Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus

Genome Rearrangement Shapes Prochlorococcus Ecological Adaptation

(2018) Wei Yan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

(2018) Paul M. Berube et al.   Scientific Data

Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome

(2017) Katinka J Apagyi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metabolic evolution and the self-organization of ecosystems

(2017) Rogier Braakman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

How clonal are bacteria over time?

(2016) B Jesse Shapiro   CURRENT OPINION IN MICROBIOLOGY

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

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

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

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

Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone

(2015) Marcia Astorga-Eló et al.   ISME Journal

Temporal dynamics ofProchlorococcuscells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans

(2015) Paul M. Berube et al.   LIMNOLOGY AND OCEANOGRAPHY

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A Neoproterozoic Transition in the Marine Nitrogen Cycle

(2014) Patricia Sánchez-Baracaldo et al.   CURRENT BIOLOGY

Physiology and evolution of nitrate acquisition in Prochlorococcus

(2014) Paul M Berube et al.   ISME Journal

BoxPlotR: a web tool for generation of box plots

(2014) Michaela Spitzer et al.   NATURE METHODS

Prochlorococcus: the structure and function of collective diversity

(2014) Steven J. Biller et al.   NATURE REVIEWS MICROBIOLOGY

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

(2014) C. Raeside et al.   mBio

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus

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

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

(2012) Rex R Malmstrom et al.   ISME Journal

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Biased gene transfer and its implications for the concept of lineage

(2011) Cheryl P Andam et al.   Biology Direct

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

(2010) Rex R Malmstrom et al.   ISME Journal

Nitrate supply from deep to near-surface waters of the North Pacific subtropical gyre

(2010) Kenneth S. Johnson et al.   NATURE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Ecosystem-specific selection pressures revealed through comparative population genomics

(2010) M. L. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biased gene transfer mimics patterns created through shared ancestry

(2010) C. P. Andam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of Prochlorococcus clades from iron-depleted oceanic regions

(2010) D. B. Rusch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Ecological Genomics of Marine Picocyanobacteria

(2009) D. J. Scanlan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes

(2009) A. C. Martiny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal