Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater

Evaluation of Monensin Transport to Shallow Groundwater after Irrigation with Dairy Lagoon Water

(2016) Sarah C. Hafner et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Addition of multiple limiting resources reduces grassland diversity

(2016) W. Stanley Harpole et al.   NATURE

Bayesian nitrate source apportionment to individual groundwater wells in the Central Valley by use of elemental and isotopic tracers

(2016) Katherine M. Ransom et al.   WATER RESOURCES RESEARCH

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

(2016) Daan R. Speth et al.   Nature Communications

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

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

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

Fecal Indicator and Pathogenic Bacteria and Their Antibiotic Resistance in Alluvial Groundwater of an Irrigated Agricultural Region with Dairies

(2015) Xunde Li et al.   JOURNAL OF ENVIRONMENTAL QUALITY

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

(2015) Christopher T. Brown et al.   NATURE

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

(2015) Mark B. Smith et al.   mBio

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Evidence for the Cooccurrence of Nitrite-Dependent Anaerobic Ammonium and Methane Oxidation Processes in a Flooded Paddy Field

(2014) Li-dong Shen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Microbial Groundwater Sampling Protocol for Fecal-Rich Environments

(2014) Thomas Harter et al.   Groundwater

Phenazine redox cycling enhances anaerobic survival inPseudomonas aeruginosaby facilitating generation of ATP and a proton-motive force

(2014) Nathaniel R. Glasser et al.   MOLECULAR MICROBIOLOGY

Shotgun metagenomic data reveals significant abundance but low diversity of “Candidatus Scalindua” marine anammox bacteria in the Arabian Sea oxygen minimum zone

(2014) Laura Villanueva et al.   Frontiers in Microbiology

Nitrogen Removal by a Nitritation-Anammox Bioreactor at Low Temperature

(2013) Ziye Hu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Antibiotic-resistant E. coli in surface water and groundwater in dairy operations in Northern California

(2013) Xunde Li et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

Comparative Genomics of Two Independently Enriched “Candidatus Kuenenia Stuttgartiensis” Anammox Bacteria

(2012) Daan R. Speth et al.   Frontiers in Microbiology

Simultaneous Nitrite-Dependent Anaerobic Methane and Ammonium Oxidation Processes

(2011) Francisca A. Luesken et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Molecular mechanism of anaerobic ammonium oxidation

(2011) Boran Kartal et al.   NATURE

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Effects of Groundwater Development on Uranium: Central Valley, California, USA

(2009) Bryant C. Jurgens et al.   Groundwater