Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities

Deciphering Diversity and Ecological Function From Marine Metagenomes

(2016) Holly M. Bik   BIOLOGICAL BULLETIN

Counts and sequences, observations that continue to change our understanding of viruses in nature

(2015) K. Eri Wommack et al.   JOURNAL OF MICROBIOLOGY

Marine Microbial Metagenomics: From Individual to the Environment

(2014) Ching-Hung Tseng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

(2014) Chris L. Dupont et al.   PLoS One

Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem

(2014) Holly M. Simon et al.   Frontiers in Microbiology

FANTOM: Functional and taxonomic analysis of metagenomes

(2013) Kemal Sanli et al.   BMC BIOINFORMATICS

Lineage specific gene family enrichment at the microscale in marine systems

(2013) Andrew E Allen et al.   CURRENT OPINION IN MICROBIOLOGY

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

Optimal colonization and growth of marine benthic diatoms on artificial substrata: protocol for a routine use in bioindication

(2013) Catherine Desrosiers et al.   JOURNAL OF APPLIED PHYCOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The Importance of Dissimilatory Nitrate Reduction to Ammonium (DNRA) in the Nitrogen Cycle of Coastal Ecosystems

(2013) Anne Giblin et al.   OCEANOGRAPHY

Function and Regulation of Isoforms of Carbon Monoxide Dehydrogenase/Acetyl Coenzyme A Synthase in Methanosarcina acetivorans

(2012) N. Matschiavelli et al.   JOURNAL OF BACTERIOLOGY

EFFECTS OF LIGHT AND SUBSTRATE ON THE BENTHIC DIATOMS IN AN OLIGOTROPHIC LAKE: A COMPARISON BETWEEN NATURAL AND ARTIFICIAL SUBSTRATES1

(2012) Hong Yang et al.   JOURNAL OF PHYCOLOGY

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

(2011) Johan Bengtsson et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

The periphyton index of trophic status PIT: a new eutrophication metric based on non-diatomaceous benthic algae in Nordic rivers

(2011) Susanne C. Schneider et al.   HYDROBIOLOGIA

Pathway-Based Functional Analysis of Metagenomes

(2011) Itai Sharon et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Microbial diversity in marine biofilms along a water quality gradient on the Great Barrier Reef

(2011) Pascal Kriwy et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Microbial Biofilms Facilitate Adhesion in Biofouling Invertebrates

(2010) John D. Zardus et al.   BIOLOGICAL BULLETIN

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

The biofilm matrix

(2010) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Marine genomics: at the interface of marine microbial ecology and biodiscovery

(2010) Karla B. Heidelberg et al.   Microbial Biotechnology

Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

(2010) Jennifer L. Edwards et al.   Genes

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

A phylogenetic approach to detect selection on the target site of the antifouling compound irgarol in tolerant periphyton communities

(2009) K. M. Eriksson et al.   ENVIRONMENTAL MICROBIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Use of diatoms to assess agricultural and coal mining impacts on streams and a multiassemblage case study

(2009) Nathan J. Smucker et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Carbohydrate Metabolism and Carbon Fixation in Roseobacter denitrificans OCh114

(2009) Kuo-Hsiang Tang et al.   PLoS One

The relevance of the community approach linking chemical and biological analyses in pollution assessment

(2009) A. Geiszinger et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Community-Level Analysis of psbA Gene Sequences and Irgarol Tolerance in Marine Periphyton

(2008) K. M. Eriksson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quorum sensing inPseudomonas aeruginosabiofilms

(2008) T. R. de Kievit   ENVIRONMENTAL MICROBIOLOGY

How much non-coding DNA do eukaryotes require?

(2008) Sebastian E. Ahnert et al.   JOURNAL OF THEORETICAL BIOLOGY

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH

A collective mechanism for phase variation in biofilms

(2008) N. Chia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA