Microbial Diversity in the Era of Omic Technologies

Culture-Independent Analysis of Aerosol Microbiology in a Metropolitan Subway System

(2013) Charles E. Robertson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Soil microbial diversity patterns of a lowland spring environment

(2013) Sotirios Vasileiadis et al.   FEMS MICROBIOLOGY ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Applications of functional gene microarrays for profiling microbial communities

(2012) Zhili He et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bacterial diversity in Cr(VI) and Cr(III)-contaminated industrial wastewaters

(2012) Katerina Katsaveli et al.   EXTREMOPHILES

Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis

(2012) T. M. Korves et al.   INDOOR AIR

Biogeography of bacterial communities exposed to progressive long-term environmental change

(2012) Ramiro Logares et al.   ISME Journal

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

(2012) Olivia U Mason et al.   ISME Journal

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

(2012) Ramiro Logares et al.   ISME Journal

Influence of geogenic factors on microbial communities in metallogenic Australian soils

(2012) Frank Reith et al.   ISME Journal

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

(2012) Manuel Martinez-Garcia et al.   PLoS One

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

(2012) K. Leung 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

Landscape of Next-Generation Sequencing Technologies

(2011) Thomas P. Niedringhaus et al.   ANALYTICAL CHEMISTRY

Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)

(2011) Noha H. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Olive-Mill Wastewater Bacterial Communities Display a Cultivar Specific Profile

(2011) George Tsiamis et al.   CURRENT MICROBIOLOGY

Development of functional gene microarrays for microbial community analysis

(2011) Zhili He et al.   CURRENT OPINION IN BIOTECHNOLOGY

Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

(2011) Sébastien Monchy et al.   ENVIRONMENTAL MICROBIOLOGY

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

(2011) Christina A. Kellogg et al.   JOURNAL OF MICROBIOLOGICAL METHODS

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Single-cell genomics

(2011) Tomer Kalisky et al.   NATURE METHODS

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

(2011) Heiko Nacke et al.   PLoS One

Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing

(2011) Purnima S. Kumar et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Microbial Metagenomics: Beyond the Genome

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

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage

(2010) Jianping Xie et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10

(2010) H. Tamaki et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

(2010) Zhili He et al.   ISME Journal

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

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

(2010) J. Rajendhran et al.   MICROBIOLOGICAL RESEARCH

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Vertical distribution of fungal communities in tallgrass prairie soil

(2010) Ari Jumpponen et al.   MYCOLOGIA

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

Lactobacillus casei Abundance Is Associated with Profound Shifts in the Infant Gut Microbiome

(2010) Michael J. Cox et al.   PLoS One

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

(2010) Terry C. Hazen et al.   SCIENCE

Bacterial symbionts in insects: balancing life and death

(2010) Harriet L. Harris et al.   SYMBIOSIS

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

(2010) Carlos W Nossa   WORLD JOURNAL OF GASTROENTEROLOGY

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing

(2009) U. S. Sagaram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Swift: primary data analysis for the Illumina Solexa sequencing platform

(2009) Nava Whiteford et al.   BIOINFORMATICS

A changing of the guard

(2009) Philip Hugenholtz et al.   ENVIRONMENTAL MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

(2009) Nikos C Kyrpides   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification

(2009) Alexander Siegl et al.   Environmental Microbiology Reports

A renaissance for the pioneering 16S rRNA gene

(2008) Susannah G Tringe et al.   CURRENT OPINION IN MICROBIOLOGY

"Candidatus Cloacamonas Acidaminovorans": Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division

(2008) E. Pelletier et al.   JOURNAL OF BACTERIOLOGY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Microbiology in the post-genomic era

(2008) Duccio Medini et al.   NATURE REVIEWS MICROBIOLOGY

A korarchaeal genome reveals insights into the evolution of the Archaea

(2008) J. G. Elkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial scaling of functional gene diversity across various microbial taxa

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

Prokaryotic community profiles at different operational stages of a Greek solar saltern

(2008) George Tsiamis et al.   RESEARCH IN MICROBIOLOGY

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

(2008) V. Acosta-Martínez et al.   SOIL BIOLOGY & BIOCHEMISTRY

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS