Next-generation sequencing technologies and their impact on microbial genomics

Changes in the intestinal microbiota from adulthood through to old age

(2012) P.W. O'Toole   CLINICAL MICROBIOLOGY AND INFECTION

Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa

(2012) María Gómez-Lozano et al.   ENVIRONMENTAL MICROBIOLOGY

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

(2012) Jennifer L Bowen et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

(2012) Elizabeth G. Wilbanks et al.   NUCLEIC ACIDS RESEARCH

Genome Sequence and Transcriptome Analysis of the Radioresistant Bacterium Deinococcus gobiensis: Insights into the Extreme Environmental Adaptations

(2012) Menglong Yuan et al.   PLoS One

RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

(2012) Ranjit Kumar et al.   PLoS One

Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition

(2012) Ellen Li et al.   PLoS One

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

(2012) Kjersti Aagaard et al.   PLoS One

Novel Bacterial Taxa in the Human Microbiome

(2012) Kristine M. Wylie et al.   PLoS One

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein

(2012) Benjamin Blasco et al.   PLoS Pathogens

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq

(2011) Yi Wang et al.   BMC GENOMICS

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

(2011) Wim Crielaard et al.   BMC Medical Genomics

RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression

(2011) Anjali Mandlik et al.   Cell Host & Microbe

Outcome of carbapenem resistant Klebsiella pneumoniae bloodstream infections

(2011) D. Ben-David et al.   CLINICAL MICROBIOLOGY AND INFECTION

Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil

(2011) Xiangyu Deng et al.   FOOD MICROBIOLOGY

Review Application of RNA-seq to reveal the transcript profile in bacteria

(2011) A.C. Pinto et al.   GENETICS AND MOLECULAR RESEARCH

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

(2011) A. D. Kostic et al.   GENOME RESEARCH

An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota

(2011) Ian B Jeffery et al.   GUT

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

An Extracytoplasmic Function Sigma Factor-Mediated Cell Surface Signaling System in Pseudomonas syringae pv. tomato DC3000 Regulates Gene Expression in Response to Heterologous Siderophores

(2011) E. Markel et al.   JOURNAL OF BACTERIOLOGY

Characterization of the Fur Regulon in Pseudomonas syringae pv. tomato DC3000

(2011) B. G. Butcher et al.   JOURNAL OF BACTERIOLOGY

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study

(2011) Louise Teixeira Cerdeira et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts

(2011) Brian M Forde et al.   Microbial Cell Factories

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation

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

Helicobacter pylori genome evolution during human infection

(2011) L. Kennemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Skin microbiome: genomics-based insights into the diversity and role of skin microbes

(2011) Heidi H. Kong   TRENDS IN MOLECULAR MEDICINE

Bacterial Antisense RNAs: How Many Are There, and What Are They Doing?

(2010) Maureen Kiley Thomason et al.   Annual Review of Genetics

Assembly of large genomes using second-generation sequencing

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

A window into third-generation sequencing

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

An antisense RNA that governs the expression kinetics of a multifunctional virulence gene

(2010) Eun-Jin Lee et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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 Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing

(2010) Peter E. Chen et al.   PLoS One

Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

(2010) Matt J. Cahill 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

Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays

(2010) Roland J. Siezen et al.   Microbial Biotechnology

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Structure and Complexity of a Bacterial Transcriptome

(2009) K. D. Passalacqua et al.   JOURNAL OF BACTERIOLOGY

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Prevalence of transcription promoters within archaeal operons and coding sequences

(2009) Tie Koide et al.   Molecular Systems Biology

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

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

(2009) Nikos C Kyrpides   NATURE BIOTECHNOLOGY

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

(2009) Marcus J. Claesson et al.   PLoS One

Ecology of the rare microbial biosphere of the Arctic Ocean

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

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Next-Generation DNA Sequencing Methods

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

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

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

Helicobacter pylori and Esophageal Cancer Risk: A Meta-analysis

(2008) F. Islami et al.   Cancer Prevention Research

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

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

A diversity profile of the human skin microbiota

(2008) E. A. Grice et al.   GENOME RESEARCH

Small Toxic Proteins and the Antisense RNAs That Repress Them

(2008) E. M. Fozo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Genome-scale analyses of health-promoting bacteria: probiogenomics

(2008) Marco Ventura et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions

(2008) Zhan Gao et al.   PLoS One

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS

Time to remove the model organism blinkers

(2008) Julian Parkhill   TRENDS IN MICROBIOLOGY

Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation

(2007) Philippe Collas   Frontiers in Bioscience-Landmark

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH