4.6 Article

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

Yuzhen Ye et al.

BIOINFORMATICS (2016)

Article Geochemistry & Geophysics

Variations in microbial carbon sources and cycling in the deep continental subsurface

Danielle N. Simkus et al.

GEOCHIMICA ET COSMOCHIMICA ACTA (2016)

Article Multidisciplinary Sciences

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

Maggie C. Y. Lau et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Biotechnology & Applied Microbiology

A survey of best practices for RNA-seq data analysis

Ana Conesa et al.

GENOME BIOLOGY (2016)

Article Biotechnology & Applied Microbiology

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

Shaman Narayanasamy et al.

GENOME BIOLOGY (2016)

Article Biochemical Research Methods

Reconstructing 16S rRNA genes in metagenomic data

Cheng Yuan et al.

BIOINFORMATICS (2015)

Article Ecology

An active atmospheric methane sink in high Arctic mineral cryosols

M. C. Y. Lau et al.

ISME JOURNAL (2015)

Article Multidisciplinary Sciences

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

Jenni Hultman et al.

NATURE (2015)

Article Multidisciplinary Sciences

Microbial community transcriptional networks are conserved in three domains at ocean basin scales

Frank O. Aylward et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biotechnology & Applied Microbiology

De novo assembly of bacterial transcriptomes from RNA-seq data

Brian Tjaden

GENOME BIOLOGY (2015)

Article Microbiology

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA

Magdalena R. Osburn et al.

FRONTIERS IN MICROBIOLOGY (2014)

Article Genetics & Heredity

tRNADB-CE: tRNA gene database well-timed in the era of big sequence data

Takashi Abe et al.

Frontiers in Genetics (2014)

Article Biotechnology & Applied Microbiology

Evaluation of de novo transcriptome assemblies from RNA-Seq data

Bo Li et al.

GENOME BIOLOGY (2014)

Article Ecology

Sizing up metatranscriptomics

Mary Ann Moran et al.

ISME JOURNAL (2013)

Article Multidisciplinary Sciences

Insights into the phylogeny and coding potential of microbial dark matter

Christian Rinke et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

Christopher S. Miller et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Cindy J. Castelle et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Marcel H. Schulz et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization

Xingpeng Jiang et al.

PLOS ONE (2012)

Review Plant Sciences

RNA-seq assembly - are we there yet?

Simon Schliesky et al.

FRONTIERS IN PLANT SCIENCE (2012)

Article Biochemical Research Methods

UCHIME improves sensitivity and speed of chimera detection

Robert C. Edgar et al.

BIOINFORMATICS (2011)

Article Environmental Sciences

Diversity of sulfate-reducing bacteria in a plant using deep geothermal energy

Mashal Alawi et al.

GRUNDWASSER (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Review Biochemical Research Methods

Computational methods for transcriptome annotation and quantification using RNA-seq

Manuel Garber et al.

NATURE METHODS (2011)

Review Genetics & Heredity

Next-generation transcriptome assembly

Jeffrey A. Martin et al.

NATURE REVIEWS GENETICS (2011)

Article Biochemistry & Molecular Biology

tRNADB-CE 2011: tRNA gene database curated manually by experts

Takashi Abe et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biotechnology & Applied Microbiology

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Christopher S. Miller et al.

GENOME BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities

Frank J. Stewart et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

De novo assembly and analysis of RNA-seq data

Gordon Robertson et al.

NATURE METHODS (2010)

Article Biochemistry & Molecular Biology

ABySS: A parallel assembler for short read sequence data

Jared T. Simpson et al.

GENOME RESEARCH (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

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

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

Article Multidisciplinary Sciences

Environmental genomics reveals a single-species ecosystem deep within earth

Dylan Chivian et al.

SCIENCE (2008)

Article Environmental Sciences

The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa

T. M. Gihring et al.

GEOMICROBIOLOGY JOURNAL (2006)

Article Multidisciplinary Sciences

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

JA Bernstein et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

5S ribosomal RNA database

M Szymanski et al.

NUCLEIC ACIDS RESEARCH (2002)