4.6 Review

Computational meta'omics for microbial community studies

Related references

Note: Only part of the references are listed.
Article Respiratory System

Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities

Yan Wei Lim et al.

JOURNAL OF CYSTIC FIBROSIS (2013)

Article Biochemical Research Methods

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

Martin Wu et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

GemSIM: general, error-model based simulator of next-generation sequencing data

Kerensa E. McElroy et al.

BMC GENOMICS (2012)

Article Biochemistry & Molecular Biology

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

Aleksandar D. Kostic et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)

Suenje J. Pamp et al.

GENOME RESEARCH (2012)

Article Biochemical Research Methods

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

Yi Wang et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Multidisciplinary Sciences

A framework for human microbiome research

Barbara A. Methe et al.

NATURE (2012)

Article Multidisciplinary Sciences

A metagenome-wide association study of gut microbiota in type 2 diabetes

Junjie Qin et al.

NATURE (2012)

Article Multidisciplinary Sciences

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower et al.

NATURE (2012)

Article Biochemical Research Methods

Predicting bacterial community assemblages using an artificial neural network approach

Peter E. Larsen et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Metagenomic microbial community profiling using unique clade-specific marker genes

Nicola Segata et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Microbiology

Genomic sequencing of uncultured microorganisms from single cells

Roger S. Lasken

NATURE REVIEWS MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Sean Powell et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

IMG/M: the integrated metagenome data management and comparative analysis system

Victor M. Markowitz et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

IMG: the integrated microbial genomes database and comparative analysis system

Victor M. Markowitz et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Kim D. Pruitt et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

The Pfam protein families database

Marco Punta et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

Toshiaki Namiki et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

Daniel R. Mende et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

Kaustubh Raosaheb Patil et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

The Most Wanted'' Taxa from the Human Microbiome for Whole Genome Sequencing

Anthony A. Fodor et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

Jens Roat Kultima et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Jason Pell et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Decade-long bacterial community dynamics in cystic fibrosis airways

Jiangchao Zhao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

Kevin J. Forsberg et al.

SCIENCE (2012)

Review Multidisciplinary Sciences

Interactions Between the Microbiota and the Immune System

Lora V. Hooper et al.

SCIENCE (2012)

Article Multidisciplinary Sciences

Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota

Nobuhiko Kamada et al.

SCIENCE (2012)

Article Cell Biology

Temporal Dynamics of the Human Vaginal Microbiota

Pawel Gajer et al.

SCIENCE TRANSLATIONAL MEDICINE (2012)

Article Biochemical Research Methods

Microbial Co-occurrence Relationships in the Human Microbiome

Karoline Faust et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota

Vanni Bucci et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Sahar Abubucker et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Inferring Correlation Networks from Genomic Survey Data

Jonathan Friedman et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS

Todd J Treangen et al.

GENOME BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

Serena Dollive et al.

GENOME BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Xochitl C. Morgan et al.

GENOME BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

Andrea K. Bartram et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biochemical Research Methods

MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks

Fabio Gori et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

SPHINX-an algorithm for taxonomic binning of metagenomic sequences

Monzoorul Haque Mohammed et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

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

Gail L. Rosen et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

MetaABC-an integrated metagenomics platform for data adjustment, binning and clustering

Chien-Hao Su et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Meta-IDBA: a de Novo assembler for metagenomic data

Yu Peng et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Aligning short reads to reference alignments and trees

Simon A. Berger et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Classifying short genomic fragments from novel lineages using composition and homology

Donovan H. Parks et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

Suparna Mitra et al.

BMC BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

Monzoorul Haque Mohammed et al.

BMC GENOMICS (2011)

Article Biotechnology & Applied Microbiology

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Bo Liu et al.

BMC GENOMICS (2011)

Review Microbiology

A chemical arms race at sea mediates algal host-virus interactions

Kay D. Bidle et al.

CURRENT OPINION IN MICROBIOLOGY (2011)

Article Biochemical Research Methods

Genovo: De Novo Assembly for Metagenomes

Jonathan Laserson et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

Jeroen Raes et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Multidisciplinary Sciences

Ecology drives a global network of gene exchange connecting the human microbiome

Chris S. Smillie et al.

NATURE (2011)

Article Multidisciplinary Sciences

Human nutrition, the gut microbiome and the immune system

Andrew L. Kau et al.

NATURE (2011)

Article Genetics & Heredity

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

Tami D. Lieberman et al.

NATURE GENETICS (2011)

Letter Biochemical Research Methods

Taxonomic metagenome sequence assignment with structured output models

Kaustubh R. Patil et al.

NATURE METHODS (2011)

Letter Biochemical Research Methods

PhymmBL expanded: confidence scores, custom databases, parallelization and more

Arthur Brady et al.

NATURE METHODS (2011)

Article Biochemical Research Methods

Bayesian community-wide culture-independent microbial source tracking

Dan Knights et al.

NATURE METHODS (2011)

Article Biochemistry & Molecular Biology

Taxonomic classification of metagenomic shotgun sequences with CARMA3

Wolfgang Gerlach et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

Maria Jose Gosalbes et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

Miguel Pignatelli et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

Les Dethlefsen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Succession of microbial consortia in the developing infant gut microbiome

Jeremy E. Koenig et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

Andrew L. Goodman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

Jeremiah J. Faith et al.

SCIENCE (2011)

Article Multidisciplinary Sciences

Rapid Pneumococcal Evolution in Response to Clinical Interventions

Nicholas J. Croucher et al.

SCIENCE (2011)

Article Multidisciplinary Sciences

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

Matthias Hess et al.

SCIENCE (2011)

Article Genetics & Heredity

ClaMS: A Classifier for Metagenomic Sequences

Amrita Pati et al.

STANDARDS IN GENOMIC SCIENCES (2011)

Review Genetics & Heredity

Gut microbiome-host interactions in health and disease

James M. Kinross et al.

GENOME MEDICINE (2011)

Article Biotechnology & Applied Microbiology

Metagenomic biomarker discovery and explanation

Nicola Segata et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences

Matthew Horton et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Treephyler: fast taxonomic profiling of metagenomes

Fabian Schreiber et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

SmashCell: a software framework for the analysis of single-cell amplified genome sequences

Eoghan D. Harrington et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

SmashCommunity: a metagenomic annotation and analysis tool

Manimozhiyan Arumugam et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics

Johannes Goll et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Fast and accurate long-read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Identifying biologically relevant differences between metagenomic communities

Donovan H. Parks et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biochemical Research Methods

DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

Tarini Shankar Ghosh et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

De novo assembly of human genomes with massively parallel short read sequencing

Ruiqiang Li et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

A global network of coexisting microbes from environmental and whole-genome sequence data

Samuel Chaffron et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

Jan-Hendrik Hehemann et al.

NATURE (2010)

Article Multidisciplinary Sciences

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin et al.

NATURE (2010)

Article Multidisciplinary Sciences

One Bacterial Cell, One Complete Genome

Tanja Woyke et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

Jay McCarren et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

Peter J. Turnbaugh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Maria G. Dominguez-Bello et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

High Frequency of Horizontal Gene Transfer in the Oceans

Lauren D. McDaniel et al.

SCIENCE (2010)

Article Multidisciplinary Sciences

A Catalog of Reference Genomes from the Human Microbiome

Karen E. Nelson et al.

SCIENCE (2010)

Article Biochemical Research Methods

Environments that Induce Synthetic Microbial Ecosystems

Niels Klitgord et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biochemical Research Methods

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

Monzoorul M. Haque et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Erik Kristiansson et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

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

Naryttza N. Diaz et al.

BMC BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Ivaylo I. Ivanov et al.

Article Ecology

Shotgun metaproteomics of the human distal gut microbiota

Nathan C. Verberkmoes et al.

ISME JOURNAL (2009)

Article Ecology

What is microbial community ecology?

Allan Konopka

ISME JOURNAL (2009)

Article Multidisciplinary Sciences

A core gut microbiome in obese and lean twins

Peter J. Turnbaugh et al.

NATURE (2009)

Article Multidisciplinary Sciences

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Dongying Wu et al.

NATURE (2009)

Article Multidisciplinary Sciences

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

Yanmei Shi et al.

NATURE (2009)

Article Multidisciplinary Sciences

Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation

Tsuneo Hakoyama et al.

NATURE (2009)

Article Multidisciplinary Sciences

Assembling the Marine Metagenome, One Cell at a Time

Tanja Woyke et al.

PLOS ONE (2009)

Article Multidisciplinary Sciences

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

Janet Jansson et al.

PLOS ONE (2009)

Article Multidisciplinary Sciences

Phage-Mediated Intergeneric Transfer of Toxin Genes

John Chen et al.

SCIENCE (2009)

Article Cell Biology

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

Peter J. Turnbaugh et al.

SCIENCE TRANSLATIONAL MEDICINE (2009)

Article Biochemical Research Methods

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

James Robert White et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Mathematical & Computational Biology

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

YUZHEN YE et al.

Journal of Bioinformatics and Computational Biology (2009)

Review Genetics & Heredity

Genomics and Evolution of Heritable Bacterial Symbionts

Nancy A. Moran et al.

ANNUAL REVIEW OF GENETICS (2008)

Article Biochemistry & Molecular Biology

An invitation to the marriage of metagenomics and metabolomics

Peter J. Turnbaugh et al.

Review Microbiology

A renaissance for the pioneering 16S rRNA gene

Susannah G. Tringe et al.

CURRENT OPINION IN MICROBIOLOGY (2008)

Review Microbiology

Worlds within worlds: evolution of the vertebrate gut microbiota

Ruth E. Ley et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Article Multidisciplinary Sciences

MetaSim-A Sequencing Simulator for Genomics and Metagenomics

Daniel C. Richter et al.

PLOS ONE (2008)

Article Multidisciplinary Sciences

Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells

Marios Giannakis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Microbial community gene expression in ocean surface waters

Jorge. Frias-Lopez et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Symbiotic gut microbes modulate human metabolic phenotypes

Min Li et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Genetics & Heredity

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

Susan M. Huse et al.

PLOS GENETICS (2008)

Article Multidisciplinary Sciences

Dissecting biological dark matter with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

Yann Marcy et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biotechnology & Applied Microbiology

Specific single-cell isolation and genomic amplification of uncultured microorganisms

Thomas Kvist et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2007)

Article Biochemistry & Molecular Biology

MEGAN analysis of metagenomic data

Daniel H. Huson et al.

GENOME RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Evolution of the core and pan-genome of Strepococcus: positive selection, recombination, and genome composition

Tristan Lefebure et al.

GENOME BIOLOGY (2007)

Article Biochemistry & Molecular Biology

metaSHARK: a WWW platform for interactive exploration of metabolic networks

Christopher Hyland et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

Metagenomic analysis of coastal RNA virus communities

Alexander I. Culley et al.

SCIENCE (2006)

Article Multidisciplinary Sciences

Toward automatic reconstruction of a highly resolved tree of life

FD Ciccarelli et al.

SCIENCE (2006)

Review Biochemistry & Molecular Biology

Metaproteomics: studying functional gene expression in microbial ecosystems

P Wilmes et al.

TRENDS IN MICROBIOLOGY (2006)

Article Biochemistry & Molecular Biology

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

R Overbeek et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Evolutionary Biology

Environmental diversity of Bacteria and Archaea

EE DeLong et al.

SYSTEMATIC BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Functional discovery via a compendium of expression profiles

TR Hughes et al.

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)