Environmental bio-monitoring with high-throughput sequencing

Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals

(2013) Gizele D. Garcia et al.   MICROBIAL ECOLOGY

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

Can You Sequence Ecology? Metagenomics of Adaptive Diversification

(2013) Christopher J. Marx   PLOS BIOLOGY

Using evolutionary tools to facilitate the prediction and prevention of host-based differentiation in biological control: a review and perspective

(2012) A.E. Vorsino et al.   ANNALS OF APPLIED BIOLOGY

Beyond the genome: community-level analysis of the microbial world

(2012) Iratxe Zarraonaindia et al.   BIOLOGY & PHILOSOPHY

Endosymbiotic bacteria as a source of carotenoids in whiteflies

(2012) D. B. Sloan et al.   Biology Letters

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Coverage evaluation of universal bacterial primers using the metagenomic datasets

(2012) Dan-Ping Mao et al.   BMC MICROBIOLOGY

Design-based spatial sampling: Theory and implementation

(2012) Jin-Feng Wang et al.   ENVIRONMENTAL MODELLING & SOFTWARE

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species

(2012) Yi Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

(2012) Andrew S. Whiteley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities

(2012) Jae-Hyung Ahn et al.   JOURNAL OF MICROBIOLOGY

Quality-Score Refinement of SSU rRNA Gene Pyrosequencing Differs Across Gene Region for Environmental Samples

(2012) Kara Bowen De León et al.   MICROBIAL ECOLOGY

Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

(2012) Nastassia V. Patin et al.   MICROBIAL ECOLOGY

Errors in ribosomal sequence datasets generated using PCR-coupled ‘panbacterial’ pyrosequencing, and the establishment of an improved approach

(2012) Erica M. Prosdocimi et al.   MOLECULAR AND CELLULAR PROBES

Using high throughput sequencing to explore the biodiversity in oral bacterial communities

(2012) P.I. Diaz et al.   Molecular Oral Microbiology

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin

(2012) Vineet K. Sharma et al.   PLoS One

Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies

(2012) Sotirios Vasileiadis et al.   PLoS One

Functional Metagenomics of Escherichia coli O157:H7 Interactions with Spinach Indigenous Microorganisms during Biofilm Formation

(2012) Michelle Q. Carter et al.   PLoS One

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

(2012) Charles K. Lee et al.   PLoS One

Detection and diversity of pathogenic Vibrio from Fiji

(2012) Reema Singh et al.   Environmental Microbiology Reports

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

A review of spatial sampling

(2012) Jin-Feng Wang et al.   Spatial Statistics

Farmland bird invertebrate food provision in arable crops

(2011) J.M. Holland et al.   ANNALS OF APPLIED BIOLOGY

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Our microbial selves: what ecology can teach us

(2011) Antonio Gonzalez et al.   EMBO REPORTS

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Integrative analysis of environmental sequences using MEGAN4

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

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Sampling and sampling strategies for environmental analysis

(2011) J. Zhang et al.   INTERNATIONAL JOURNAL OF ENVIRONMENTAL ANALYTICAL CHEMISTRY

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Rethinking microbial diversity analysis in the high throughput sequencing era

(2011) Leandro N. Lemos et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Getting pharmaceutical R&D back on target

(2011) Mark E Bunnage   Nature Chemical Biology

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth 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

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Accessing the Soil Metagenome for Studies of Microbial Diversity

(2010) Tom O. Delmont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

GPU-BLAST: using graphics processors to accelerate protein sequence alignment

(2010) P. D. Vouzis et al.   BIOINFORMATICS

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen 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

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes

(2010) Michael J Raupach et al.   Frontiers in Zoology

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

(2010) Jonathan Kennedy et al.   Marine Drugs

Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology

(2010) MARTIN UNTERSEHER et al.   MOLECULAR ECOLOGY

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Analysis of the predator community of a subterranean herbivorous insect based on polymerase chain reaction

(2009) Jonathan G. Lundgren et al.   ECOLOGICAL APPLICATIONS

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

Towards an optimal sampling strategy to assess groundwater biodiversity: comparison across six European regions

(2009) M.-J. DOLE-OLIVIER et al.   FRESHWATER BIOLOGY

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

(2009) Ben Temperton et al.   ISME Journal

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

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

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

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Spatial Heterogeneity of Water Quality in a Highly Degraded Tropical Freshwater Ecosystem

(2008) Luis Zambrano et al.   ENVIRONMENTAL MANAGEMENT

DNA barcoding insect-host plant associations

(2008) J. A Jurado-Rivera et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY

Allocation of Sampling Effort to Optimize Efficiency of Watershed-Level Ichthyofaunal Inventories

(2008) Katherine L. Smith et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY