An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids

Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs

(2019) Lily Momper et al.   FREE RADICAL BIOLOGY AND MEDICINE

Dating phototrophic microbial lineages with reticulate gene histories

(2018) C. Magnabosco et al.   Geobiology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Early photosynthetic eukaryotes inhabited low-salinity habitats

(2017) Patricia Sánchez-Baracaldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecogenomics and Taxonomy of Cyanobacteria Phylum

(2017) Juline M. Walter et al.   Frontiers in Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time

(2016) Josef C. Uyeda et al.   PLoS One

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Correlation between methyl anthranilate level and percentage of pollen in Spanish citrus honey

(2015) Marisol Juan-Borrás et al.   INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY

Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils

(2015) Bettina E. Schirrmeister et al.   PALAEONTOLOGY

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

An integrated phylogenomic approach toward pinpointing the origin of mitochondria

(2015) Zhang Wang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

(2014) Blaise Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Strong Genome-Wide Selection Early in the Evolution of Prochlorococcus Resulted in a Reduced Genome through the Loss of a Large Number of Small Effect Genes

(2014) Zhiyi Sun et al.   PLoS One

The plastid ancestor originated among one of the major cyanobacterial lineages

(2014) Jesús A. G. Ochoa de Alda et al.   Nature Communications

New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability

(2013) Matteo P. Ferla et al.   PLoS One

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

Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

(2012) Tal Dagan et al.   Genome Biology and Evolution

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

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A congruent phylogenomic signal places eukaryotes within the Archaea

(2012) T. A. Williams et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

(2011) Alexis Criscuolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dating the cyanobacterial ancestor of the chloroplast

(2010) Luisa I Falcón et al.   ISME Journal

Differential Gene Retention in Plastids of Common Recent Origin

(2010) A. Reyes-Prieto et al.   MOLECULAR BIOLOGY AND EVOLUTION

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis

(2009) PATRICK J. KEELING   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor

(2008) O. Deusch et al.   MOLECULAR BIOLOGY AND EVOLUTION