Reverse vaccinology in the 21st century: improvements over the original design

Structural Insight into the Mechanism of DNA-Binding Attenuation of the Neisserial Adhesin Repressor NadR by the Small Natural Ligand 4-Hydroxyphenylacetic Acid

(2012) Sébastien Brier et al.   BIOCHEMISTRY

Literature mining of host–pathogen interactions: comparing feature-based supervised learning and language-based approaches

(2012) Thanh Thieu et al.   BIOINFORMATICS

Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation

(2012) Teerasak E-komon et al.   BMC BIOINFORMATICS

Multi High-Throughput Approach for Highly Selective Identification of Vaccine Candidates: the Group A Streptococcus Case

(2012) Giuliano Bensi et al.   MOLECULAR & CELLULAR PROTEOMICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

Immune epitope database analysis resource

(2012) Y. Kim et al.   NUCLEIC ACIDS RESEARCH

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

(2011) Charles Ansong et al.   BMC GENOMICS

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Population genetics and evolution of the pan-genome of Streptococcus pneumoniae

(2011) Alessandro Muzzi et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

(2011) Wei Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

(2011) R. R. Chaudhuri et al.   MICROBIOLOGY-SGM

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Single-cell genomics

(2011) Tomer Kalisky et al.   NATURE METHODS

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

The Streptococcus pneumoniae Pilus-1 Displays a Biphasic Expression Pattern

(2011) Gabriella De Angelis et al.   PLoS One

Investigating pathogen biology at the level of the proteome

(2011) Phillip Cash   PROTEOMICS

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

A comprehensive analysis of Bordetella pertussis surface proteome and identification of new immunogenic proteins

(2011) Burcu E. Tefon et al.   VACCINE

In Vivo Expression of Salmonella enterica Serotype Typhi Genes in the Blood of Patients with Typhoid Fever in Bangladesh

(2011) Alaullah Sheikh et al.   PLoS Neglected Tropical Diseases

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival

(2011) Hebert Echenique-Rivera et al.   PLoS Pathogens

The Cost of Virulence: Retarded Growth of Salmonella Typhimurium Cells Expressing Type III Secretion System 1

(2011) Alexander Sturm et al.   PLoS Pathogens

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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Bacillus anthracis genome organization in light of whole transcriptome sequencing

(2010) Jeffrey Martin et al.   BMC BIOINFORMATICS

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

(2010) David Goudenege et al.   BMC MICROBIOLOGY

Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods

(2010) Ulrike Mäder et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bacterial proteomics and identification of potential vaccine targets

(2010) Matthew S Walters et al.   Expert Review of Proteomics

Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies

(2010) Lihua Cheng et al.   GYNECOLOGIC ONCOLOGY

Reverse Vaccinology: Developing Vaccines in the Era of Genomics

(2010) Alessandro Sette et al.   IMMUNITY

Characterization of Diverse Subvariants of the Meningococcal Factor H (fH) Binding Protein for Their Ability To Bind fH, To Mediate Serum Resistance, and To Induce Bactericidal Antibodies

(2010) Kate L. Seib et al.   INFECTION AND IMMUNITY

Genome-based approaches to vaccine development

(2010) Marirosa Mora et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea

(2010) N. Y. Yu et al.   NUCLEIC ACIDS RESEARCH

By-passing in vitro screening—next generation sequencing technologies applied to antibody display and in silico candidate selection

(2010) U. Ravn et al.   NUCLEIC ACIDS RESEARCH

Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

(2010) Matt J. Cahill et al.   PLoS One

Qualitative and quantitative assessment of meningococcal antigens to evaluate the potential strain coverage of protein-based vaccines

(2010) J. Donnelly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

(2010) A. Git et al.   RNA

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Comparing microarrays and next-generation sequencing technologies for microbial ecology research

(2010) Seong Woon Roh et al.   TRENDS IN BIOTECHNOLOGY

Next-generation sequencing technologies for DNA methylation analyses in cancer genomics

(2010) Stefan T Boerno et al.   Epigenomics

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Variation of the factor H-binding protein of Neisseria meningitidis

(2009) C. Brehony et al.   MICROBIOLOGY-SGM

Surfome Analysis as a Fast Track to Vaccine Discovery

(2009) Francesco Doro et al.   MOLECULAR & CELLULAR PROTEOMICS

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

Emergent bistability by a growth-modulating positive feedback circuit

(2009) Cheemeng Tan et al.   Nature Chemical Biology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

(2009) Marco Albrecht et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

Genome flexibility in Neisseria meningitidis

(2009) Christoph Schoen et al.   VACCINE

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

A Novel Phase Variation Mechanism in the Meningococcus Driven by a Ligand-Responsive Repressor and Differential Spacing of Distal Promoter Elements

(2009) Matteo M. E. Metruccio et al.   PLoS Pathogens

Pili in Gram-negative and Gram-positive bacteria — structure, assembly and their role in disease

(2008) T. Proft et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

A Second Pilus Type in Streptococcus pneumoniae Is Prevalent in Emerging Serotypes and Mediates Adhesion to Host Cells

(2008) F. Bagnoli et al.   JOURNAL OF BACTERIOLOGY

Sequence Variation in Group AStreptococcusPili and Association of Pilus Backbone Types with Lancefield T Serotypes

(2008) Fabiana Falugi et al.   JOURNAL OF INFECTIOUS DISEASES

Streptococcus pneumoniaeContains 3rlrAPilus Variants That Are Clonally Related

(2008) Monica Moschioni et al.   JOURNAL OF INFECTIOUS DISEASES

Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins

(2008) Bing Niu et al.   MOLECULAR DIVERSITY

PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis

(2008) Jia-Ming Chang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY

Benchmarking B cell epitope prediction: Underperformance of existing methods

(2004) Martin J. Blythe et al.   PROTEIN SCIENCE

Sequence conserved for subcellular localization

(2002) Rajesh Nair et al.   PROTEIN SCIENCE