Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion

(2021) Jordan Vacheron et al.   Communications Biology

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Next-generation physiology approaches to study microbiome function at single cell level

(2020) Roland Hatzenpichler et al.   NATURE REVIEWS MICROBIOLOGY

Role of PstS on the pathogenesis of Acinetobacter baumannii under microaerobiosis and normoxia

(2020) María Luisa Gil-Marqués et al.   JOURNAL OF INFECTIOUS DISEASES

Metabolic Heterogeneity and Cross-Feeding in Bacterial Multicellular Systems

(2020) Christopher R. Evans et al.   TRENDS IN MICROBIOLOGY

Spatial Ecology of the Human Tongue Dorsum Microbiome

(2020) Steven A. Wilbert et al.   Cell Reports

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

(2020) Sydney B. Blattman et al.   Nature Microbiology

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

(2020) Fabian Imdahl et al.   Nature Microbiology

Highly multiplexed spatial mapping of microbial communities

(2020) Hao Shi et al.   NATURE

Metabolic Microenvironments Drive Microbial Differentiation and Antibiotic Resistance

(2020) Tatyana L. Povolotsky et al.   TRENDS IN GENETICS

Structural and Functional Characterization of the Type Three Secretion System (T3SS) Needle of Pseudomonas aeruginosa

(2019) Charlotte Lombardi et al.   Frontiers in Microbiology

Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae

(2019) Britta E. Rued et al.   mBio

Bacteria and archaea on Earth and their abundance in biofilms

(2019) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface

(2019) Sankalp Malhotra et al.   CLINICAL MICROBIOLOGY REVIEWS

Heterogeneity in surface sensing suggests a division of labor in Pseudomonas aeruginosa populations

(2019) Catherine R Armbruster et al.   eLife

Transcriptional regulation of central carbon metabolism in Pseudomonas aeruginosa

(2019) Stephen K. Dolan et al.   Microbial Biotechnology

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

NanoSIMS imaging reveals metabolic stratification within current-producing biofilms

(2019) Grayson L. Chadwick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental drivers of metabolic heterogeneity in clonal microbial populations

(2019) Frank Schreiber et al.   CURRENT OPINION IN BIOTECHNOLOGY

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Gluconeogenic precursor availability regulates flux through the glyoxylate shunt in Pseudomonas aeruginosa

(2018) Audrey Crousilles et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion

(2018) Federico Bocci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic interactions between dynamic bacterial subpopulations

(2018) Adam Z Rosenthal et al.   eLife

The Glyoxylate Shunt, 60 Years On

(2018) Stephen K. Dolan et al.   Annual Review of Microbiology

Metabolism in dense microbial colonies: 13C metabolic flux analysis of E. coli grown on agar identifies two distinct cell populations with acetate cross-feeding

(2018) Eric Wolfsberg et al.   METABOLIC ENGINEERING

CdrA Interactions within the Pseudomonas aeruginosa Biofilm Matrix Safeguard It from Proteolysis and Promote Cellular Packing

(2018) Courtney Reichhardt et al.   mBio

A Surface-Induced Asymmetric Program Promotes Tissue Colonization by Pseudomonas aeruginosa

(2018) Benoît-Joseph Laventie et al.   Cell Host & Microbe

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa

(2017) David W. Basta et al.   mBio

Identification of a neural crest stem cell niche by Spatial Genomic Analysis

(2017) Antti Lignell et al.   Nature Communications

An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence

(2017) Jeanyoung Jo et al.   eLife

Microbial interactions and community assembly at microscales

(2016) Otto X Cordero et al.   CURRENT OPINION IN MICROBIOLOGY

SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells

(2016) Stella Stylianidou et al.   MOLECULAR MICROBIOLOGY

Spatial structure, cooperation and competition in biofilms

(2016) Carey D. Nadell et al.   NATURE REVIEWS MICROBIOLOGY

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling

(2016) William H. DePas et al.   mBio

Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms

(2016) Lynne Turnbull et al.   Nature Communications

Cystic fibrosis lung environment and Pseudomonas aeruginosa infection

(2016) Anjali Y. Bhagirath et al.   BMC Pulmonary Medicine

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

(2016) Frank Schreiber et al.   Nature Microbiology

Heavy water and15N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats

(2015) Sebastian H. Kopf et al.   ENVIRONMENTAL MICROBIOLOGY

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

(2015) Evert Bosdriesz et al.   FEBS Journal

Origin and Impact of Nitric Oxide in Pseudomonas aeruginosa Biofilms

(2015) Francesca Cutruzzolà et al.   JOURNAL OF BACTERIOLOGY

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

The Tailocin Tale: Peeling off Phage Tails

(2015) Maarten G.K. Ghequire et al.   TRENDS IN MICROBIOLOGY

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation

(2015) Elise S. Cowley et al.   mBio

Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk

(2015) Sebastian Schulz et al.   PLoS Pathogens

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

(2014) Harry M. T. Choi et al.   ACS Nano

Phenotypic bistability in Escherichia coli's central carbon metabolism

(2014) O. Kotte et al.   Molecular Systems Biology

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Catalase (KatA) Plays a Role in Protection against Anaerobic Nitric Oxide in Pseudomonas aeruginosa

(2014) Shengchang Su et al.   PLoS One

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biofilms, flagella, and mechanosensing of surfaces by bacteria

(2014) Robert Belas   TRENDS IN MICROBIOLOGY

Oxygen Limitation within a Bacterial Aggregate

(2014) A. K. Wessel et al.   mBio

The hierarchy quorum sensing network in Pseudomonas aeruginosa

(2014) Jasmine Lee et al.   Protein & Cell

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Bacterial Community Morphogenesis Is Intimately Linked to the Intracellular Redox State

(2013) L. E. P. Dietrich et al.   JOURNAL OF BACTERIOLOGY

Stabilization of cooperative virulence by the expression of an avirulent phenotype

(2013) Médéric Diard et al.   NATURE

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

(2013) Samuel O Skinner et al.   Nature Protocols

The Extra-Cytoplasmic Function Sigma Factor SigX Modulates Biofilm and Virulence-Related Properties in Pseudomonas aeruginosa

(2013) Gwendoline Gicquel et al.   PLoS One

Chromosomal Organization and Segregation in Pseudomonas aeruginosa

(2013) Isabelle Vallet-Gely et al.   PLoS Genetics

Pseudomonas aeruginosaTwitching Motility: Type IV Pili in Action

(2012) Lori L. Burrows   Annual Review of Microbiology

Combined treatment ofPseudomonas aeruginosabiofilms with bacteriophages and chlorine

(2012) Yanyan Zhang et al.   BIOTECHNOLOGY AND BIOENGINEERING

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

(2012) Omri Wurtzel et al.   PLoS Pathogens

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

The clinical impact of bacterial biofilms

(2011) Niels Høiby et al.   International Journal of Oral Science

Regulation and Function of Versatile Aerobic and Anaerobic Respiratory Metabolism in Pseudomonas aeruginosa

(2011) Hiroyuki Arai   Frontiers in Microbiology

Pseudomonas aeruginosauses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix

(2010) Bradley R. Borlee et al.   MOLECULAR MICROBIOLOGY

Compensatory periplasmic nitrate reductase activity supports anaerobic growth of Pseudomonas aeruginosa PAO1 in the absence of membrane nitrate reductase

(2009) Nadine E. Van Alst et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Differential expression of multiple terminal oxidases for aerobic respiration inPseudomonas aeruginosa

(2009) Takuro Kawakami et al.   ENVIRONMENTAL MICROBIOLOGY

The type III secretion system of Pseudomonas aeruginosa: infection by injection

(2009) Alan R. Hauser   NATURE REVIEWS MICROBIOLOGY

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas aeruginosabiofilms in the respiratory tract of cystic fibrosis patients

(2009) Thomas Bjarnsholt et al.   PEDIATRIC PULMONOLOGY

Bistability, Epigenetics, and Bet-Hedging in Bacteria

(2008) Jan-Willem Veening et al.   Annual Review of Microbiology

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Physiological heterogeneity in biofilms

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

Structure–Function Aspects of PstS in Multi-Drug–Resistant Pseudomonas aeruginosa

(2008) Olga Zaborina et al.   PLoS Pathogens