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

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

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

A Side by Side Comparison of Bruker Biotyper and VITEK MS: Utility of MALDI-TOF MS Technology for Microorganism Identification in a Public Health Reference Laboratory

(2015) Simon Lévesque et al.   PLoS One

The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

(2014) Veronica N. Kos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics

(2014) Anke Penzlin et al.   BIOINFORMATICS

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Sub-Typing of Extended-Spectrum-β-Lactamase-Producing Isolates from a Nosocomial Outbreak: Application of a 10-Loci Generic Escherichia coli Multi-Locus Variable Number Tandem Repeat Analysis

(2014) Nahid Karami et al.   PLoS One

Bacterial resistance mechanism: what proteomics can elucidate

(2013) Thais Bergamin Lima et al.   FASEB JOURNAL

A simple shotgun proteomics method for rapid bacterial identification

(2013) Dobryan M. Tracz et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Handling the 3-methylcytosine lesion by six human DNA polymerases members of the B-, X- and Y-families

(2013) Antonia Furrer et al.   NUCLEIC ACIDS RESEARCH

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli?

(2012) Hajer Radhouani et al.   Journal of 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

Metagenomic abundance estimation and diagnostic testing on species level

(2012) Martin S. Lindner et al.   NUCLEIC ACIDS RESEARCH

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

(2011) Benjamin J. Diament et al.   JOURNAL OF PROTEOME RESEARCH

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Double-Blind Characterization of Non-Genome-Sequenced Bacteria by Mass Spectrometry-Based Proteomics

(2010) R. E. Jabbour et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Missing genes in the annotation of prokaryotic genomes

(2010) Andrew S Warren et al.   BMC BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

(2010) Andreas Dotsch et al.   BMC GENOMICS

Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens

(2010) Yvonne Pfeifer et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

A Protein Processing Filter Method for Bacterial Identification by Mass Spectrometry-Based Proteomics

(2010) Rabih E. Jabbour et al.   JOURNAL OF PROTEOME RESEARCH

Mass spectrometry tools for the classification and identification of bacteria

(2009) Sascha Sauer et al.   NATURE REVIEWS MICROBIOLOGY

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

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