Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River

Microbial ecological succession during municipal solid waste decomposition

(2018) Bryan F. Staley et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity

(2017) Emma Ransom-Jones et al.   mSphere

Change in microbial community in landfill refuse contaminated with antibiotics facilitates denitrification more than the increase in ARG over long-term

(2017) Dong Wu et al.   Scientific Reports

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0

(2016) Hideto Takami et al.   DNA RESEARCH

Municipal Solid Waste Landfills Harbor Distinct Microbiomes

(2016) Blake W. Stamps et al.   Frontiers in 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

Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing

(2015) Thorsten Köchling et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

An anaerobic dynamic membrane bioreactor (AnDMBR) for landfill leachate treatment: Performance and microbial community identification

(2014) Zhenfang Xie et al.   BIORESOURCE TECHNOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis

(2014) Regina Hoo et al.   PLoS One

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial diversity and dynamics during methane production from municipal solid waste

(2013) Christopher A. Bareither et al.   WASTE MANAGEMENT

Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate

(2013) J. Gabarró et al.   WATER RESEARCH

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

Nitrogen removal through different pathways in an aged refuse bioreactor treating mature landfill leachate

(2012) Bing Xie et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Evaluation method for the potential functionome harbored in the genome and metagenome

(2012) Hideto Takami et al.   BMC GENOMICS

The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters

(2012) James E. McDonald et al.   ENVIRONMENTAL MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Characterization and Phylogenetic Diversity of Carboxymethyl Cellulase Producing Bacillus Species from a Landfill Ecosystem

(2011) Suresh Korpole et al.   INDIAN JOURNAL OF MICROBIOLOGY

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

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

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Polyamine biosynthesis and transport mechanisms are crucial for fitness and pathogenesis of Streptococcus pneumoniae

(2010) P. Shah et al.   MICROBIOLOGY-SGM

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer

(2008) Traian Brad et al.   FEMS MICROBIOLOGY ECOLOGY

A Tripartite Efflux Pump Involved in Gastrointestinal Colonization by Klebsiella pneumoniae Confers a Tolerance Response to Inorganic Acid

(2008) S. Coudeyras et al.   INFECTION AND IMMUNITY