Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq

Dormancy Is Not Necessary or Sufficient for Bacterial Persistence

(2013) Mehmet A. Orman et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A problem of persistence: still more questions than answers?

(2013) Nathalie Q. Balaban et al.   NATURE REVIEWS MICROBIOLOGY

Detection of viable but non-culturable staphylococci in biofilms from central venous catheters negative on standard microbiological assays

(2012) G. Zandri et al.   CLINICAL MICROBIOLOGY AND INFECTION

Characterization of a mazEF Toxin-Antitoxin Homologue from Staphylococcus equorum

(2012) C. F. Schuster et al.   JOURNAL OF BACTERIOLOGY

Heterogeneity in Pseudomonas aeruginosa Biofilms Includes Expression of Ribosome Hibernation Factors in the Antibiotic-Tolerant Subpopulation and Hypoxia-Induced Stress Response in the Metabolically Active Population

(2012) K. S. Williamson et al.   JOURNAL OF BACTERIOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

New-found fundamentals of bacterial persistence

(2012) Cyrielle I. Kint et al.   TRENDS IN MICROBIOLOGY

Superoxide Dismutases Are Involved in Candida albicans Biofilm Persistence against Miconazole

(2011) Anna Bink et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

SYBR green as a fluorescent probe to evaluate the biofilm physiological state of Staphylococcus epidermidis, using flow cytometry

(2011) Filipe Cerca et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Heterogeneous bacterial persisters and engineering approaches to eliminate them

(2011) Kyle R Allison et al.   CURRENT OPINION IN MICROBIOLOGY

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Evidence for persisters in Staphylococcus epidermidis RP62a planktonic cultures and biofilms

(2011) J. A. Shapiro et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Staphylococcus epidermidis biofilms with higher proportions of dormant bacteria induce a lower activation of murine macrophages

(2011) F. Cerca et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies

(2011) M. Fauvart et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Viable but non-culturable (VBNC) bacteria: Gene expression in planktonic and biofilm cells

(2011) J.T. Trevors   JOURNAL OF MICROBIOLOGICAL METHODS

Modulation of poly-N-acetylglucosamine accumulation within mature Staphylococcus epidermidis biofilms grown in excess glucose

(2011) Filipe Cerca et al.   MICROBIOLOGY AND IMMUNOLOGY

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Metabolite-enabled eradication of bacterial persisters by aminoglycosides

(2011) Kyle R. Allison et al.   NATURE

Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response

(2011) Matej Butala et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Protocol Dependence of Sequencing-Based Gene Expression Measurements

(2011) Tal Raz et al.   PLoS One

Molecular basis of Staphylococcus epidermidis infections

(2011) Michael Otto   Seminars in Immunopathology

Characterization and Transcriptome Analysis of Mycobacterium tuberculosis Persisters

(2011) I. Keren et al.   mBio

Persister Cells

(2010) Kim Lewis   Annual Review of Microbiology

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Exit from dormancy in microbial organisms

(2010) Jonathan Dworkin et al.   NATURE REVIEWS MICROBIOLOGY

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

Bacterial persistence: some new insights into an old phenomenon

(2009) R. Jayaraman   JOURNAL OF BIOSCIENCES

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

Characterization and virulence retention of viable but nonculturable Vibrio harveyi

(2008) Fengrong Sun et al.   FEMS MICROBIOLOGY ECOLOGY

Tolerance of dormant and active cells in Pseudomonas aeruginosa PA01 biofilm to antimicrobial agents

(2008) Jaeeun Kim et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY