Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics

Deciphering Multifactorial Resistance Phenotypes inAcinetobacter baumanniiby Genomics and Targeted Label-free Proteomics

(2017) Tiphaine Cecchini et al.   MOLECULAR & CELLULAR PROTEOMICS

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics

(2017) Fredrik Boulund et al.   MOLECULAR & CELLULAR PROTEOMICS

A Novel Peptidomic Approach to Strain Typing of Clinical Acinetobacter baumannii Isolates Using Mass Spectrometry

(2016) H. Wang et al.   CLINICAL CHEMISTRY

Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus

(2016) Anders Jensen et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: Principle and applications

(2016) Adele Bourmaud et al.   PROTEOMICS

Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics

(2016) Roger Karlsson et al.   Frontiers in Microbiology

Evolution of Orbitrap Mass Spectrometry Instrumentation

(2015) Shannon Eliuk et al.   Annual Review of Analytical Chemistry

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

(2015) Michael Richter et al.   BIOINFORMATICS

Global, regional, and national causes of child mortality in 2000–13, with projections to inform post-2015 priorities: an updated systematic analysis

(2015) Li Liu et al.   LANCET

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Proteotyping: Proteomic characterization, classification and identification of microorganisms – A prospectus

(2015) Roger Karlsson et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Rapid Bacterial Identification, Resistance, Virulence and Type Profiling using Selected Reaction Monitoring Mass Spectrometry

(2015) Yannick Charretier et al.   Scientific Reports

Phylogenomics and systematics in Pseudomonas

(2015) Margarita Gomila et al.   Frontiers in Microbiology

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database

(2015) Roxana Beaz-Hidalgo et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Detection of Mycobacterium tuberculosis Peptides in the Exosomes of Patients with Active and Latent M. tuberculosis Infection Using MRM-MS

(2014) Nicole A. Kruh-Garcia et al.   PLoS One

Parallel Evolution of Streptococcus pneumoniae and Streptococcus mitis to Pathogenic and Mutualistic Lifestyles

(2014) M. Kilian 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

Proteotyping for the rapid identification of influenza virus and other biopathogens

(2013) Kevin M. Downard   CHEMICAL SOCIETY REVIEWS

Identification and Validation of Specific Markers ofBacillus anthracisSpores by Proteomics and Genomics Approaches

(2013) Jérôme Chenau et al.   MOLECULAR & CELLULAR PROTEOMICS

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

(2013) W. Florian Fricke et al.   NATURE REVIEWS GENETICS

Strain-Level Typing and Identification of Bacteria Using Mass Spectrometry-Based Proteomics

(2012) Roger Karlsson et al.   JOURNAL OF PROTEOME RESEARCH

Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)

(2012) Angus I. Lamond et al.   MOLECULAR & CELLULAR PROTEOMICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Developing an integrated proteo-genomic approach for the characterisation of biomarkers for the identification of Bacillus anthracis

(2011) Raju V. Misra et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Rapid Differentiation of Seasonal and Pandemic H1N1 Influenza through Proteotyping of Viral Neuraminidase with Mass Spectrometry

(2010) Alexander B. Schwahn et al.   ANALYTICAL CHEMISTRY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

(2010) Claudio Donati et al.   GENOME BIOLOGY

Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates

(2009) Katherine L O'Brien et al.   LANCET

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying and Characterizing Bacteria in an Era of Genomics and Proteomics

(2008) David Emerson et al.   BIOSCIENCE

X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers

(2007) Robert D. Bjornson et al.   JOURNAL OF PROTEOME RESEARCH