Patrick S. G. Chain

Whole-genome-based phylogeny and divergence of the genus Brucella.

Genomics. Genome project standards in a new era of sequencing.

The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.

Genomics for key players in the N cycle from guinea pigs to the next frontier.

Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts.

Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide.

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics.

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia.

Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies.

Genome sequence of Kingella kingae septic arthritis isolate PYKK081.

Complete genome sequence of Francisella philomiragia ATCC 25017.

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.

Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T.

Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2.

Genome sequence of the hepatitis C virus subtype 6n isolated from malaysia.

Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46.

Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360).

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.

Recruiting human microbiome shotgun data to site-specific reference genomes.

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.

Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.

Standards for sequencing viral genomes in the era of high-throughput sequencing.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Draft Genome Assembly of Acinetobacter baumannii ATCC 19606.

Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains.

Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.

Rapid evaluation and quality control of next generation sequencing data with FaQCs.

Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.

Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial).

CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA.

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Building International Genomics Collaboration for Global Health Security.

ADEPT, a dynamic next generation sequencing data error-detection program with trimming.

Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.

Draft Genome Sequence of Sorghum Grain Mold Fungus Epicoccum sorghinum, a Producer of Tenuazonic Acid.

Ten Genome Sequences of Human and Livestock Isolates of from the Country of Georgia.

Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera.

Displays Altered Stress Responses While Enhancing Biofilm Formation by in Mixed-Species Consortium.

Complete Genome Sequences of Historic Clostridioides difficile Food-Dwelling Ribotype 078 Strains in Canada Identical to That of the Historic Human Clinical Strain M120 in the United Kingdom.

Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions.

Bacterial spores, from ecology to biotechnology.

Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in and Resistance to Extreme Conditions.

Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus.

Novel Insights Into the Spread of Enteric Pathogens Using Genomics.

MicroRNA in Pancreatic Cancer: From Biology to Therapeutic Potential.

Advances and Challenges in Metatranscriptomic Analysis.

Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing.

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis.

The National Microbiome Data Collaborative: enabling microbiome science.

Uncovering the Core Microbiome and Distribution of Palmerolide in Across the Anvers Island Archipelago Antarctica.

Roadmap for naming uncultivated Archaea and Bacteria.

Genomic Analysis of Diverse Members of the Fungal Genus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate.

A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays.

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.

The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice.

Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi.

DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli.

Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya.

Epigenetic regulation of gene expression in Shiga toxin-producing : Transcriptomic data.

Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data.

Widespread bacterial diversity within the bacteriome of fungi.

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian.

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes.

Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients.

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing O145:H28.

Advances and Challenges in Fluorescence Hybridization for Visualizing Fungal Endobacteria.

Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain.

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles.

Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns.

Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns.

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.

The Coronavirus Standards Working Group's roadmap for improved population testing.

Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods.

A centralized resource for bacterial-fungal interactions research.

Diversity of fungal microbiome obtained from plant rhizoplanes.

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.

Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi.

Identification of mobile genetic elements with geNomad.

Metabolic versatility of from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes.

Genomic and Phenotypic Characterization of Shiga Toxin-Producing Strains Isolated from Wild Birds in a Major Agricultural Region in California.

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance.

Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between with spp.

The complete genome sequence of probiotic ATCC 9224 isolated from sour milk.

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

Combining compositional data sets introduces error in covariance network reconstruction.

A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics.

Fabricated devices for performing bacterial-fungal interaction experiments across scales.

Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes.

Erratum for Longley et al., "Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes".