4.5 Article

Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

Le Huang et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Microbiology

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Stephanie A. Eichorst et al.

ENVIRONMENTAL MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

Alexander Crits-Christoph et al.

NATURE (2018)

Article Biochemistry & Molecular Biology

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

A global atlas of the dominant bacteria found in soil

Manuel Delgado-Baquerizo et al.

SCIENCE (2018)

Article Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Christian M. K. Sieber et al.

NATURE MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Genome-centric view of carbon processing in thawing permafrost

Ben J. Woodcroft et al.

NATURE (2018)

Article Multidisciplinary Sciences

Structure and function of the global topsoil microbiome

Mohammad Bahram et al.

NATURE (2018)

Article Biochemical Research Methods

Sipros Ensemble improves database searching and filtering for complex metaproteomics

Xuan Guo et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2017)

Review Microbiology

Embracing the unknown: disentangling the complexities of the soil microbiome

Noah Fierer

NATURE REVIEWS MICROBIOLOGY (2017)

Article Biochemical Research Methods

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

Yu-Wei Wu et al.

BIOINFORMATICS (2016)

Article Biotechnology & Applied Microbiology

Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

Helen Decleyre et al.

BMC GENOMICS (2016)

Article Multidisciplinary Sciences

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Karthik Anantharaman et al.

NATURE COMMUNICATIONS (2016)

Article Microbiology

A new view of the tree of life

Laura A. Hug et al.

NATURE MICROBIOLOGY (2016)

Review Microbiology

Bacterial molybdoenzymes: old enzymes for new purposes

Silke Leimkuehler et al.

FEMS MICROBIOLOGY REVIEWS (2016)

Article Microbiology

XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments

Martin Taubert et al.

ENVIRONMENTAL MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Itai Sharon et al.

GENOME RESEARCH (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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Review Biotechnology & Applied Microbiology

PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference

Jan T. Keltjens et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Binning metagenomic contigs by coverage and composition

Johannes Alneberg et al.

NATURE METHODS (2014)

Article Multidisciplinary Sciences

Tackling soil diversity with the assembly of large, complex metagenomes

Adina Chuang Howe et al.

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

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Review Biotechnology & Applied Microbiology

Microbial carbohydrate esterases deacetylating plant polysaccharides

Peter Biely

BIOTECHNOLOGY ADVANCES (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

Sarah A. Placella et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Geochemistry & Geophysics

Stability of YREE complexes with the trihydroxamate siderophore desferrioxamine B at seawater ionic strength

Emily A. Christenson et al.

GEOCHIMICA ET COSMOCHIMICA ACTA (2011)

Article Biotechnology & Applied Microbiology

Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacteriurn radiotolerans

Yoshihisa Hibi et al.

JOURNAL OF BIOSCIENCE AND BIOENGINEERING (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Quantification of Burkholderia coxL Genes in Hawaiian Volcanic Deposits

C. F. Weber et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

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 Computer Science, Interdisciplinary Applications

Feature Selection with the Boruta Package

Miron B. Kursa et al.

JOURNAL OF STATISTICAL SOFTWARE (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Biochemical Research Methods

Universal sample preparation method for proteome analysis

Jacek R. Wisniewski et al.

NATURE METHODS (2009)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

Species interactions reverse grassland responses to changing climate

K. B. Suttle et al.

SCIENCE (2007)

Review Biochemical Research Methods

Interpretation of shotgun proteomic data - The protein inference problem

AI Nesvizhskii et al.

MOLECULAR & CELLULAR PROTEOMICS (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biotechnology & Applied Microbiology

Large-scale analysis of the yeast proteome by multidimensional protein identification technology

MP Washburn et al.

NATURE BIOTECHNOLOGY (2001)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)