A Primer on Metagenomics

Effects of Experimental Choices and Analysis Noise on Surveys of the "Rare Biosphere"

(2009) T. J. Hamp et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

Genome sequence data: management, storage, and visualization

(2009) Jacqueline Batley et al.   BIOTECHNIQUES

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

(2009) Katharina J Hoff et al.   BMC BIOINFORMATICS

Methods for comparative metagenomics

(2009) Daniel H Huson et al.   BMC BIOINFORMATICS

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

(2009) Weizhong Li   BMC BIOINFORMATICS

A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment

(2009) Shani Tzahor et al.   BMC GENOMICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Planning the Human Variome Project: The Spain report

(2009) Jim Kaput et al.   HUMAN MUTATION

Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

(2009) Jennifer M. Brulc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Managing and Analyzing Next-Generation Sequence Data

(2009) Brent G. Richter et al.   PLoS Computational Biology

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

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

MetaMine - A tool to detect and analyse gene patterns in their environmental context

(2008) Uta Bohnebeck et al.   BMC BIOINFORMATICS

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

(2008) Shibu Yooseph et al.   BMC 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

Scratching the surface of the rare biosphere with ribosomal sequence tag primers

(2008) Josh D. Neufeld et al.   FEMS MICROBIOLOGY LETTERS

The new paradigm of flow cell sequencing

(2008) R. A. Holt et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Species richness in soil bacterial communities: A proposed approach to overcome sample size bias

(2008) Noha H. Youssef et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

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

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

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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

Biological roles of specific peptides in enzymes

(2008) Yasmine Meroz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Short read fragment assembly of bacterial genomes

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