Next-generation sequencing technologies for environmental DNA research

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Bar-Coded Pyrosequencing Reveals the Responses of PBDE-Degrading Microbial Communities to Electron Donor Amendments

(2012) Meiying Xu et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing

(2011) Renato Andreotti et al.   BMC MICROBIOLOGY

Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest (Poland)

(2011) Rafał Kowalczyk et al.   FOREST ECOLOGY AND MANAGEMENT

Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation

(2011) Melanie A. Jones et al.   GENETICS IN MEDICINE

Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota

(2011) Matteo Serino et al.   GUT

Human papillomavirus genotyping by 454 next generation sequencing technology

(2011) Luisa Barzon et al.   JOURNAL OF CLINICAL VIROLOGY

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

(2011) SANNE BOESSENKOOL et al.   MOLECULAR ECOLOGY

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

(2011) KENNETH ANDERSEN et al.   MOLECULAR ECOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

(2011) Eun-Joon Lee et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Heiko Nacke et al.   PLoS One

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

(2011) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode

(2011) Kevin S. Burgess et al.   Methods in Ecology and Evolution

High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species

(2011) Orly Razgour et al.   Ecology and Evolution

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models

(2010) E F Murphy et al.   GUT

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

(2010) Johannes Rousk et al.   ISME Journal

Assessment of soil fungal communities using pyrosequencing

(2010) Young Woon Lim et al.   JOURNAL OF MICROBIOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Ecometagenetics confirm high tropical rainforest nematode diversity

(2010) DOROTA L. PORAZINSKA et al.   MOLECULAR ECOLOGY

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

(2010) J. H. SØNSTEBØ et al.   Molecular Ecology Resources

Vertical distribution of fungal communities in tallgrass prairie soil

(2010) Ari Jumpponen et al.   MYCOLOGIA

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

(2009) Eeva M Soininen et al.   Frontiers in Zoology

Universal DNA-Based Methods for Assessing the Diet of Grazing Livestock and Wildlife from Feces

(2009) Anthony Pegard et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing

(2009) Vladimir Lazarevic et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach

(2009) ALICE VALENTINI et al.   Molecular Ecology Resources

Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology

(2009) IAN P. ADAMS et al.   MOLECULAR PLANT PATHOLOGY

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince 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

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

(2009) James Haile et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human gut microbiota in obesity and after gastric bypass

(2009) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Enrichment of sequencing targets from the human genome by solution hybridization

(2009) Ryan Tewhey et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico

(2008) Mya Breitbart et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial carbon processing by generalist species in the coastal ocean

(2008) Xiaozhen Mou et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

(2008) Shannon J. Williamson et al.   PLoS One

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

(2008) Anders F. Andersson et al.   PLoS One

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

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

Microbial community gene expression in ocean surface waters

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

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris 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

Single-molecule DNA sequencing technologies for future genomics research

(2008) Pushpendra K. Gupta   TRENDS IN BIOTECHNOLOGY

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS