Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

(2021) Caitlin M. Singleton et al.   Nature Communications

Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes

(2020) Lin Ye et al.   Microbiome

Correlation between bacterial community structure and performance efficiency of a full-scale wastewater treatment plant

(2020) Amani A. Al Ali et al.   Journal of Water Process Engineering

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Global diversity and biogeography of bacterial communities in wastewater treatment plants

(2019) Linwei Wu et al.   Nature Microbiology

Use and abuse of correlation analyses in microbial ecology

(2019) Alex Carr et al.   ISME Journal

KEGG Mapper for inferring cellular functions from protein sequences

(2019) Minoru Kanehisa et al.   PROTEIN SCIENCE

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

(2019) Steven J. Robbins et al.   Nature Microbiology

Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study

(2019) Xiaole Yin et al.   ENVIRONMENT INTERNATIONAL

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

High resolution time series reveals cohesive but short-lived communities in coastal plankton

(2018) Antonio M. Martin-Platero et al.   Nature Communications

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems

(2018) Yulin Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

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 dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

(2017) Benjamin J Tully et al.   ISME Journal

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach

(2016) Yuanqing Chao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly

(2016) James S Griffin et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions

(2016) Nataliya M. Shchegolkova et al.   Frontiers in Microbiology

High taxonomic variability despite stable functional structure across microbial communities

(2016) Stilianos Louca et al.   Nature Ecology & Evolution

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Biofilm-specific antibiotic tolerance and resistance

(2015) I. Olsen   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

The activated sludge ecosystem contains a core community of abundant organisms

(2015) Aaron M Saunders et al.   ISME Journal

Microbial Surface Colonization and Biofilm Development in Marine Environments

(2015) Hongyue Dang et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Functionally relevant diversity of closely related Nitrospira in activated sludge

(2014) Christiane Gruber-Dorninger et al.   ISME Journal

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

(2014) Inka Vanwonterghem et al.   ISME Journal

Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant

(2014) Feng Ju et al.   ISME Journal

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants

(2013) Feng Ju et al.   ENVIRONMENTAL MICROBIOLOGY

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

Lake microbial communities are resilient after a whole-ecosystem disturbance

(2012) Ashley Shade et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge

(2012) Ke Yu et al.   PLoS One

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Profiling bulking and foaming bacteria in activated sludge by high throughput sequencing

(2012) Feng Guo et al.   WATER RESEARCH

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

(2011) Li C Xia et al.   BMC Systems Biology

Community assembly: alternative stable states or alternative transient states?

(2011) Tadashi Fukami et al.   ECOLOGY LETTERS

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

(2011) Tong Zhang et al.   ISME Journal

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Inadequately Treated Wastewater as a Source of Human Enteric Viruses in the Environment

(2010) Anthony I. Okoh et al.   International Journal of Environmental Research and Public Health

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea

(2009) George F. Wells et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION