Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

Microbial carbon use efficiency predicted from genome-scale metabolic models

(2019) Mustafa Saifuddin et al.   Nature Communications

Ultrarare marine microbes contribute to key sulphur-related ecosystem functions

(2018) Dimitri Kalenitchenko et al.   MOLECULAR ECOLOGY

The lost world of Cuatro Ciénegas Basin, a relictual bacterial niche in a desert oasis

(2018) Valeria Souza et al.   eLife

The Ecology and Evolution of Stoichiometric Phenotypes

(2017) Miguel C. Leal et al.   TRENDS IN ECOLOGY & EVOLUTION

Bacterial Unculturability and the Formation of Intercellular Metabolic Networks

(2017) Samay Pande et al.   TRENDS IN MICROBIOLOGY

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

(2017) Zarraz M.-P. Lee et al.   Frontiers in Microbiology

Disengaging from statistical significance

(2016) Kenneth J. Rothman   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

Interaction between lithification and resource availability in the microbialites of Río Mesquites, Cuatro Ciénegas, México

(2015) J. R. Corman et al.   Geobiology

The physiology and ecological implications of efficient growth

(2015) Benjamin RK Roller et al.   ISME Journal

The fickle P value generates irreproducible results

(2015) Lewis G Halsey et al.   NATURE METHODS

Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number

(2015) Zsuzsanna Gyorfy et al.   NUCLEIC ACIDS RESEARCH

Response of a Stoichiometrically Imbalanced Ecosystem to Manipulation of Nutrient Supplies and Ratios

(2015) Zarraz M. Lee et al.   PLoS One

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

(2014) Sascha Krause et al.   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

General Models for the Spectra of Surface Area Scaling Strategies of Cells and Organisms: Fractality, Geometric Dissimilitude, and Internalization

(2013) Jordan G. Okie   AMERICAN NATURALIST

Selection on GGU and CGU Codons in the High Expression Genes in Bacteria

(2013) Siddhartha Sankar Satapathy et al.   JOURNAL OF MOLECULAR EVOLUTION

Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis

(2013) K. Yano et al.   MICROBIOLOGY-SGM

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Environmental shaping of codon usage and functional adaptation across microbial communities

(2013) Maša Roller et al.   NUCLEIC ACIDS RESEARCH

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

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

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

(2012) Lisa Zeigler Allen et al.   ISME Journal

Lifestyles and phylogeny explain bird life histories

(2012) F. S. Dobson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

(2011) Matthew D. Wallenstein et al.   BIOGEOCHEMISTRY

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Bacterial community assembly based on functional genes rather than species

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

Genomic and functional adaptation in surface ocean planktonic prokaryotes

(2010) Shibu Yooseph et al.   NATURE

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Contrasting trait responses in plant communities to experimental and geographic variation in precipitation

(2010) Brody Sandel et al.   NEW PHYTOLOGIST

Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life

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

No evidence for elemental-based streamlining of prokaryotic genomes

(2010) Sara Vieira-Silva et al.   TRENDS IN ECOLOGY & EVOLUTION

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Niches, body sizes, and the disassembly of mammal communities on the Sunda Shelf islands

(2009) J. G. Okie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

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

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

Trait-Based Community Ecology of Phytoplankton

(2008) Elena Litchman et al.   Annual Review of Ecology Evolution and Systematics

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands

(2008) Yin Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes

(2008) S. Subramanian   GENETICS

Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage

(2008) P. G. Higgs et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of an extreme climatic event on community assembly

(2008) K. M. Thibault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extreme polyploidy in a large bacterium

(2008) J. E. Mendell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA