Trade-off between taxon diversity and functional diversity in European lake ecosystems

www.freshwaterecology.info – An online tool that unifies, standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences

(2015) Astrid Schmidt-Kloiber et al.   ECOLOGICAL INDICATORS

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Microbial community transcriptional networks are conserved in three domains at ocean basin scales

(2015) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome analyses to investigate symbiotic relationships between marine protists

(2015) Sergio Balzano et al.   Frontiers in Microbiology

Transcriptomics in the tropics: Total RNA-based profiling of Costa Rican bromeliad-associated communities

(2015) Shana K. Goffredi et al.   Computational and Structural Biotechnology Journal

Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

(2014) Aurélie Chambouvet et al.   BMC MICROBIOLOGY

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures

(2014) Anderson B. Mayfield et al.   MOLECULAR ECOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Effects of Silver Nitrate and Silver Nanoparticles on a Planktonic Community: General Trends after Short-Term Exposure

(2014) Jens Boenigk et al.   PLoS One

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Trophic complexity enhances ecosystem functioning in an aquatic detritus-based model system

(2013) Jérémy Jabiol et al.   JOURNAL OF ANIMAL ECOLOGY

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

(2013) Alexander Eiler et al.   PLoS One

Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach

(2012) Franck Lejzerowicz et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Testing the stress-gradient hypothesis with aquatic detritivorous invertebrates: insights for biodiversity-ecosystem functioning research

(2012) V. Fugère et al.   JOURNAL OF ANIMAL ECOLOGY

Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

(2012) Heath J. Mills et al.   Frontiers in Microbiology

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Functional and phylogenetic diversity as predictors of biodiversity–ecosystem-function relationships

(2011) Dan F. B. Flynn et al.   ECOLOGY

Has the Earth’s sixth mass extinction already arrived?

(2011) Anthony D. Barnosky et al.   NATURE

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

(2011) Meng Qi et al.   PLoS One

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

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

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA