Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

(2016) Alexander Eiler et al.   ISME Journal

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

A new view of the tree of life

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

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

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

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

(2014) Trevor W Ghylin et al.   ISME Journal

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing

(2014) Rohit Ghai et al.   MOLECULAR ECOLOGY

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)

(2013) F Heinrich et al.   AQUATIC MICROBIAL ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

(2013) Katarzyna Zaremba-Niedzwiedzka et al.   GENOME BIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

(2012) Sarahi L Garcia et al.   ISME Journal

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

(2012) Emily L Kara et al.   ISME Journal

In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake

(2012) Michaela M Salcher et al.   ISME Journal

Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns

(2012) Stefan Rösel et al.   MICROBIAL ECOLOGY

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

Coherent dynamics and association networks among lake bacterioplankton taxa

(2011) Alexander Eiler et al.   ISME Journal

Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake

(2011) Michaela M. Salcher et al.   LIMNOLOGY AND OCEANOGRAPHY

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

(2011) C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)

(2009) R. Logares et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

(2008) Ainslie E.F. Little et al.   Annual Review of Microbiology

Genomic patterns of recombination, clonal divergence and environment in marine microbial populations

(2008) Konstantinos T Konstantinidis et al.   ISME Journal

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE