Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
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Title
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective
Authors
Keywords
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Journal
BRIEFINGS IN BIOINFORMATICS
Volume 13, Issue 6, Pages 728-742
Publisher
Oxford University Press (OUP)
Online
2012-09-11
DOI
10.1093/bib/bbs039
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Note: Only part of the references are listed.- A de novo metagenomic assembly program for shotgun DNA reads
- (2012) Binbin Lai et al. BIOINFORMATICS
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- (2012) Chengwei Luo et al. PLoS One
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- (2012) Ian Holmes et al. PLoS One
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- (2012) Manuel Martinez-Garcia et al. PLoS One
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- (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
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- (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
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- (2011) Wolfgang Gerlach et al. NUCLEIC ACIDS RESEARCH
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- (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
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- 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!
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- Metagenomic Analyses: Past and Future Trends
- (2010) Carola Simon et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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- (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
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- (2010) Donovan H. Parks et al. BIOINFORMATICS
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- (2010) David Goudenege et al. BMC MICROBIOLOGY
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- (2010) Susan M. Huse et al. ENVIRONMENTAL MICROBIOLOGY
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- (2009) Katharina J Hoff et al. BMC BIOINFORMATICS
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- MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes
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- 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
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- A Bioinformatician's Guide to Metagenomics
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- The minimum information about a genome sequence (MIGS) specification
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- Phylogenetic classification of short environmental DNA fragments
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- 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
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