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

A de novo metagenomic assembly program for shotgun DNA reads

(2012) Binbin Lai et al.   BIOINFORMATICS

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

(2012) Chengwei Luo et al.   PLoS One

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

(2012) Manuel Martinez-Garcia et al.   PLoS One

Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use

(2012) M. Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) V. Iverson et al.   SCIENCE

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Joint Analysis of Multiple Metagenomic Samples

(2012) Yael Baran et al.   PLoS Computational Biology

The great screen anomaly—a new frontier in product discovery through functional metagenomics

(2011) David Matthias Ekkers et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio

(2011) H. C. M. Leung et al.   BIOINFORMATICS

Bambus 2: scaffolding metagenomes

(2011) Sergey Koren et al.   BIOINFORMATICS

Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore

(2011) Binquan Luan et al.   BIOPHYSICAL JOURNAL

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Replication, lies and lesser-known truths regarding experimental design in environmental microbiology

(2011) Jay T. Lennon   ENVIRONMENTAL MICROBIOLOGY

The genomic standards consortium: bringing standards to life for microbial ecology

(2011) Pelin Yilmaz et al.   ISME Journal

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo 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

Genovo: De Novo Assembly for Metagenomes

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

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Single-cell genomics

(2011) Tomer Kalisky et al.   NATURE METHODS

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Isaam Saeed 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

The Pfam protein families database

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

CoMet—a web server for comparative functional profiling of metagenomes

(2011) Thomas Lingner et al.   NUCLEIC ACIDS RESEARCH

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

(2011) M. Hess et al.   SCIENCE

TSdb: A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates

(2011) Min Zhao et al.   Science China-Life Sciences

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

The Genomic Standards Consortium

(2011) Dawn Field et al.   PLOS BIOLOGY

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Treephyler: fast taxonomic profiling of metagenomes

(2010) F. Schreiber et al.   BIOINFORMATICS

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

(2010) Johannes Goll et al.   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

(2010) David Goudenege et al.   BMC MICROBIOLOGY

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

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

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database

(2010) Byung H Park et al.   GLYCOBIOLOGY

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

(2010) Marc Weber et al.   ISME Journal

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

(2010) Arantxa Peña et al.   ISME Journal

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

(2010) Yanmei Shi et al.   ISME Journal

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho 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

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

GENETACK: FRAMESHIFT IDENTIFICATION IN PROTEIN-CODING SEQUENCES BY THE VITERBI ALGORITHM

(2010) IVAN ANTONOV et al.   Journal of Bioinformatics and Computational Biology

Gene prediction in metagenomic fragments: A large scale machine learning approach

(2009) Katharina J Hoff et al.   BMC 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

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

(2009) Wolfgang Gerlach et al.   BMC BIOINFORMATICS

Unsupervised statistical clustering of environmental shotgun sequences

(2009) Andrey Kislyuk et al.   BMC BIOINFORMATICS

The effect of sequencing errors on metagenomic gene prediction

(2009) Katharina J Hoff   BMC GENOMICS

Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group

(2009) Anke Meyerdierks et al.   ENVIRONMENTAL MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Orphelia: predicting genes in metagenomic sequencing reads

(2009) Katharina J. Hoff et al.   NUCLEIC ACIDS RESEARCH

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification

(2008) Christian Martin et al.   BIOINFORMATICS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Binning sequences using very sparse labels within a metagenome

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

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

(2008) Patrick D Schloss et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

The rational exploration of microbial diversity

(2008) Christopher Quince et al.   ISME Journal

"Candidatus Cloacamonas Acidaminovorans": Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division

(2008) E. Pelletier et al.   JOURNAL OF BACTERIOLOGY

A Bioinformatician's Guide to Metagenomics

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

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database: recent advances

(2008) M. H. Saier et al.   NUCLEIC ACIDS RESEARCH

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata

(2008) Lynette Hirschman et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML)

(2008) Renzo Kottmann et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing

(2007) Chon-Kit Kenneth Chan et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY