Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

(2013) Hannah M Doll et al.   BMC MICROBIOLOGY

Sequencing the human microbiome in health and disease

(2013) M. J. Cox et al.   HUMAN MOLECULAR GENETICS

Ecology, Diversity, and Evolution of Magnetotactic Bacteria

(2013) C. T. Lefevre et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Comparative microbial ecology study of the sediments and the water column of the Río Tinto, an extreme acidic environment

(2012) Antonio García-Moyano et al.   FEMS MICROBIOLOGY ECOLOGY

Geomicrobiology of extremely acidic subsurface environments

(2012) David Barrie Johnson   FEMS MICROBIOLOGY ECOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic life in biofilms formed in a uranium mine

(2012) Isabel Zirnstein et al.   MicrobiologyOpen

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Measuring diversity: the importance of species similarity

(2011) Tom Leinster et al.   ECOLOGY

Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community

(2011) Ryan S. Mueller et al.   ENVIRONMENTAL MICROBIOLOGY

Algal diversity in flowing waters at an acidic mine drainage “barrens” in central Pennsylvania, USA

(2011) Radha Prasanna et al.   FOLIA MICROBIOLOGICA

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

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

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature

(2010) Vincent J Denef et al.   ISME Journal

Microbial community structure across the tree of life in the extreme Río Tinto

(2010) Linda A Amaral-Zettler et al.   ISME Journal

Active community profiling via capillary electrophoresis single-strand conformation polymorphism analysis of amplified 16S rRNA and 16S rRNA genes

(2010) Sage R. Hiibel et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond

(2010) J. Rajendhran et al.   MICROBIOLOGICAL RESEARCH

Ecological distribution and population physiology defined by proteomics in a natural microbial community

(2010) Ryan S Mueller et al.   Molecular Systems Biology

Enigmatic, ultrasmall, uncultivated Archaea

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

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities

(2009) B. J. Baker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Cultivation and quantitative proteomic analyses of acidophilic microbial communities

(2009) Christopher P Belnap et al.   ISME Journal

Metals, minerals and microbes: geomicrobiology and bioremediation

(2009) G. M. Gadd   MICROBIOLOGY-SGM

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

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

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

(2008) Stephen J Bent et al.   ISME Journal

Natural acidophilic biofilm communities reflect distinct organismal and functional organization

(2008) Paul Wilmes et al.   ISME Journal

Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon

(2008) Luis R Comolli et al.   ISME Journal

Emerging patterns in the comparative analysis of phylogenetic community structure

(2008) S. M. VAMOSI et al.   MOLECULAR ECOLOGY

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics