Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs

Resource allocation and metabolism: the search for governing principles

(2018) Markus Basan   CURRENT OPINION IN MICROBIOLOGY

Rapid Growth of Uropathogenic Escherichia coli during Human Urinary Tract Infection

(2018) Valerie S. Forsyth et al.   mBio

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

(2018) Philip Burnham et al.   Nature Communications

Nonantibiotic prevention and management of recurrent urinary tract infection

(2018) Néha Sihra et al.   Nature Reviews Urology

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections

(2017) Henry L. Schreiber et al.   Science Translational Medicine

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Urinary tract infections: epidemiology, mechanisms of infection and treatment options

(2015) Ana L. Flores-Mireles et al.   NATURE REVIEWS MICROBIOLOGY

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Human Urine Decreases Function and Expression of Type 1 Pili in Uropathogenic Escherichia coli

(2015) Sarah E. Greene et al.   mBio

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Host-specific induction ofEscherichia colifitness genes during human urinary tract infection

(2014) Sargurunathan Subashchandrabose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Vivo mRNA Profiling of Uropathogenic Escherichia coli from Diverse Phylogroups Reveals Common and Group-Specific Gene Expression Profiles

(2014) P. Bielecki et al.   mBio

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distribution of uropathogenic virulence genes in Escherichia coli isolated from patients with urinary tract infection

(2013) Mouna Tarchouna et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The ClermontEscherichia coliphylo-typing method revisited: improvement of specificity and detection of new phylo-groups

(2012) Olivier Clermont et al.   Environmental Microbiology Reports

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Bacterial growth laws and their applications

(2011) Matthew Scott et al.   CURRENT OPINION IN BIOTECHNOLOGY

What defines extraintestinal pathogenic Escherichia coli?

(2011) Christian-Daniel Köhler et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The epidemiology of urinary tract infection

(2010) Betsy Foxman   Nature Reviews Urology

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Escherichia coli Global Gene Expression in Urine from Women with Urinary Tract Infection

(2010) Erin C. Hagan et al.   PLoS Pathogens

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Waging War against Uropathogenic Escherichia coli: Winning Back the Urinary Tract

(2009) K. E. Sivick et al.   INFECTION AND IMMUNITY

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

Fitness of Escherichia coli during Urinary Tract Infection Requires Gluconeogenesis and the TCA Cycle

(2009) Christopher J. Alteri et al.   PLoS Pathogens