Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline
出版年份 2016 全文链接
标题
Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline
作者
关键词
Sequence alignment, Sequence assembly tools, Mammalian genomics, Mice, Sequence databases, RNA sequencing, Taxonomy, Microbial taxonomy
出版物
PLoS One
Volume 11, Issue 1, Pages e0146423
出版商
Public Library of Science (PLoS)
发表日期
2016-01-13
DOI
10.1371/journal.pone.0146423
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation
- (2014) Andrew Toseland et al. BMC GENOMICS
- Saccharide breakdown and fermentation by the honey bee gut microbiome
- (2014) Fredrick J. Lee et al. ENVIRONMENTAL MICROBIOLOGY
- An integrated catalog of reference genes in the human gut microbiome
- (2014) Junhua Li et al. NATURE BIOTECHNOLOGY
- Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation
- (2014) Albi Celaj et al. Microbiome
- Gene expression of lactobacilli in murine forestomach biofilms
- (2014) Clarissa Schwab et al. Microbial Biotechnology
- Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052: genome-wide transcriptional analysis with RNA-Seq
- (2013) Yi Wang et al. Biotechnology for Biofuels
- A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
- (2013) Milkha M Leimena et al. BMC GENOMICS
- Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment
- (2013) Vincent P Richards et al. BMC GENOMICS
- Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
- (2013) Ya Yang et al. BMC GENOMICS
- A multi-omic analysis of an Enterococcus faecium mutant reveals specific genetic mutations and dramatic changes in mRNA and protein expression
- (2013) De Chang et al. BMC MICROBIOLOGY
- IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology
- (2013) Henry C.M. Leung et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
- (2013) Brian J Haas et al. Nature Protocols
- Sequence assembly demystified
- (2013) Niranjan Nagarajan et al. NATURE REVIEWS GENETICS
- Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in Beer
- (2013) Vanessa Pittet et al. PLoS One
- Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies
- (2012) Milkha M. Leimena et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
- (2012) Evguenia Kopylova et al. BIOINFORMATICS
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
- (2012) Jian Ye et al. BMC BIOINFORMATICS
- Dietary protein – its role in satiety, energetics, weight loss and health
- (2012) Margriet S. Westerterp-Plantenga et al. BRITISH JOURNAL OF NUTRITION
- Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
- (2012) C. Lozupone et al. GENOME RESEARCH
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
- (2012) Toshiaki Namiki et al. NUCLEIC ACIDS RESEARCH
- Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing
- (2012) Xuejian Xiong et al. PLoS One
- Dietary Protein Affects Gene Expression and Prevents Lipid Accumulation in the Liver in Mice
- (2012) Jessica Schwarz et al. PLoS One
- SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
- (2012) Ruibang Luo et al. GigaScience
- Quality control and preprocessing of metagenomic datasets
- (2011) R. Schmieder et al. BIOINFORMATICS
- Integrative analysis of environmental sequences using MEGAN4
- (2011) D. H. Huson et al. GENOME RESEARCH
- Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
- (2011) Chris L Dupont et al. ISME Journal
- Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
- (2011) Petr Baldrian et al. ISME Journal
- Enterotypes of the human gut microbiome
- (2011) Manimozhiyan Arumugam et al. NATURE
- iPath2.0: interactive pathway explorer
- (2011) Takuji Yamada et al. NUCLEIC ACIDS RESEARCH
- Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
- (2011) G. D. Wu et al. SCIENCE
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Obesity, Diabetes, and Gut Microbiota: The hygiene hypothesis expanded?
- (2010) G. Musso et al. DIABETES CARE
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- Do nutrient-gut-microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes?
- (2010) M. Diamant et al. Obesity Reviews
- Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
- (2010) P. J. Turnbaugh et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing
- (2009) D. R. Yoder-Himes et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Shifting the genomic gold standard for the prokaryotic species definition
- (2009) Michael Richter et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome
- (2008) Tim Urich et al. PLoS One
- Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
- (2008) Jack A. Gilbert et al. PLoS One
- Microbial community gene expression in ocean surface waters
- (2008) J. Frias-Lopez et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Publish 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 MoreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started