Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data

Evaluation of different molecular and phenotypic methods for identification of environmental Burkholderia cepacia complex

(2019) João Pedro Rueda Furlan et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

(2018) Takuro Nunoura et al.   SCIENCE

Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces

(2018) C. Urbaniak et al.   Scientific Reports

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates

(2018) Michal Strejcek et al.   Frontiers in Microbiology

Safety and Accuracy of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Highly Pathogenic Organisms

(2017) James T. Rudrik et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Research priorities for harnessing plant microbiomes in sustainable agriculture

(2017) Posy E. Busby et al.   PLOS BIOLOGY

Applications of MALDI-TOF MS in environmental microbiology

(2016) Inês C. Santos et al.   ANALYST

16S-ARDRA and MALDI-TOF mass spectrometry as tools for identification of Lactobacillus bacteria isolated from poultry

(2016) Marta Dec et al.   BMC MICROBIOLOGY

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria

(2016) Bo Zhu et al.   ISME Journal

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

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Improving survival and storage stability of bacteria recalcitrant to freeze-drying: a coordinated study by European culture collections

(2015) Jindrich Peiren et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

(2013) A. E. Clark et al.   CLINICAL MICROBIOLOGY REVIEWS

Culture conditions and sample preparation methods affect spectrum quality and reproducibility during profiling ofStaphylococcus aureuswith matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

(2013) J.E. Goldstein et al.   LETTERS IN APPLIED MICROBIOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

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

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

MALDI TOF MS profiling of bacteria at the strain level: A review

(2012) Todd R. Sandrin et al.   MASS SPECTROMETRY REVIEWS

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Comparison of Direct Colony Method versus Extraction Method for Identification of Gram-Positive Cocci by Use of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

(2011) A. A. Alatoom et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication

(2011) Jonas Ghyselinck et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology

(2011) Martin Welker et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories

(2010) S. Q. van Veen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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