Analysis of plant microbe interactions in the era of next generation sequencing technologies

Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase

(2018) Daniel J. G. Lahr et al.   BIOTECHNIQUES

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

(2014) L. Maignien et al.   mBio

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Filtering duplicate reads from 454 pyrosequencing data

(2013) Susanne Balzer et al.   BIOINFORMATICS

Using state machines to model the Ion Torrent sequencing process and to improve read error rates

(2013) D. Golan et al.   BIOINFORMATICS

RACER: Rapid and accurate correction of errors in reads

(2013) Lucian Ilie et al.   BIOINFORMATICS

Base calling for high-throughput short-read sequencing: dynamic programming solutions

(2013) Shreepriya Das et al.   BMC BIOINFORMATICS

Routine performance and errors of 454 HLA exon sequencing in diagnostics

(2013) Norbert Niklas et al.   BMC BIOINFORMATICS

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology

(2013) Jue Ruan et al.   BMC GENOMICS

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

(2013) Sarah K Bowman et al.   BMC GENOMICS

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

(2013) Fabio Gori et al.   BMC GENOMICS

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

(2013) Andrea R Ottesen et al.   BMC MICROBIOLOGY

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

(2013) H. Nagasaki et al.   DNA RESEARCH

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

(2013) Etienne Yergeau et al.   ISME Journal

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

(2013) Terrence H Bell et al.   ISME Journal

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Application of Natural Blends of Phytochemicals Derived from the Root Exudates ofArabidopsisto the Soil Reveal That Phenolic-related Compounds Predominantly Modulate the Soil Microbiome

(2013) Dayakar V. Badri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples

(2013) Jennifer J. Mosher et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland

(2013) Xiao-Tao Jiang et al.   MICROBIAL ECOLOGY

A glimpse into past, present, and future DNA sequencing

(2013) Marcos Morey et al.   MOLECULAR GENETICS AND METABOLISM

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Updating benchtop sequencing performance comparison

(2013) Sebastian Jünemann et al.   NATURE BIOTECHNOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen

(2013) Karnika Thakur et al.   PLoS One

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen et al.   PLoS One

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

(2013) John M. Gaspar et al.   PLoS One

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

(2013) Paul Igor Costea et al.   PLoS One

Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample

(2013) Aakrosh Ratan et al.   PLoS One

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Choosing a Benchtop Sequencing Machine to Characterise Helicobacter pylori Genomes

(2013) Timothy T. Perkins et al.   PLoS One

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

(2013) Nora Rieber et al.   PLoS One

Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes

(2013) Seung Chul Shin et al.   PLoS One

Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere

(2013) Andrea R. Ottesen et al.   PLoS One

Season, Irrigation, Leaf Age, and Escherichia coli Inoculation Influence the Bacterial Diversity in the Lettuce Phyllosphere

(2013) Thomas R. Williams et al.   PLoS One

Water Regime Influences Bulk Soil and Rhizosphere of Cereus jamacaru Bacterial Communities in the Brazilian Caatinga Biome

(2013) Vanessa Nessner Kavamura et al.   PLoS One

Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study of Endophytes in Eucalyptus grandis Reveals High Taxonomic Diversity

(2013) Martin Kemler et al.   PLoS One

Distinct Phyllosphere Bacterial Communities on Arabidopsis Wax Mutant Leaves

(2013) Eva E. Reisberg et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

(2013) N. A. Bokulich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

(2013) Wei Shao et al.   Retrovirology

Peregrine

(2013) Stanley A. Langevin et al.   RNA Biology

Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton

(2013) Haiwei Luo et al.   Environmental Microbiology Reports

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

(2013) A. Shade et al.   mBio

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

(2013) Lauren M. Bragg et al.   PLoS Computational Biology

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome

(2013) Sagar Chhabra et al.   MicrobiologyOpen

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community

(2012) Christopher W. Marshall et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mining of unexplored habitats for novel chitinases—chiA as a helper gene proxy in metagenomics

(2012) Mariana Silvia Cretoiu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

Bioinformatics clouds for big data manipulation

(2012) Lin Dai et al.   Biology Direct

Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications

(2012) Ina Vandenbroucke et al.   BIOTECHNIQUES

Efficient error correction for next-generation sequencing of viral amplicons

(2012) Pavel Skums et al.   BMC BIOINFORMATICS

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Rapid transcriptome characterization and parsing of sequences in a non-model host-pathogen interaction; pea-Sclerotinia sclerotiorum

(2012) Xiaofeng Zhuang et al.   BMC GENOMICS

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Metagenomic analysis: the challenge of the data bonanza

(2012) C. I. Hunter et al.   BRIEFINGS IN BIOINFORMATICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

(2012) C. De Filippo et al.   BRIEFINGS IN BIOINFORMATICS

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Recent advances in nanopore sequencing

(2012) Raj D. Maitra et al.   ELECTROPHORESIS

Advances in computational analysis of metagenome sequences

(2012) Colin F. Davenport et al.   ENVIRONMENTAL MICROBIOLOGY

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

(2012) Acácio A. Navarrete et al.   FEMS MICROBIOLOGY ECOLOGY

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Transcriptome analysis of enriched Golovinomyces orontii haustoria by deep 454 pyrosequencing

(2012) Ralf Weßling et al.   FUNGAL GENETICS AND BIOLOGY

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Pyrosequencing Reveals Bacterial Diversity in the Rhizosphere of ThreePhragmites australisEcotypes

(2012) Wei Zhang et al.   GEOMICROBIOLOGY JOURNAL

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

(2012) Gurdeep Rastogi et al.   ISME Journal

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties

(2012) Anja B Dohrmann et al.   ISME Journal

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

(2012) J Gregory Caporaso et al.   ISME Journal

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

(2012) S. D. Brown et al.   JOURNAL OF BACTERIOLOGY

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

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

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

(2012) Ramiro Logares et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Metagenomic Analysis of the Rhizosphere Soil Microbiome with Respect to Phytic Acid Utilization

(2012) Yusuke Unno et al.   MICROBES AND ENVIRONMENTS

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Succession of root-associated fungi in Pisum sativum during a plant growth cycle as examined by 454 pyrosequencing

(2012) L. Yu et al.   PLANT AND SOIL

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

(2012) Chengwei Luo et al.   PLoS One

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

(2012) Konstantinos Mavromatis et al.   PLoS One

Library Preparation and Multiplex Capture for Massive Parallel Sequencing Applications Made Efficient and Easy

(2012) Mårten Neiman et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Bacterial anoxygenic photosynthesis on plant leaf surfaces

(2012) Nof Atamna-Ismaeel et al.   Environmental Microbiology Reports

ANALYSIS OF CONTEXT-DEPENDENT ERRORS FOR ILLUMINA SEQUENCING

(2012) IRINA ABNIZOVA et al.   Journal of Bioinformatics and Computational Biology

Landscape of Next-Generation Sequencing Technologies

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

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

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

Identification and Targeted Cultivation of Abundant Novel Freshwater Sphingomonads and Analysis of Their Population Substructure

(2011) Mareike Jogler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

(2011) Neil R. Gottel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Correcting errors in short reads by multiple alignments

(2011) L. Salmela et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

(2011) Phuong Nguyen et al.   BMC GENOMICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Base-calling for next-generation sequencing platforms

(2011) C. Ledergerber et al.   BRIEFINGS IN BIOINFORMATICS

An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud

(2011) Andreas Wilke et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Microbial rhodopsins on leaf surfaces of terrestrial plants

(2011) Nof Atamna-Ismaeel et al.   ENVIRONMENTAL MICROBIOLOGY

Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA

(2011) N. J. Parkinson 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

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Sequencing technologies and genome sequencing

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

The impact of next-generation sequencing on genomics

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

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction

(2011) DIANA FERNANDEZ et al.   MOLECULAR PLANT PATHOLOGY

Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis

(2011) A. Sessitsch et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq)

(2011) Lira Mamanova et al.   Nature Protocols

Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing

(2011) Alex J. Dumbrell et al.   NEW PHYTOLOGIST

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

(2011) Noah Rosenzweig et al.   PLANT DISEASE

Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves

(2011) A. Tremblay et al.   PLANT PATHOLOGY

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

(2011) Shingo Suzuki 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

Bacterial adaptation to life in association with plants - A proteomic perspective from culture to in situ conditions

(2011) Claudia Knief et al.   PROTEOMICS

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Correction of sequencing errors in a mixed set of reads

(2010) L. Salmela   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu 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

Recent advances in single-molecule sequencing

(2010) Regina Treffer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Effect of the herbicide glyphosate on glyphosate-tolerant maize rhizobacterial communities: a comparison with pre-emergency applied herbicide consisting of a combination of acetochlor and terbuthylazine

(2010) Jorge Barriuso et al.   ENVIRONMENTAL MICROBIOLOGY

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves

(2010) Amanda J. Redford et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing

(2010) C. Lind et al.   HUMAN IMMUNOLOGY

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Nanopore Sequencing: Electrical Measurements of the Code of Life

(2010) Winston Timp et al.   IEEE TRANSACTIONS ON NANOTECHNOLOGY

BIPES, a cost-effective high-throughput method for assessing microbial diversity

(2010) Hong-Wei Zhou et al.   ISME Journal

Next Generation Molecular Ecology

(2010) DIETHARD TAUTZ et al.   MOLECULAR ECOLOGY

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

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

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

Reference-Free Validation of Short Read Data

(2010) Jan Schröder et al.   PLoS One

Deep Sequencing of the Vaginal Microbiota of Women with HIV

(2010) Ruben Hummelen et al.   PLoS One

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions

(2010) Adrian C. Newton et al.   TRENDS IN MICROBIOLOGY

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

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

(2010) Andrew Adey et al.   GENOME BIOLOGY

Next-Generation Sequencing: From Basic Research to Diagnostics

(2009) K. V. Voelkerding et al.   CLINICAL CHEMISTRY

Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach

(2009) Erica Lumini et al.   ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

(2009) W. Zhang et al.   MICROBIOLOGY-SGM

Complete Genome Sequence of Citrus Huanglongbing Bacterium, ‘CandidatusLiberibacter asiaticus’ Obtained Through Metagenomics

(2009) Yongping Duan et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

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

An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota

(2009) D. V. Badri et al.   PLANT PHYSIOLOGY

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

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

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

(2009) Gabriella Rozera et al.   Retrovirology

Perspectives and Challenges of Emerging Single-Molecule DNA Sequencing Technologies

(2009) Mingsheng Xu et al.   Small

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

(2008) Jean-Marc Aury et al.   BMC GENOMICS

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

(2008) J. A. Reinhardt et al.   GENOME RESEARCH

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

(2008) Yaniv Erlich et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

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

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

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