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

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus

(2017) Nadav Kashtan et al.   ISME Journal

panX: pan-genome analysis and exploration

(2017) Wei Ding et al.   NUCLEIC ACIDS RESEARCH

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

Global genetic capacity for mixotrophy in marine picocyanobacteria

(2016) Alexis P Yelton et al.   ISME Journal

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Prochlorococcus: the structure and function of collective diversity

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

GEOTRACES: Changing the Way We Explore Ocean Chemistry

(2014) Robert Anderson et al.   OCEANOGRAPHY

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

(2014) Steven J. Biller et al.   Scientific Data

Stabilizing the foundation of the house that ‘omics builds: the evolving value of cultured isolates to marine microbiology

(2013) Michael S Rappé   CURRENT OPINION IN MICROBIOLOGY

Dynamic biogeochemical provinces in the global ocean

(2013) Gabriel Reygondeau et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

(2013) Libusha Kelly et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

IMG 4 version of the integrated microbial genomes comparative analysis system

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

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Effect of Temperature on Photosynthesis and Growth in Marine Synechococcus spp.

(2013) K. R. M. Mackey et al.   PLANT PHYSIOLOGY

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

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

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

The virocell concept and environmental microbiology

(2012) Patrick Forterre   ISME Journal

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

(2012) Rex R Malmstrom et al.   ISME Journal

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

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

Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

(2012) Jana Grote et al.   Standards in Genomic Sciences

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Dependence of the Cyanobacterium Prochlorococcus on Hydrogen Peroxide Scavenging Microbes for Growth at the Ocean's Surface

(2011) J. Jeffrey Morris et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Complete Genome Sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a Representative of the SAR116 Clade in the Alphaproteobacteria

(2010) H.-M. Oh et al.   JOURNAL OF BACTERIOLOGY

How Many Bootstrap Replicates Are Necessary?

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

Prochlorococcus: Advantages and Limits of Minimalism

(2009) Frédéric Partensky et al.   Annual Review of Marine Science

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

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY