4.7 Article

Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters

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。
Article Microbiology

Flood Season Microbiota from the Amazon Basin Lakes: Analysis with Metagenome Sequencing

Cello Dias Santos Junior et al.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2019)

Article Biotechnology & Applied Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Biotechnology & Applied Microbiology

Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal

Pedro J. Cabello-Yeves et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

A snapshot on prokaryotic diversity of the Solimoes River basin (Amazon, Brazil)

D. Toyama et al.

GENETICS AND MOLECULAR RESEARCH (2017)

Article Ecology

Expression patterns of elemental cycling genes in the Amazon River Plume

Brandon M. Satinsky et al.

ISME JOURNAL (2017)

Review Ecology

Where less may be more: how the rare biosphere pulls ecosystems strings

Alexandre Jousset et al.

ISME JOURNAL (2017)

Article Biotechnology & Applied Microbiology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Robert M. Bowers et al.

NATURE BIOTECHNOLOGY (2017)

Review Environmental Sciences

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

Naofumi Kamimura et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2017)

Article Microbiology

Bacterial Biogeography across the Amazon River-Ocean Continuum

Mary Doherty et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Microbiology

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs

Pedro J. Cabello-Yeves et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Microbiology

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

Pedro J. Cabello-Yeves et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Environmental Sciences

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

Brandon M. Satinsky et al.

FRONTIERS IN MARINE SCIENCE (2017)

Article Environmental Sciences

Carbon Dioxide Emissions along the Lower Amazon River

Henrique O. Sawakuchi et al.

FRONTIERS IN MARINE SCIENCE (2017)

Article Biochemistry & Molecular Biology

The Pfam protein families database: towards a more sustainable future

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biotechnology & Applied Microbiology

Regulation of Polyhydroxybutyrate Synthesis in the Soil Bacterium Bradyrhizobium diazoefficiens

J. I. Quelas et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Inhibition of lignin-derived phenolic compounds to cellulase

Lei Qin et al.

BIOTECHNOLOGY FOR BIOFUELS (2016)

Article Environmental Sciences

The reactivity of plant-derived organic matter and the potential importance of priming effects along the lower Amazon River

Nicholas D. Ward et al.

JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES (2016)

Article Microbiology

Metagenomics Analysis of Microorganisms in Freshwater Lakes of the Amazon Basin

Danyelle Toyama et al.

GENOME ANNOUNCEMENTS (2016)

Article Biochemical Research Methods

Sambamba: fast processing of NGS alignment formats

Artem Tarasov et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Article Biochemistry & Molecular Biology

Microbial species delineation using whole genome sequences

Neha J. Varghese et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

UniProt: a hub for protein information

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biotechnology & Applied Microbiology

Metagenome-assembled genomes uncover a global brackish microbiome

Luisa W. Hugerth et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

The SILVA and All-species Living Tree Project (LTP) taxonomic frameworks

Pelin Yilmaz et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Microspatial gene expression patterns in the Amazon River Plume

Brandon M. Satinsky et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Emilie E. L. Muller et al.

NATURE COMMUNICATIONS (2014)

Article Geosciences, Multidisciplinary

Degradation of terrestrially derived macromolecules in the Amazon River

Nicholas D. Ward et al.

NATURE GEOSCIENCE (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 Biochemistry & Molecular Biology

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

Yanbin Yin et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River

Rohit Ghai et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

The role of terrestrially derived organic carbon in the coastal ocean: A changing paradigm and the priming effect

Thomas S. Bianchi

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

New Abundant Microbial Groups in Aquatic Hypersaline Environments

Rohit Ghai et al.

SCIENTIFIC REPORTS (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL 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 Water Resources

Water and sediment runoff at the Amazon River mouth

V. N. Mikhailov

WATER RESOURCES (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan N. Price et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biotechnology & Applied Microbiology

Community-wide analysis of microbial genome sequence signatures

Gregory J. Dick et al.

GENOME BIOLOGY (2009)

Article Geosciences, Multidisciplinary

Biophysical controls on organic carbon fluxes in fluvial networks

Tom J. Battin et al.

NATURE GEOSCIENCE (2008)

Review Multidisciplinary Sciences

Climate change, deforestation, and the fate of the Amazon

Yadvinder Malhi et al.

SCIENCE (2008)

Article Biochemical Research Methods

Dendroscope: An interactive viewer for large phylogenetic trees

Daniel H. Huson et al.

BMC BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

The periplasmic binding protein of a tripartite tricarboxylate transporter is involved in signal transduction

R Antoine et al.

JOURNAL OF MOLECULAR BIOLOGY (2005)

Article Oceanography

Influence of the Amazon River on the surface optical properties of the western tropical North Atlantic Ocean

R Del Vecchio et al.

JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS (2004)

Article Biochemical Research Methods

The COG database: an updated version includes eukaryotes

RL Tatusov et al.

BMC BIOINFORMATICS (2003)

Review Microbiology

The tripartite tricarboxylate transporter (TTT) family

B Winnen et al.

RESEARCH IN MICROBIOLOGY (2003)