DRAM for distilling microbial metabolism to automate the curation of microbiome function
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Title
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Authors
Keywords
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Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-07-23
DOI
10.1093/nar/gkaa621
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Note: Only part of the references are listed.- Clades of huge phages from across Earth’s ecosystems
- (2020) Basem Al-Shayeb et al. NATURE
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- (2020) Hiroyuki Imachi et al. NATURE
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- (2019) Edoardo Pasolli et al. CELL
- Evolution of Immune Systems From Viruses and Transposable Elements
- (2019) Felix Broecker et al. Frontiers in Microbiology
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- (2019) Carolina M. Mizuno et al. Nature Communications
- Novel insights from uncultivated genomes of the global human gut microbiome
- (2019) Stephen Nayfach et al. NATURE
- A new genomic blueprint of the human gut microbiota
- (2019) Alexandre Almeida et al. NATURE
- Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
- (2019) Ho Bin Jang et al. NATURE BIOTECHNOLOGY
- Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans
- (2019) Abigail J. Johnson et al. Cell Host & Microbe
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- (2019) Evan Bolyen et al. NATURE BIOTECHNOLOGY
- MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
- (2019) Dongwan D. Kang et al. PeerJ
- Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
- (2019) Robert D. Stewart et al. NATURE BIOTECHNOLOGY
- KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold
- (2019) Takuya Aramaki et al. BIOINFORMATICS
- Profiling of Protein Degraders in Cultures of Human Gut Microbiota
- (2019) Alberto Amaretti et al. Frontiers in Microbiology
- An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
- (2019) Xiaoli Dong et al. Frontiers in Genetics
- Salmonella -Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut
- (2018) Jikang Wu et al. INFECTION AND IMMUNITY
- The social network of microorganisms — how auxotrophies shape complex communities
- (2018) Karsten Zengler et al. NATURE REVIEWS MICROBIOLOGY
- dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
- (2018) Han Zhang et al. NUCLEIC ACIDS RESEARCH
- Branched-chain amino acids in health and disease: metabolism, alterations in blood plasma, and as supplements
- (2018) Milan Holeček Nutrition & Metabolism
- The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
- (2018) Benjamin J. Tully et al. Scientific Data
- Stability of the human faecal microbiome in a cohort of adult men
- (2018) Raaj S. Mehta et al. Nature Microbiology
- Host-linked soil viral ecology along a permafrost thaw gradient
- (2018) Joanne B. Emerson et al. Nature Microbiology
- Genome-centric view of carbon processing in thawing permafrost
- (2018) Ben J. Woodcroft et al. NATURE
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
- Development of a gut microbe–targeted nonlethal therapeutic to inhibit thrombosis potential
- (2018) Adam B. Roberts et al. NATURE MEDICINE
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- Minimum Information about an Uncultivated Virus Genome (MIUViG)
- (2018) Simon Roux et al. NATURE BIOTECHNOLOGY
- Dietary metabolism, the gut microbiome, and heart failure
- (2018) W. H. Wilson Tang et al. Nature Reviews Cardiology
- The Pfam protein families database in 2019
- (2018) Sara El-Gebali et al. NUCLEIC ACIDS RESEARCH
- Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland
- (2018) Garrett J. Smith et al. mBio
- Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
- (2018) Lindsey M. Solden et al. Nature Microbiology
- Microbial nitrogen limitation in the mammalian large intestine
- (2018) Aspen T. Reese et al. Nature Microbiology
- Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
- (2018) Rebecca A. Daly et al. Nature Microbiology
- dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
- (2017) Matthew R Olm et al. ISME Journal
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- (2017) Robert M Bowers et al. NATURE BIOTECHNOLOGY
- MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
- (2017) Martin Steinegger et al. NATURE BIOTECHNOLOGY
- Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions
- (2017) Jordan C. Angle et al. Nature Communications
- PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
- (2017) Julian R. Garneau et al. Scientific Reports
- A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data
- (2016) Elizabeth T. Hobbs et al. Algorithms for Molecular Biology
- Viral metabolic reprogramming in marine ecosystems
- (2016) Bonnie L Hurwitz et al. CURRENT OPINION IN MICROBIOLOGY
- RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria
- (2016) Kelly C Wrighton et al. ISME Journal
- Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
- (2016) François Enault et al. ISME Journal
- Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
- (2016) Simon Roux et al. NATURE
- Role of glutamatergic neurotransmission in the enteric nervous system and brain-gut axis in health and disease
- (2016) Viviana Filpa et al. NEUROPHARMACOLOGY
- UniProt: the universal protein knowledgebase
- (2016) NUCLEIC ACIDS RESEARCH
- W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
- (2016) Jana Trifinopoulos et al. NUCLEIC ACIDS RESEARCH
- KEGG: new perspectives on genomes, pathways, diseases and drugs
- (2016) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- Decoupling function and taxonomy in the global ocean microbiome
- (2016) S. Louca et al. SCIENCE
- Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
- (2016) Karthik Anantharaman et al. Nature Communications
- Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
- (2016) Anna Heintz-Buschart et al. Nature Microbiology
- Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales
- (2016) Rebecca A. Daly et al. Nature Microbiology
- A new view of the tree of life
- (2016) Laura A. Hug et al. Nature Microbiology
- Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks
- (2015) John A. Gerlt et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Personalized Nutrition by Prediction of Glycemic Responses
- (2015) David Zeevi et al. CELL
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Complex archaea that bridge the gap between prokaryotes and eukaryotes
- (2015) Anja Spang et al. NATURE
- The Phyre2 web portal for protein modeling, prediction and analysis
- (2015) Lawrence A Kelley et al. Nature Protocols
- Rising to the challenge: accelerated pace of discovery transforms marine virology
- (2015) Jennifer R. Brum et al. NATURE REVIEWS MICROBIOLOGY
- VirSorter: mining viral signal from microbial genomic data
- (2015) Simon Roux et al. PeerJ
- UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
- (2014) B. E. Suzek et al. BIOINFORMATICS
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- Methane dynamics regulated by microbial community response to permafrost thaw
- (2014) Carmody K. McCalley et al. NATURE
- A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase
- (2014) T. Ticak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
- (2013) Kishori M Konwar et al. BMC BIOINFORMATICS
- Genomes from Metagenomics
- (2013) I. Sharon et al. SCIENCE
- Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta
- (2013) H. J. Haiser et al. SCIENCE
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- Diversity, stability and resilience of the human gut microbiota
- (2012) Catherine A. Lozupone et al. NATURE
- Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme
- (2012) S. Craciun et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
- (2012) K. C. Wrighton et al. SCIENCE
- The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
- (2012) Dirk Gevers et al. PLOS BIOLOGY
- Integrative genomics viewer
- (2011) James T Robinson et al. NATURE BIOTECHNOLOGY
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- Pectin – An emerging new bioactive food polysaccharide
- (2011) Ellen G. Maxwell et al. TRENDS IN FOOD SCIENCE & TECHNOLOGY
- PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
- (2010) Nancy Y. Yu et al. BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs
- (2010) Patricia L. Tavormina et al. Environmental Microbiology Reports
- MEROPS: the peptidase database
- (2009) Neil D. Rawlings et al. NUCLEIC ACIDS RESEARCH
- The RAST Server: Rapid Annotations using Subsystems Technology
- (2008) Ramy K Aziz et al. BMC GENOMICS
- MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes
- (2008) H. Noguchi et al. DNA RESEARCH
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