Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

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

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

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

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

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

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

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

Novel Bacterial Taxa in the Human Microbiome

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

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization

(2012) Xingpeng Jiang et al.   PLoS One

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

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

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

(2012) S. L. Jorgensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems

(2012) L. A. Levin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Seasonality in Ocean Microbial Communities

(2012) S. J. Giovannoni et al.   SCIENCE

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Virtual metagenome reconstruction from 16S rRNA gene sequences

(2012) Shujiro Okuda et al.   Nature Communications

Joint Analysis of Multiple Metagenomic Samples

(2012) Yael Baran et al.   PLoS Computational Biology

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust 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

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

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

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

(2012) ZEEHASHAM RASHEED et al.   Journal of Bioinformatics and Computational Biology

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson 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

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

(2011) Yu-Wei Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

(2011) Xingpeng Jiang et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

(2011) Isaam Saeed et al.   NUCLEIC ACIDS RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

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

KEGG for integration and interpretation of large-scale molecular data sets

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

Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life

(2011) E. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

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

(2010) Fabio Gori et al.   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS

Vaginal microbiome of reproductive-age women

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

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Unsupervised statistical clustering of environmental shotgun sequences

(2009) Andrey Kislyuk et al.   BMC BIOINFORMATICS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Binning sequences using very sparse labels within a metagenome

(2008) Chon-Kit Chan et al.   BMC BIOINFORMATICS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology