Computational meta'omics for microbial community studies

Intestinal Microbiota Containing Barnesiella Species Cures Vancomycin-Resistant Enterococcus faecium Colonization

(2013) Carles Ubeda et al.   INFECTION AND IMMUNITY

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

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

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

(2012) C. Lozupone et al.   GENOME RESEARCH

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

(2012) Sünje J. Pamp et al.   GENOME RESEARCH

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason 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

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

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

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

(2012) Yan Wei Lim et al.   Journal of Cystic Fibrosis

A framework for human microbiome research

(2012)   NATURE

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Predicting bacterial community assemblages using an artificial neural network approach

(2012) Peter E Larsen et al.   NATURE METHODS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   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

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

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

(2012) Chengwei Luo et al.   PLoS One

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

(2012) Kaustubh Raosaheb Patil et al.   PLoS One

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

(2012) Anthony A. Fodor et al.   PLoS One

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decade-long bacterial community dynamics in cystic fibrosis airways

(2012) J. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

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

(2012) N. Kamada et al.   SCIENCE

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

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

(2012) Vanni Bucci et al.   PLoS Computational Biology

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS

(2012) Todd J Treangen et al.   GENOME BIOLOGY

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

(2012) Serena Dollive et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

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

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2011) Chien-Hao Su et al.   BIOINFORMATICS

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra et al.   BMC BIOINFORMATICS

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

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

(2011) Monzoorul Mohammed et al.   BMC GENOMICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

The Genome of Th17 Cell-Inducing Segmented Filamentous Bacteria Reveals Extensive Auxotrophy and Adaptations to the Intestinal Environment

(2011) Andrew Sczesnak et al.   Cell Host & Microbe

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

(2011) Kay D Bidle et al.   CURRENT OPINION IN MICROBIOLOGY

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

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

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Genovo: De Novo Assembly for Metagenomes

(2011) Jonathan Laserson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2011) J. Raes et al.   Molecular Systems Biology

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

(2011) Chris S. Smillie et al.   NATURE

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

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

(2011) Arthur Brady et al.   NATURE METHODS

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

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

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

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

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

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

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

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

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

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

(2011) Miguel Pignatelli et al.   PLoS One

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface

(2011) Xiaoxiao Li et al.   PLoS One

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

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

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

(2011) J. J. Faith et al.   SCIENCE

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

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

(2011) M. Hess et al.   SCIENCE

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

The secret languages of coevolved symbioses: Insights from the Euprymna scolopes–Vibrio fischeri symbiosis

(2011) Margaret McFall-Ngai et al.   SEMINARS IN IMMUNOLOGY

ClaMS: A Classifier for Metagenomic Sequences

(2011) Amrita Pati et al.   Standards in Genomic Sciences

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

(2010) Fabio Gori et al.   BIOINFORMATICS

Treephyler: fast taxonomic profiling of metagenomes

(2010) F. Schreiber et al.   BIOINFORMATICS

SmashCell: a software framework for the analysis of single-cell amplified genome sequences: Fig. 1.

(2010) Eoghan D. Harrington et al.   BIOINFORMATICS

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

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

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

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

(2010) Johannes Goll et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

(2010) Lucie Bittner et al.   Biology Direct

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

(2010) Tarini Ghosh et al.   BMC BIOINFORMATICS

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

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

(2010) S. Chaffron et al.   GENOME RESEARCH

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

(2010) Marc Weber et al.   ISME Journal

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

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

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

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

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

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

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

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

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

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

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

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

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

(2009) Matthew Horton et al.   BIOINFORMATICS

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

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

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

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

(2009) Weizhong Li   BMC BIOINFORMATICS

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

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

(2009) R. Li et al.   GENOME RESEARCH

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

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

(2009) Yanmei Shi et al.   NATURE

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

(2009) Tsuneo Hakoyama et al.   NATURE

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

Phage-Mediated Intergeneric Transfer of Toxin Genes

(2009) J. Chen et al.   SCIENCE

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

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

(2009) YUZHEN YE et al.   Journal of Bioinformatics and Computational Biology

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

A renaissance for the pioneering 16S rRNA gene

(2008) Susannah G Tringe et al.   CURRENT OPINION IN MICROBIOLOGY

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

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

(2008) M. Giannakis 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

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics