Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
Published 2014 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
Authors
Keywords
-
Journal
PLoS One
Volume 9, Issue 8, Pages e105776
Publisher
Public Library of Science (PLoS)
Online
2014-08-23
DOI
10.1371/journal.pone.0105776
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
- (2013) C. S. Oehmen et al. BIOINFORMATICS
- Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities
- (2013) Sharon Greenblum et al. CURRENT OPINION IN BIOTECHNOLOGY
- Insights into the phylogeny and coding potential of microbial dark matter
- (2013) Christian Rinke et al. NATURE
- Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
- (2013) Mads Albertsen et al. NATURE BIOTECHNOLOGY
- Functional and evolutionary implications of gene orthology
- (2013) Toni Gabaldón et al. NATURE REVIEWS GENETICS
- Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups
- (2013) Dongying Wu et al. PLoS One
- Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
- (2013) R. Levy et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
- (2013) Rogan Carr et al. PLoS Computational Biology
- MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
- (2013) Todd J Treangen et al. GENOME BIOLOGY
- The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
- (2012) Andreas Wilke et al. BMC BIOINFORMATICS
- Ultrafast clustering algorithms for metagenomic sequence analysis
- (2012) W. Li et al. BRIEFINGS IN BIOINFORMATICS
- 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
- 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
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
- (2012) Jens Roat Kultima et al. PLoS One
- Bioinformatics for the Human Microbiome Project
- (2012) Dirk Gevers 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
- Integrative analysis of environmental sequences using MEGAN4
- (2011) D. H. Huson et al. GENOME RESEARCH
- eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
- (2011) S. Powell et al. NUCLEIC ACIDS RESEARCH
- Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
- (2011) David R. Kelley et al. NUCLEIC ACIDS RESEARCH
- IMG: the integrated microbial genomes database and comparative analysis system
- (2011) V. M. Markowitz 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
- KEGG for integration and interpretation of large-scale molecular data sets
- (2011) M. Kanehisa et al. NUCLEIC ACIDS RESEARCH
- The Pfam protein families database
- (2011) M. Punta et al. NUCLEIC ACIDS RESEARCH
- Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees
- (2011) Dongying Wu et al. PLoS One
- Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
- (2011) S. Greenblum et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
- (2010) Jesse R. Zaneveld et al. NUCLEIC ACIDS RESEARCH
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- PyNAST: a flexible tool for aligning sequences to a template alignment
- (2009) J. G. Caporaso et al. BIOINFORMATICS
- A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
- (2009) Dongying Wu et al. NATURE
- 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
- Improved base calling for the Illumina Genome Analyzer using machine learning strategies
- (2009) Martin Kircher et al. GENOME BIOLOGY
- Metagenomics: Read Length Matters
- (2008) K. E. Wommack et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Annotation of metagenome short reads using proxygenes
- (2008) D. Dalevi 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
- A core gut microbiome in obese and lean twins
- (2008) Peter J. Turnbaugh et al. NATURE
- Evolution of Mammals and Their Gut Microbes
- (2008) R. E. Ley et al. SCIENCE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More