Patrick S. G. Chain

Bioscience Division, Los Alamos National Laboratory

Affiliated withLos Alamos National Laboratory

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 3	2025

Other Publications

Article	Year
Whole-genome-based phylogeny and divergence of the genus Brucella. Journal of bacteriology\| PubMed ID: 19201792	2009
Genomics. Genome project standards in a new era of sequencing. Science (New York, N.Y.)\| PubMed ID: 19815760	2009
The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PloS one\| PubMed ID: 21390229	2011
Genomics for key players in the N cycle from guinea pigs to the next frontier. Methods in enzymology\| PubMed ID: 21514469	2011
Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. Journal of bacteriology\| PubMed ID: 21551308	2011
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature biotechnology\| PubMed ID: 21552244	2011
Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts. Journal of bacteriology\| PubMed ID: 21685287	2011
Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide. Journal of bacteriology\| PubMed ID: 21705610	2011
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current opinion in biotechnology\| PubMed ID: 22154470	2012
Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Briefings in functional genomics\| PubMed ID: 22199376	2011
Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PloS one\| PubMed ID: 22536372	2012
Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases\| PubMed ID: 22551038	2012
Genome sequence of Kingella kingae septic arthritis isolate PYKK081. Journal of bacteriology\| PubMed ID: 22582375	2012
Complete genome sequence of Francisella philomiragia ATCC 25017. Journal of bacteriology\| PubMed ID: 22628499	2012
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME journal\| PubMed ID: 22717885	2012
Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. Journal of bacteriology\| PubMed ID: 23105050	2012
Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2. PloS one\| PubMed ID: 23133618	2012
Genome sequence of the hepatitis C virus subtype 6n isolated from malaysia. Genome announcements\| PubMed ID: 23409272	2013
Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46. Genome announcements\| PubMed ID: 23599293	2013
Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360). Genome announcements\| PubMed ID: 23640195	2013
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature communications\| PubMed ID: 23673639	2013
Recruiting human microbiome shotgun data to site-specific reference genomes. PloS one\| PubMed ID: 24454771	2014
Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one\| PubMed ID: 24743558	2014
Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin. Genome announcements\| PubMed ID: 24855308	2014
Standards for sequencing viral genomes in the era of high-throughput sequencing. mBio\| PubMed ID: 24939889	2014
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS biology\| PubMed ID: 25093819	2014
Draft Genome Assembly of Acinetobacter baumannii ATCC 19606. Genome announcements\| PubMed ID: 25146140	2014
Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains. Genome announcements\| PubMed ID: 25212618	2014
Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Scientific reports\| PubMed ID: 25270300	2014
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. The ISME journal\| PubMed ID: 25361395	2015
Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC bioinformatics\| PubMed ID: 25408143	2014
Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes. Genome announcements\| PubMed ID: 25593267	2015
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic acids research\| PubMed ID: 25765641	2015
Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. PloS one\| PubMed ID: 25794000	2015
Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial). Frontiers in microbiology\| PubMed ID: 26217314	2015
CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA. PloS one\| PubMed ID: 26305456	2015
Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Standards in genomic sciences\| PubMed ID: 26380642	2015
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in microbiology\| PubMed ID: 26583008	2015
Building International Genomics Collaboration for Global Health Security. Frontiers in public health\| PubMed ID: 26697418	2015
ADEPT, a dynamic next generation sequencing data error-detection program with trimming. BMC bioinformatics\| PubMed ID: 26928302	2016
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 Zo... Genome biology and evolution\| PubMed ID: 27289094	2016
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic acids research\| PubMed ID: 27899609	2017
Draft Genome Sequence of Sorghum Grain Mold Fungus Epicoccum sorghinum, a Producer of Tenuazonic Acid. Genome announcements\| PubMed ID: 28126937	2017
Ten Genome Sequences of Human and Livestock Isolates of from the Country of Georgia. Genome announcements\| PubMed ID: 28495766	2017
Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. International journal of systematic and evolutionary microbiology\| PubMed ID: 29111971	2018
Displays Altered Stress Responses While Enhancing Biofilm Formation by in Mixed-Species Consortium. Frontiers in cellular and infection microbiology\| PubMed ID: 29326887	2017
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... Microbiology resource announcements\| PubMed ID: 30533668	2018
Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. Advances in applied microbiology\| PubMed ID: 30798804	2019
Bacterial spores, from ecology to biotechnology. Advances in applied microbiology\| PubMed ID: 30798805	2019
Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in and Resistance to Extreme Conditions. Frontiers in microbiology\| PubMed ID: 30804904	2019
Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 30891596	2020
Novel Insights Into the Spread of Enteric Pathogens Using Genomics. The Journal of infectious diseases\| PubMed ID: 31538189	2020
MicroRNA in Pancreatic Cancer: From Biology to Therapeutic Potential. Genes\| PubMed ID: 31557962	2019
Advances and Challenges in Metatranscriptomic Analysis. Frontiers in genetics\| PubMed ID: 31608125	2019
Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing. The Journal of infectious diseases\| PubMed ID: 31751454	2020
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Scientific reports\| PubMed ID: 32015354	2020
A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis. mSystems\| PubMed ID: 32047060	2020
The National Microbiome Data Collaborative: enabling microbiome science. Nature reviews. Microbiology\| PubMed ID: 32350400
Uncovering the Core Microbiome and Distribution of Palmerolide in Across the Anvers Island Archipelago Antarctica. Marine drugs\| PubMed ID: 32498449	2020
Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology\| PubMed ID: 32514073
Genomic Analysis of Diverse Members of the Fungal Genus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate. G3 (Bethesda, Md.)\| PubMed ID: 32580939	2020
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays. Bioinformatics (Oxford, England)\| PubMed ID: 32777813	2021
Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology\| PubMed ID: 33184503
The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice. Life (Basel, Switzerland)\| PubMed ID: 33374112	2020
Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS microbiology ecology\| PubMed ID: 33440006	2021
DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food microbiology\| PubMed ID: 33494894	2021
Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS neglected tropical diseases\| PubMed ID: 33524010	2021
Epigenetic regulation of gene expression in Shiga toxin-producing : Transcriptomic data. Data in brief\| PubMed ID: 34307800	2021
Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data. Bio-protocol\| PubMed ID: 34595290	2017
Widespread bacterial diversity within the bacteriome of fungi. Communications biology\| PubMed ID: 34621007	2021
Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian. Frontiers in chemistry\| PubMed ID: 35004620	2021
Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes. Frontiers in genetics\| PubMed ID: 35096026	2021
Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients. Human microbiome journal\| PubMed ID: 35506046	2019
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. Bioinformatics (Oxford, England)\| PubMed ID: 35561186	2022
Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing O145:H28. Microorganisms\| PubMed ID: 35630311	2022
Advances and Challenges in Fluorescence Hybridization for Visualizing Fungal Endobacteria. Frontiers in microbiology\| PubMed ID: 35722318	2022
Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain. Microbiology resource announcements\| PubMed ID: 35924938	2022
Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles. Frontiers in microbiology\| PubMed ID: 35935195	2022
Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns. bioRxiv : the preprint server for biology\| PubMed ID: 36032969	2022
Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses\| PubMed ID: 36298683	2022
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. Frontiers in bioinformatics\| PubMed ID: 36303775	2021
The Coronavirus Standards Working Group's roadmap for improved population testing. Nature biotechnology\| PubMed ID: 36323792	2022
Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS global public health\| PubMed ID: 36962439	2022
A centralized resource for bacterial-fungal interactions research. Fungal biology\| PubMed ID: 37142360	2023
Diversity of fungal microbiome obtained from plant rhizoplanes. The Science of the total environment\| PubMed ID: 37295515	2023
The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. Microbiome\| PubMed ID: 37626434	2023
Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Communications biology\| PubMed ID: 37723238	2023
Identification of mobile genetic elements with geNomad. Nature biotechnology\| PubMed ID: 37735266	2024
Metabolic versatility of from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes. Frontiers in microbiology\| PubMed ID: 37799600	2023
Genomic and Phenotypic Characterization of Shiga Toxin-Producing Strains Isolated from Wild Birds in a Major Agricultural Region in California. Microorganisms\| PubMed ID: 38004814	2023
Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. Astrobiology\| PubMed ID: 38079228	2023
Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between with spp. Frontiers in fungal biology\| PubMed ID: 38155707	2023
The complete genome sequence of probiotic ATCC 9224 isolated from sour milk. Microbiology resource announcements\| PubMed ID: 38488370	2024
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses\| PubMed ID: 38543795	2024
Combining compositional data sets introduces error in covariance network reconstruction. ISME communications\| PubMed ID: 38812718	2024
A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 38819573	2024
Fabricated devices for performing bacterial-fungal interaction experiments across scales. Frontiers in microbiology\| PubMed ID: 39171270	2024
Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes. mSphere\| PubMed ID: 39189783	2024
Erratum for Longley et al., "Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes". mSphere\| PubMed ID: 39555927	2024

Article	Year
Whole-genome-based phylogeny and divergence of the genus Brucella. Journal of bacteriology\| PubMed ID: 19201792	2009
Genomics. Genome project standards in a new era of sequencing. Science (New York, N.Y.)\| PubMed ID: 19815760	2009
The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PloS one\| PubMed ID: 21390229	2011
Genomics for key players in the N cycle from guinea pigs to the next frontier. Methods in enzymology\| PubMed ID: 21514469	2011
Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. Journal of bacteriology\| PubMed ID: 21551308	2011
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature biotechnology\| PubMed ID: 21552244	2011
Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts. Journal of bacteriology\| PubMed ID: 21685287	2011
Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide. Journal of bacteriology\| PubMed ID: 21705610	2011
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current opinion in biotechnology\| PubMed ID: 22154470	2012
Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Briefings in functional genomics\| PubMed ID: 22199376	2011
Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PloS one\| PubMed ID: 22536372	2012
Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases\| PubMed ID: 22551038	2012
Genome sequence of Kingella kingae septic arthritis isolate PYKK081. Journal of bacteriology\| PubMed ID: 22582375	2012
Complete genome sequence of Francisella philomiragia ATCC 25017. Journal of bacteriology\| PubMed ID: 22628499	2012
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME journal\| PubMed ID: 22717885	2012
Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. Journal of bacteriology\| PubMed ID: 23105050	2012
Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2. PloS one\| PubMed ID: 23133618	2012
Genome sequence of the hepatitis C virus subtype 6n isolated from malaysia. Genome announcements\| PubMed ID: 23409272	2013
Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46. Genome announcements\| PubMed ID: 23599293	2013
Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360). Genome announcements\| PubMed ID: 23640195	2013
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature communications\| PubMed ID: 23673639	2013
Recruiting human microbiome shotgun data to site-specific reference genomes. PloS one\| PubMed ID: 24454771	2014
Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one\| PubMed ID: 24743558	2014
Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin. Genome announcements\| PubMed ID: 24855308	2014
Standards for sequencing viral genomes in the era of high-throughput sequencing. mBio\| PubMed ID: 24939889	2014
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS biology\| PubMed ID: 25093819	2014
Draft Genome Assembly of Acinetobacter baumannii ATCC 19606. Genome announcements\| PubMed ID: 25146140	2014
Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains. Genome announcements\| PubMed ID: 25212618	2014
Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Scientific reports\| PubMed ID: 25270300	2014
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. The ISME journal\| PubMed ID: 25361395	2015
Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC bioinformatics\| PubMed ID: 25408143	2014
Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes. Genome announcements\| PubMed ID: 25593267	2015
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic acids research\| PubMed ID: 25765641	2015
Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. PloS one\| PubMed ID: 25794000	2015
Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial). Frontiers in microbiology\| PubMed ID: 26217314	2015
CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA. PloS one\| PubMed ID: 26305456	2015
Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Standards in genomic sciences\| PubMed ID: 26380642	2015
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in microbiology\| PubMed ID: 26583008	2015
Building International Genomics Collaboration for Global Health Security. Frontiers in public health\| PubMed ID: 26697418	2015
ADEPT, a dynamic next generation sequencing data error-detection program with trimming. BMC bioinformatics\| PubMed ID: 26928302	2016
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 Zo... Genome biology and evolution\| PubMed ID: 27289094	2016
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic acids research\| PubMed ID: 27899609	2017
Draft Genome Sequence of Sorghum Grain Mold Fungus Epicoccum sorghinum, a Producer of Tenuazonic Acid. Genome announcements\| PubMed ID: 28126937	2017
Ten Genome Sequences of Human and Livestock Isolates of from the Country of Georgia. Genome announcements\| PubMed ID: 28495766	2017
Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. International journal of systematic and evolutionary microbiology\| PubMed ID: 29111971	2018
Displays Altered Stress Responses While Enhancing Biofilm Formation by in Mixed-Species Consortium. Frontiers in cellular and infection microbiology\| PubMed ID: 29326887	2017
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... Microbiology resource announcements\| PubMed ID: 30533668	2018
Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. Advances in applied microbiology\| PubMed ID: 30798804	2019
Bacterial spores, from ecology to biotechnology. Advances in applied microbiology\| PubMed ID: 30798805	2019
Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in and Resistance to Extreme Conditions. Frontiers in microbiology\| PubMed ID: 30804904	2019
Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 30891596	2020
Novel Insights Into the Spread of Enteric Pathogens Using Genomics. The Journal of infectious diseases\| PubMed ID: 31538189	2020
MicroRNA in Pancreatic Cancer: From Biology to Therapeutic Potential. Genes\| PubMed ID: 31557962	2019
Advances and Challenges in Metatranscriptomic Analysis. Frontiers in genetics\| PubMed ID: 31608125	2019
Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing. The Journal of infectious diseases\| PubMed ID: 31751454	2020
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Scientific reports\| PubMed ID: 32015354	2020
A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis. mSystems\| PubMed ID: 32047060	2020
The National Microbiome Data Collaborative: enabling microbiome science. Nature reviews. Microbiology\| PubMed ID: 32350400
Uncovering the Core Microbiome and Distribution of Palmerolide in Across the Anvers Island Archipelago Antarctica. Marine drugs\| PubMed ID: 32498449	2020
Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology\| PubMed ID: 32514073
Genomic Analysis of Diverse Members of the Fungal Genus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate. G3 (Bethesda, Md.)\| PubMed ID: 32580939	2020
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays. Bioinformatics (Oxford, England)\| PubMed ID: 32777813	2021
Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology\| PubMed ID: 33184503
The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice. Life (Basel, Switzerland)\| PubMed ID: 33374112	2020
Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS microbiology ecology\| PubMed ID: 33440006	2021
DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food microbiology\| PubMed ID: 33494894	2021
Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS neglected tropical diseases\| PubMed ID: 33524010	2021
Epigenetic regulation of gene expression in Shiga toxin-producing : Transcriptomic data. Data in brief\| PubMed ID: 34307800	2021
Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data. Bio-protocol\| PubMed ID: 34595290	2017
Widespread bacterial diversity within the bacteriome of fungi. Communications biology\| PubMed ID: 34621007	2021
Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian. Frontiers in chemistry\| PubMed ID: 35004620	2021
Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes. Frontiers in genetics\| PubMed ID: 35096026	2021
Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients. Human microbiome journal\| PubMed ID: 35506046	2019
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. Bioinformatics (Oxford, England)\| PubMed ID: 35561186	2022
Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing O145:H28. Microorganisms\| PubMed ID: 35630311	2022
Advances and Challenges in Fluorescence Hybridization for Visualizing Fungal Endobacteria. Frontiers in microbiology\| PubMed ID: 35722318	2022
Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain. Microbiology resource announcements\| PubMed ID: 35924938	2022
Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles. Frontiers in microbiology\| PubMed ID: 35935195	2022
Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns. bioRxiv : the preprint server for biology\| PubMed ID: 36032969	2022
Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses\| PubMed ID: 36298683	2022
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. Frontiers in bioinformatics\| PubMed ID: 36303775	2021
The Coronavirus Standards Working Group's roadmap for improved population testing. Nature biotechnology\| PubMed ID: 36323792	2022
Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS global public health\| PubMed ID: 36962439	2022
A centralized resource for bacterial-fungal interactions research. Fungal biology\| PubMed ID: 37142360	2023
Diversity of fungal microbiome obtained from plant rhizoplanes. The Science of the total environment\| PubMed ID: 37295515	2023
The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. Microbiome\| PubMed ID: 37626434	2023
Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Communications biology\| PubMed ID: 37723238	2023
Identification of mobile genetic elements with geNomad. Nature biotechnology\| PubMed ID: 37735266	2024
Metabolic versatility of from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes. Frontiers in microbiology\| PubMed ID: 37799600	2023
Genomic and Phenotypic Characterization of Shiga Toxin-Producing Strains Isolated from Wild Birds in a Major Agricultural Region in California. Microorganisms\| PubMed ID: 38004814	2023
Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. Astrobiology\| PubMed ID: 38079228	2023
Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between with spp. Frontiers in fungal biology\| PubMed ID: 38155707	2023
The complete genome sequence of probiotic ATCC 9224 isolated from sour milk. Microbiology resource announcements\| PubMed ID: 38488370	2024
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses\| PubMed ID: 38543795	2024
Combining compositional data sets introduces error in covariance network reconstruction. ISME communications\| PubMed ID: 38812718	2024
A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 38819573	2024
Fabricated devices for performing bacterial-fungal interaction experiments across scales. Frontiers in microbiology\| PubMed ID: 39171270	2024
Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes. mSphere\| PubMed ID: 39189783	2024
Erratum for Longley et al., "Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes". mSphere\| PubMed ID: 39555927	2024