Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

Venom peptides cathelicidin and lycotoxin cause strong inhibition of Escherichia coli ATP synthase

(2016) Sofiya Azim et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

(2015) Gelio Alves et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Multilocus sequence analysis (MLSA) in prokaryotic taxonomy

(2015) Stefanie P. Glaeser et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Biomarker- and similarity coefficient-based approaches to bacterial mixture characterization using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)

(2015) Lin Zhang et al.   Scientific Reports

Genomic insights into the taxonomic status of the Bacillus cereus group

(2015) Yang Liu et al.   Scientific Reports

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

(2015) Neelja Singhal et al.   Frontiers in Microbiology

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

(2015) Jan P Meier-Kolthoff et al.   Standards in Genomic Sciences

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

When should a DDH experiment be mandatory in microbial taxonomy?

(2013) Jan P. Meier-Kolthoff et al.   ARCHIVES OF MICROBIOLOGY

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Highly parallelized inference of large genome-based phylogenies

(2013) Jan P. Meier-Kolthoff et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Bacillus weihenstephanensischaracteristics are present inBacillus cereusandBacillus mycoidesstrains

(2013) Brahim Soufiane et al.   FEMS MICROBIOLOGY LETTERS

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Complete Genome Sequence of Bacillus thuringiensis Serovar finitimus Strain YBT-020

(2011) Y. Zhu et al.   JOURNAL OF BACTERIOLOGY

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

Inhibition of Escherichia coli ATP synthase by amphibian antimicrobial peptides

(2010) Thomas F. Laughlin et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Genome of a Bacillus Isolate Causing Anthrax in Chimpanzees Combines Chromosomal Properties of B. cereus with B. anthracis Virulence Plasmids

(2010) Silke R. Klee et al.   PLoS One

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

(2009) Markus Göker et al.   PLoS One

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS