A Bayesian non-parametric mixed-effects model of microbial growth curves

Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth

(2019) Francesca M. L. Bushell et al.   Frontiers in Microbiology

Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains

(2017) Jenny L. Draper et al.   mBio

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

(2017) Byoung-Mo Koo et al.   Cell Systems

Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis

(2017) Cynthia L. Darnell et al.   mSystems

Quantifying Variability in Growth and Thermal Inactivation Kinetics of Lactobacillus plantarum

(2016) D. C. Aryani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

Detecting differential growth of microbial populations with Gaussian process regression

(2016) Peter D. Tonner et al.   GENOME RESEARCH

Estimating Variance Components in Functional Linear Models With Applications to Genetic Heritability

(2016) Matthew Reimherr et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A note on statistical repeatability and study design for high-throughput assays

(2016) George Nicholson et al.   STATISTICS IN MEDICINE

Inter-laboratory evolution of a model organism and its epistatic effects on mutagenesis screens

(2016) Michael D. Bradley et al.   Scientific Reports

High-throughput bacterial functional genomics in the sequencing era

(2015) Andrew N Gray et al.   CURRENT OPINION IN MICROBIOLOGY

Quantifying strain variability in modeling growth of Listeria monocytogenes

(2015) D.C. Aryani et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Bayesian hierarchical modelling for inferring genetic interactions in yeast

(2015) Jonathan Heydari et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

Systems biology approaches to defining transcription regulatory networks in halophilic archaea

(2015) Cynthia L. Darnell et al.   METHODS

A Regulatory Hierarchy Controls the Dynamic Transcriptional Response to Extreme Oxidative Stress in Archaea

(2015) Peter D. Tonner et al.   PLoS Genetics

Microbial growth and physiology: a call for better craftsmanship

(2015) Thomas Egli   Frontiers in Microbiology

The Antibacterial Activity of Acetic Acid against Biofilm-Producing Pathogens of Relevance to Burns Patients

(2015) Fenella D. Halstead et al.   PLoS One

Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

(2014) Karlyn D. Beer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A system-level model for the microbial regulatory genome

(2014) A. N. Brooks et al.   Molecular Systems Biology

Strain variability of the behavior of foodborne bacterial pathogens: A review

(2013) Alexandra Lianou et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Engineering improved ethanol production in Escherichia coli with a genome-wide approach

(2013) Lauren B.A. Woodruff et al.   METABOLIC ENGINEERING

The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium

(2013) James A. Imlay   NATURE REVIEWS MICROBIOLOGY

Role of Oxidative Stress in Persister Tolerance

(2012) Yanxia Wu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon

(2012) Kriti Sharma et al.   BMC GENOMICS

The Arrhenius Equation Revisited

(2012) Micha Peleg et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Variation of cardinal growth parameters and growth limits according to phylogenetic affiliation in the Bacillus cereus Group. Consequences for risk assessment

(2012) Frédéric Carlin et al.   FOOD MICROBIOLOGY

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

(2012) B. Ryall et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Microbial Growth Curves: What the Models Tell Us and What They Cannot

(2011) Micha Peleg et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Modeling of Clostridium perfringens vegetative cell inactivation in beef-in-sauce products: A meta-analysis using mixed linear models

(2011) S. Jaloustre et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness

(2011) Anna Zakrzewska et al.   MOLECULAR BIOLOGY OF THE CELL

Supervised normalization of microarrays

(2010) Brigham H. Mecham et al.   BIOINFORMATICS

A random effect multiplicative heteroscedastic model for bacterial growth

(2010) Ricardo Cao et al.   BMC BIOINFORMATICS

Hierarchical Bayesian Modelling for Saccharomyces cerevisiae population dynamics

(2010) Aymé Spor et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Coordination of frontline defense mechanisms under severe oxidative stress

(2010) Amardeep Kaur et al.   Molecular Systems Biology

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

(2010) Anastasia Baryshnikova et al.   NATURE METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Effects of temperature, pH and sugar concentration on the growth parameters of Saccharomyces cerevisiae, S. kudriavzevii and their interspecific hybrid

(2009) F. Noé Arroyo-López et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Quantifying the heterogeneous heat response ofEscherichia coliunder dynamic temperatures

(2009) E. Van Derlinden et al.   JOURNAL OF APPLIED MICROBIOLOGY