi.org/10.1128/jb.01148-06openalex-snapshot

Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6

inferredcites →https://doi.org/10.1128/jb.187.24.8340-8349.2005openalex-snapshot

Catabolite Control Protein A (CcpA) Contributes to Virulence and Regulation of Sugar Metabolism in Streptococcus pneumoniae

inferredcites →https://doi.org/10.1128/jcm.36.12.3514-3519.1998openalex-snapshot

Identification of Three Major Clones of Multiply Antibiotic-Resistant Streptococcus pneumoniae in Taiwanese Hospitals by Multilocus Sequence Typing

inferredcites →https://doi.org/10.1128/jcm.39.7.2565-2571.2001openalex-snapshot

Nomenclature of Major Antimicrobial-Resistant Clones of Streptococcus pneumoniae Defined by the Pneumococcal Molecular Epidemiology Network

inferredcites →https://doi.org/10.1128/jvi.02547-05openalex-snapshot

Effects of Random Mutations in the Human Immunodeficiency Virus Type 1 Transcriptional Promoter on Viral Fitness in Different Host Cell Environments

inferredcites →https://doi.org/10.1128/mbio.00950-16openalex-snapshot

Multidrug Intrinsic Resistance Factors in Staphylococcus aureus Identified by Profiling Fitness within High-Diversity Transposon Libraries

inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.114751openalex-snapshot

Systematic Mapping of Genetic Interaction Networks

inferredcites →https://doi.org/10.1146/annurev.mi.33.100179.000553openalex-snapshot

The Mechanism of the Irreversible Antimicrobial Effects of Penicillins: How the Beta-Lactam Antibiotics Kill and Lyse Bacteria

inferredcites →https://doi.org/10.1186/1471-2105-8-212openalex-snapshot

Optimization based automated curation of metabolic reconstructions

inferredcites →https://doi.org/10.1186/1471-2164-13-734openalex-snapshot

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

inferredcites →https://doi.org/10.1186/1476-4598-8-34openalex-snapshot

Discovery of gene expression-based pharmacodynamic biomarker for a p53 context-specific anti-tumor drug Wee1 inhibitor

inferredcites →https://doi.org/10.1186/1752-0509-6-5openalex-snapshot

Identifying co-targets to fight drug resistance based on a random walk model

inferredcites →https://doi.org/10.1186/1752-0509-8-68openalex-snapshot

Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1371/journal.pcbi.1002085openalex-snapshot

Robust Network Topologies for Generating Switch-Like Cellular Responses

inferredcites →https://doi.org/10.1371/journal.pgen.1004518openalex-snapshot

Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection

inferredcites →https://doi.org/10.1371/journal.pone.0054717openalex-snapshot

Global Transcriptional Profiling of Longitudinal Clinical Isolates of Mycobacterium tuberculosis Exhibiting Rapid Accumulation of Drug Resistance

inferredcites →https://doi.org/10.1371/journal.pone.0057370openalex-snapshot

Downregulation of yidC in Escherichia coli by Antisense RNA Expression Results in Sensitization to Antibacterial Essential Oils Eugenol and Carvacrol

inferredcites →https://doi.org/10.1371/journal.pone.0079475openalex-snapshot

The Transcriptional Landscape of Campylobacter jejuni under Iron Replete and Iron Limited Growth Conditions

inferredcites →https://doi.org/10.1371/journal.ppat.1005869openalex-snapshot

Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome

inferredcites →https://doi.org/10.3389/fmicb.2015.00001openalex-snapshot

One Juliet and four Romeos: VeA and its methyltransferases

inferredcites →https://doi.org/10.3390/metabo5020291openalex-snapshot

Computational Metabolomics Operations at BioCyc.org

inferredcites →https://doi.org/10.5860/choice.34-6252openalex-snapshot

Understanding the control of metabolism

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bioinformatics/btx320openalex-snapshot

MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization

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