First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

An Expanded Genomic Representation of the Phylum Cyanobacteria

(2014) Rochelle M. Soo et al.   Genome Biology and Evolution

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques

(2013) Inka Vanwonterghem et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

IMG/M 4 version of the integrated metagenome comparative analysis system

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

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Ecophysiology of Uncultured Filamentous Anaerobes Belonging to the Phylum KSB3 That Cause Bulking in Methanogenic Granular Sludge

(2011) Takeshi Yamada et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

(2011) Alexandra Sirota-Madi et al.   BMC GENOMICS

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Gliding Motility Revisited: How Do the Myxobacteria Move without Flagella?

(2010) E. M. F. Mauriello et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Comparative Genomic Analysis of Fruiting Body Formation in Myxococcales

(2010) S. Huntley et al.   MOLECULAR BIOLOGY AND EVOLUTION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Chemotaxis-Like Regulatory Systems: Unique Roles in Diverse Bacteria

(2009) John R. Kirby   Annual Review of Microbiology

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

(2009) Delphine Rivière et al.   ISME Journal

Comparative Analysis of Bacterial and Archaeal Communities in Methanogenic Sludge Granules from Upflow Anaerobic Sludge Blanket Reactors Treating Various Food-Processing, High-Strength Organic Wastewaters

(2009) Takashi Narihiro et al.   MICROBES AND ENVIRONMENTS

Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance

(2009) Takeshi Yamada et al.   MICROBES AND ENVIRONMENTS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic circuitry controlling motility behaviors ofMyxococcus xanthus

(2008) Tâm Mignot et al.   BIOESSAYS

Filamentous granular sludge bulking in a laboratory scale UASB reactor

(2008) Jinye Li et al.   BIORESOURCE TECHNOLOGY

The surprisingly diverse ways that prokaryotes move

(2008) Ken F. Jarrell et al.   NATURE REVIEWS MICROBIOLOGY

High-rate anaerobic wastewater treatment: diversifying from end-of-the-pipe treatment to resource-oriented conversion techniques

(2008) Jules B. van Lier   WATER SCIENCE AND TECHNOLOGY

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

(2007) Rotem Sorek et al.   NATURE REVIEWS MICROBIOLOGY