Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics

(2015) Jie Ren et al.   BIOINFORMATICS

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

(2015) Huan Fan et al.   BMC GENOMICS

Fast alignment-free sequence comparison using spaced-word frequencies

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

kmacs: the k -mismatch average common substring approach to alignment-free sequence comparison

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

Genome sequencing defines phylogeny and spread of methicillin-resistantStaphylococcus aureusin a high transmission setting

(2014) Steven Y.C. Tong et al.   GENOME RESEARCH

Extraction of high quality k-words for alignment-free sequence comparison

(2014) Upuli Gunasinghe et al.   JOURNAL OF THEORETICAL BIOLOGY

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

(2014) Sebastian Horwege et al.   NUCLEIC ACIDS RESEARCH

Molecular phylogenetics before sequences

(2014) Mark A Ragan et al.   RNA Biology

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Inferring phylogenies of evolving sequences without multiple sequence alignment

(2014) Cheong Xin Chan et al.   Scientific Reports

Next-generation phylogenomics

(2013) Cheong Xin Chan et al.   Biology Direct

Alignment-free phylogenetics and population genetics

(2013) B. Haubold   BRIEFINGS IN BIOINFORMATICS

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

(2013) O. Bonham-Carter et al.   BRIEFINGS IN BIOINFORMATICS

Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

(2013) Kai Song et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

(2013) Huiguang Yi et al.   NUCLEIC ACIDS RESEARCH

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

(2013) P. M. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

(2011) Anne Kupczok et al.   Algorithms for Molecular Biology

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

(2011) David J Russell et al.   BMC BIOINFORMATICS

Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

(2011) John W Stiller   BMC EVOLUTIONARY BIOLOGY

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella

(2011) Elizabeth Skippington et al.   BMC GENOMICS

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

(2011) John A. Fuerst et al.   NATURE REVIEWS MICROBIOLOGY

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using jackknife to assess the quality of gene order phylogenies

(2010) Jian Shi et al.   BMC BIOINFORMATICS

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome Biology and Evolution

Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics

(2010) Lin Wan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Computing the Distribution of a Tree Metric

(2009) D. Bryant et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Estimating Mutation Distances from Unaligned Genomes

(2009) Bernhard Haubold et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

(2009) S.-R. Jun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method

(2008) David M. Gordon et al.   ENVIRONMENTAL MICROBIOLOGY

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

The Impact of Reticulate Evolution on Genome Phylogeny

(2008) Robert G. Beiko et al.   SYSTEMATIC BIOLOGY

Dynamics of Genome Rearrangement in Bacterial Populations

(2008) Aaron E. Darling et al.   PLoS Genetics