Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
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Title
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
Authors
Keywords
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Journal
Nature Communications
Volume 12, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-03-31
DOI
10.1038/s41467-021-22203-2
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Note: Only part of the references are listed.- Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
- (2021) Krithika Arumugam et al. npj Biofilms and Microbiomes
- Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes
- (2020) Lin Ye et al. Microbiome
- Accurate and complete genomes from metagenomes
- (2020) Lin-Xing Chen et al. GENOME RESEARCH
- MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge
- (2020) Marta Nierychlo et al. WATER RESEARCH
- Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants
- (2020) Marta Nierychlo et al. Frontiers in Microbiology
- Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
- (2020) Morten Simonsen Dueholm et al. mBio
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
- (2019) Edoardo Pasolli et al. CELL
- Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman–FISH
- (2019) Eustace Y. Fernando et al. ISME Journal
- Assembly of long, error-prone reads using repeat graphs
- (2019) Mikhail Kolmogorov et al. NATURE BIOTECHNOLOGY
- Interactive Tree Of Life (iTOL) v4: recent updates and new developments
- (2019) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess
- (2019) Han Gao et al. WATER RESEARCH
- Re-evaluating the microbiology of the enhanced biological phosphorus removal process
- (2019) Per Halkjær Nielsen et al. CURRENT OPINION IN BIOTECHNOLOGY
- Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories
- (2019) Alon Shaiber et al. mBio
- MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
- (2019) Dongwan D. Kang et al. PeerJ
- Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification
- (2019) Florian P Breitwieser et al. BIOINFORMATICS
- Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
- (2019) Robert D. Stewart et al. NATURE BIOTECHNOLOGY
- Common principles and best practices for engineering microbiomes
- (2019) Christopher E. Lawson et al. NATURE REVIEWS MICROBIOLOGY
- GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
- (2019) Pierre-Alain Chaumeil et al. BIOINFORMATICS
- Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies
- (2019) Volkan Sevim et al. Scientific Data
- Minimap2: pairwise alignment for nucleotide sequences
- (2018) Heng Li BIOINFORMATICS
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
- (2018) Cindy J. Castelle et al. CELL
- Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
- (2018) Christian M. K. Sieber et al. Nature Microbiology
- Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution
- (2018) Andrew M. Boddicker et al. ISME Journal
- Distinct Microbial Community Performing Dissimilatory Nitrate Reduction to Ammonium (DNRA) in a High C/NO3− Reactor
- (2018) Pokchat Chutivisut et al. MICROBES AND ENVIRONMENTS
- 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
- Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants
- (2018) Martin H. Andersen et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation
- (2017) Sergey Koren et al. GENOME RESEARCH
- 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
- Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation
- (2017) Norisuke Ushiki et al. JOURNAL OF BIOSCIENCE AND BIOENGINEERING
- 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
- MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups
- (2017) Simon Jon McIlroy et al. Database-The Journal of Biological Databases and Curation
- Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
- (2017) Ryan R. Wick et al. PLoS Computational Biology
- Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
- (2017) Donovan H. Parks et al. Nature Microbiology
- Microbial biotechnology and circular economy in wastewater treatment
- (2017) Per Halkjaer Nielsen Microbial Biotechnology
- MultiQC: summarize analysis results for multiple tools and samples in a single report
- (2016) Philip Ewels et al. BIOINFORMATICS
- Fast and sensitive taxonomic classification for metagenomics with Kaiju
- (2016) Peter Menzel et al. Nature Communications
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.
- (2015) Ryan R. Wick et al. BIOINFORMATICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
- (2015) Ben O Oyserman et al. ISME Journal
- Diverse uncultivated ultra-small bacterial cells in groundwater
- (2015) Birgit Luef et al. Nature Communications
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- Metagenomic characterization of ‘Candidatus Defluviicoccus tetraformis strain TFO71’, a tetrad-forming organism, predominant in an anaerobic-aerobic membrane bioreactor with deteriorated biological phosphorus removal
- (2014) Masaru K. Nobu et al. ENVIRONMENTAL MICROBIOLOGY
- Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems
- (2014) Simon Jon McIlroy et al. ENVIRONMENTAL MICROBIOLOGY
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
- (2014) Xuesong He et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Anticipating the next century of wastewater treatment
- (2014) M. C. M. van Loosdrecht et al. SCIENCE
- ‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity
- (2013) Simon J McIlroy et al. ISME Journal
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
- (2013) Mads Albertsen et al. NATURE BIOTECHNOLOGY
- Using Tablet for visual exploration of second-generation sequencing data
- (2012) I. Milne et al. BRIEFINGS IN BIOINFORMATICS
- Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode
- (2012) Mamoru Oshiki et al. MICROBES AND ENVIRONMENTS
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- Nitrous oxide emissions from wastewater treatment processes
- (2012) Y. Law et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
- (2011) William A. Walters et al. BIOINFORMATICS
- Accelerated Profile HMM Searches
- (2011) Sean R. Eddy PLoS Computational Biology
- mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization
- (2010) L. Safak Yilmaz et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
- (2010) Frederick A Matsen et al. BMC BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- FragGeneScan: predicting genes in short and error-prone reads
- (2010) Mina Rho et al. NUCLEIC ACIDS RESEARCH
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- (2009) P. D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Infernal 1.0: inference of RNA alignments
- (2009) E. P. Nawrocki et al. BIOINFORMATICS
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
- (2009) S. Capella-Gutierrez et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge
- (2008) Fernando Morgan-Sagastume et al. FEMS MICROBIOLOGY ECOLOGY
- PHA-accumulating microorganisms in full-scale wastewater treatment plants
- (2008) Mamoru Oshiki et al. WATER SCIENCE AND TECHNOLOGY
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