The co-transcriptome of uropathogenicEscherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions

Peroxisome Proliferator-Activated Receptor-  Regulates the Expression of Alveolar Macrophage Macrophage Colony-Stimulating Factor

(2014) T. L. Bonfield et al.   JOURNAL OF IMMUNOLOGY

Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations

(2014) D. Willner et al.   mBio

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

(2013) Carlo Vittorio Cannistraci et al.   BIOINFORMATICS

Uropathogenic Escherichia coli virulence and innate immune responses during urinary tract infection

(2013) Glen C Ulett et al.   CURRENT OPINION IN MICROBIOLOGY

Changes in Psp protein binding partners, localization and behaviour upon activation of theYersinia enterocoliticaphage shock protein response

(2013) Saori Yamaguchi et al.   MOLECULAR MICROBIOLOGY

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

(2013) James A. Imlay   NATURE REVIEWS MICROBIOLOGY

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

(2013) Michael S. Humphrys et al.   PLoS One

Cyclosporine A Impairs Nucleotide Binding Oligomerization Domain (Nod1)-Mediated Innate Antibacterial Renal Defenses in Mice and Human Transplant Recipients

(2013) Emilie Tourneur et al.   PLoS Pathogens

Stress Relief during Host Infection: The Phage Shock Protein Response Supports Bacterial Virulence in Various Ways

(2013) Andrew J. Darwin   PLoS Pathogens

Deep sequencing-based transcriptome profiling analysis of Oryzias melastigma exposed to PFOS

(2012) Qiansheng Huang et al.   AQUATIC TOXICOLOGY

Uropathogenic Escherichia coli Mediated Urinary Tract Infection

(2012) Makrina Totsika et al.   CURRENT DRUG TARGETS

Genome-Wide Mapping of Cystitis Due to Streptococcus agalactiae and Escherichia coli in Mice Identifies a Unique Bladder Transcriptome That Signifies Pathogen-Specific Antimicrobial Defense against Urinary Tract Infection

(2012) Chee K. Tan et al.   INFECTION AND IMMUNITY

YbcL of Uropathogenic Escherichia coli Suppresses Transepithelial Neutrophil Migration

(2012) Megan E. Lau et al.   INFECTION AND IMMUNITY

Recent findings about the Yersinia enterocolitica phage shock protein response

(2012) Saori Yamaguchi et al.   JOURNAL OF MICROBIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection

(2012) Qinghua Nie et al.   PLoS One

Extracellular histones promote thrombin generation through platelet-dependent mechanisms: involvement of platelet TLR2 and TLR4

(2011) F. Semeraro et al.   BLOOD

Role of c-MYC in alternative activation of human macrophages and tumor-associated macrophage biology

(2011) O. M. Pello et al.   BLOOD

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

(2011) Franc Llorens et al.   BMC GENOMICS

Urinary tract infections in women

(2011) Stefano Salvatore et al.   European Journal of Obstetrics & Gynecology and Reproductive Biology

Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages

(2011) Nilesh J. Bokil et al.   IMMUNOBIOLOGY

Molecular Characterization of UpaB and UpaC, Two New Autotransporter Proteins of Uropathogenic Escherichia coli CFT073

(2011) Luke P. Allsopp et al.   INFECTION AND IMMUNITY

Innate Transcriptional Networks Activated in Bladder in Response to Uropathogenic Escherichia coli Drive Diverse Biological Pathways and Rapid Synthesis of IL-10 for Defense against Bacterial Urinary Tract Infection

(2011) B. L. Duell et al.   JOURNAL OF IMMUNOLOGY

Extracellular Histones Are Mediators of Death through TLR2 and TLR4 in Mouse Fatal Liver Injury

(2011) J. Xu et al.   JOURNAL OF IMMUNOLOGY

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Deep-Sequencing Analysis of the Mouse Transcriptome Response to Infection with Brucella melitensis Strains of Differing Virulence

(2011) Fangkun Wang et al.   PLoS One

Identification of citrullinated histone H3 as a potential serum protein biomarker in a lethal model of lipopolysaccharide-induced shock

(2011) Yongqing Li et al.   SURGERY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Intracellular Lifestyles and Immune Evasion Strategies of UropathogenicEscherichia coli

(2010) David A. Hunstad et al.   Annual Review of Microbiology

Anti-apoptosis and cell survival: A review

(2010) Liam Portt et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes

(2010) Carlo Vittorio Cannistraci et al.   BIOINFORMATICS

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

(2010) Li-xin Xiang et al.   BMC GENOMICS

Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

(2010) Anita Ordas et al.   FISH & SHELLFISH IMMUNOLOGY

UpaH Is a Newly Identified Autotransporter Protein That Contributes to Biofilm Formation and Bladder Colonization by Uropathogenic Escherichia coli CFT073

(2010) L. P. Allsopp et al.   INFECTION AND IMMUNITY

The phage shock protein PspA facilitates divalent metal transport and is required for virulence of Salmonella enterica sv. Typhimurium

(2010) Joyce E. Karlinsey et al.   MOLECULAR MICROBIOLOGY

The epidemiology of urinary tract infection

(2010) Betsy Foxman   Nature Reviews Urology

Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing

(2010) Shuqi Xiao et al.   PLoS One

Host Imprints on Bacterial Genomes—Rapid, Divergent Evolution in Individual Patients

(2010) Jaroslaw Zdziarski et al.   PLoS Pathogens

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

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

Pathogen Recognition and Inflammatory Signaling in Innate Immune Defenses

(2009) T. H. Mogensen   CLINICAL MICROBIOLOGY REVIEWS

Conditioning of Uropathogenic Escherichia coli for Enhanced Colonization of Host

(2009) J. M. Bower et al.   INFECTION AND IMMUNITY

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

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

Induction of Salmonella pathogenicity island 1 under different growth conditions can affect Salmonella-host cell interactions in vitro

(2009) J. A. Ibarra et al.   MICROBIOLOGY-SGM

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

(2009) Zoltán Hegedűs et al.   MOLECULAR IMMUNOLOGY

Extracellular histones are major mediators of death in sepsis

(2009) Jun Xu et al.   NATURE MEDICINE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Antimicrobial mechanisms of phagocytes and bacterial evasion strategies

(2009) Ronald S. Flannagan et al.   NATURE REVIEWS MICROBIOLOGY

Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability

(2009) D. Jager et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G-CSF induction early in uropathogenicEscherichia coliinfection of the urinary tract modulates host immunity

(2008) Molly A. Ingersoll et al.   CELLULAR MICROBIOLOGY

UropathogenicEscherichia coliAL511 requires flagellum to enter renal collecting duct cells

(2008) Christophe Pichon et al.   CELLULAR MICROBIOLOGY

Origins and virulence mechanisms of uropathogenic Escherichia coli

(2008) Travis J. Wiles et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Virulence properties of asymptomatic bacteriuria Escherichia coli

(2008) A MABBETT et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH