Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

(2012) Yu Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Purification and Characterization of the Acetone Carboxylase of Cupriavidus metallidurans Strain CH34

(2012) Caroline Rosier et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

(2012) Kim M. Handley et al.   FEMS MICROBIOLOGY ECOLOGY

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

Semi-Automatic In Silico Gap Closure Enabled De Novo Assembly of Two Dehalobacter Genomes from Metagenomic Data

(2012) Shuiquan Tang et al.   PLoS One

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

(2012) S. L. Jorgensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor

(2012) Tomonori Kindaichi et al.   WATER SCIENCE AND TECHNOLOGY

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

(2012) Hajnalka Kiss et al.   Standards in Genomic Sciences

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains

(2012) Shivakumara Siddaramappa et al.   Standards in Genomic Sciences

Natural Niche for Organohalide-Respiring Chloroflexi

(2011) Mark J. Krzmarzick et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard

(2011) A. Teske et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cloning, functional expression, biochemical characterization, and structural analysis of a haloalkane dehalogenase from Plesiocystis pacifica SIR-1

(2011) Martin Hesseler et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus

(2011) Kuo-Hsiang Tang et al.   BMC GENOMICS

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

(2011) Xueju Lin et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal

(2011) Vitaly V. Kadnikov et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial community composition in sediments resists perturbation by nutrient enrichment

(2011) Jennifer L Bowen et al.   ISME Journal

Identification and Characterization of a Re-Citrate Synthase in Dehalococcoides Strain CBDB1

(2011) E. Marco-Urrea et al.   JOURNAL OF BACTERIOLOGY

The Evolution of Respiratory Chain Complex I from a Smaller Last Common Ancestor Consisting of 11 Protein Subunits

(2011) Vamsi K. Moparthi et al.   JOURNAL OF MOLECULAR EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

(2011) Dongying Wu et al.   PLoS One

Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)

(2011) Yun-juan Chang et al.   Standards in Genomic Sciences

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

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

(2010) Manuel Stark et al.   BMC GENOMICS

Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war

(2010) Iain C. Sutcliffe   ENVIRONMENTAL MICROBIOLOGY

High abundance of JS-1- andChloroflexi-relatedBacteriain deeply buried marine sediments revealed by quantitative, real-time PCR

(2010) Anna Blazejak et al.   FEMS MICROBIOLOGY ECOLOGY

Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)

(2010) Hajnalka Kiss et al.   Standards in Genomic Sciences

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T)

(2010) Amrita Pati et al.   Standards in Genomic Sciences

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

(2010) M. Ahsanul Islam et al.   PLoS Computational Biology

Variations in Archaeal and Bacterial Diversity Associated with the Sulfate-Methane Transition Zone in Continental Margin Sediments (Santa Barbara Basin, California)

(2009) B. K. Harrison et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria

(2009) S. Yabe et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Changes in Community Structure of Sediment Bacteria Along the Florida Coastal Everglades Marsh–Mangrove–Seagrass Salinity Gradient

(2009) Makoto Ikenaga et al.   MICROBIAL ECOLOGY

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

(2009) Dongying Wu et al.   PLoS One

Sequence- and activity-based screening of microbial genomes for novel dehalogenases

(2009) Wing Yiu Chan et al.   Microbial Biotechnology

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

(2009) Paul J. McMurdie et al.   PLoS Genetics

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The surprisingly diverse ways that prokaryotes move

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

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY