Robert Edwards

Publications

• Perspective on taxonomic classification of uncultivated viruses
• Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics
• Organizing the bacterial annotation space with amino acid sequence embeddings
• The StkSR Two-Component System Influences Colistin Resistance in Acinetobacter baumannii
• Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers
• PHANOTATE: a novel approach to gene identification in phage genomes
• Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
• Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
• Diel population and functional synchrony of microbial communities on coral reefs
• Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology
• Prodigious Prevotella phages
• Ten simple rules and a template for creating workflows-as-applications
• Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale
• The utility of dust for forensic intelligence
• Latitude and chlorophyll a density drive the distribution of carbohydrate-active enzymes in the planktonic microbial fraction of the epipelagic zone
• Confidence for exploratory machine learning
• Abolishment of morphology-based taxa and change to binomial species names
• Global Whale Shark (Rhincodon typus) microbiome: regional taxonomic flexibility and functional stability
• Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities
• Deep immune profiling of the maternal-fetal interface with mild SARS-CoV-2 infection
• Phage and bacteria diversification through a prophage acquisition ratchet
• Hecatomb: An End-to-End Research Platform for Viral Metagenomics
• Erratum: A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation (mSystems (2021) 6:1 (e00773-20) DOI: 10.1128/mSystems.00773-20)
• RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content
• Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
• MultiPhATE2: Code for Functional Annotation and Comparison of Bacteriophage Genomes
• A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation
• NCBI’s Virus Discovery Codeathon: Building “FIVE”—The Federated Index of Viral Experiments API Index
• NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements
• RaFAH: A superior method for virus-host prediction
• How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research
• Gut microbiota represent a major thermogenic biomass
• Gut Microbiota Represent a Major Thermogenic Biomass
• Single-cell gene expression links SARS-CoV-2 infection and gut serotonin
• Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents
• The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
• `Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market
• Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus)
• Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes
• Predicting the capsid architecture of phages from metagenomic data
• Fastq-pair: efficient synchronization of paired-end fastq files
• Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network
• Standardized bacteriophage purification for personalized phage therapy
• A distinct contractile injection system gene cluster found in a majority of healthy adult human microbiomes
• Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes
• Philympics 2021: Prophage Predictions Perplex Programs
• MultiPhATE2
• No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study
• hafeZ: Active prophage identification through read mapping
• Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
• Computational approaches to predict bacteriophage-host relationships
• Aging and Intermittent Fasting Impact on Transcriptional Regulation and Physiological Responses of Adult Drosophila Neuronal and Muscle Tissues
• Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
• Kullback Leibler divergence in complete bacterial and phage genomes
• Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle
• Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
• PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive
• Surgical Removal of Gut Bacteria Biomass Promotes Weight Gain via Suppression of Energy Expenditure
• Biological chlorine cycling in the Arctic Coastal Plain
• PMAnalyzer: a new web interface for bacterial growth curve analysis
• Corrigendum: Lytic to temperate switching of viral communities
• Global microbialization of coral reefs
• Corrigendum: Allelic variation contributes to bacterial host specificity
• A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
• Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater
• Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes
• Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut
• Growth Score: a single metric to define growth in 96-well phenotype assays
• Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin and Cylindrospermopsin Synthetase Genes
• From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
• Dietary Fat and Carbohydrate Content Modulate Energy Expenditure via Gut Bacteria
• Variability and host density independence in inductions-based estimates of environmental lysogeny
• Elucidating genomic gaps using phenotypic profiles
• Using viromes to predict novel immune proteins in non-model organisms
• Lytic to temperate switching of viral communities
• Genomics to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus)
• Genomic, proteomic, and phylogenetic analysis of spounaviruses indicates paraphyly of the order Caudovirales
• Taxonomy proposal: To create one (1) new family, Herelleviridae, in the order Caudovirales
• The biomass and composition of the gut microbiota modify anaerobic metabolism
• Benchmark data sets, software results and reference data for the first CAMI challenge
• THEA: A novel approach to gene identification in phage genomes
• PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets
• Development of a shark health matrix using metabolomics coupled with metagenomics
• Suppl Methods for Biogeochemistry paper
• The skin microbiome of elasmobranchs follows phylosymbosis, but in teleost fishes the microbiomes converge
• Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
• Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages
• Genomics to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus).
• A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes
• linsalrob/fasta_validator
• multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
• Charting the diversity of uncultured viruses of Archaea and Bacteria
• Phage genome annotation using the RAST pipeline
• Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
• Searching the sequence read archive using Jetstream and Wrangler
• Some of the most interesting CASP11 targets through the eyes of their authors
• An agile functional analysis of metagenomic data using SUPER-FOCUS
• Prophage genomics reveals patterns in phage genome organization and replication
• Critical Assessment of Metagenome Interpretation - a benchmark of metagenomics software
• ­Growth Score: A single metric to define growth in 96-well phenotype assays
• Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors
• The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
• RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
• A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
• Microbial genomic taxonomy
• Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities
• Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis
• Real time metagenomics: using k-mers to annotate metagenomes
• FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
• A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes
• Reference-independent comparative metagenomics using cross-assembly: crAss
• Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
• Microbial taxonomy in the post-genomic era: rebuilding from scratch?
• Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals
• Multivariate analysis of functional metagenomes
• Combining de novo and reference-guided assembly with scaffold_builder
• Explaining microbial phenotypes on a genomic scale: GWAS for microbes
• Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux
• Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems
• Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data
• SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
• Genomic taxonomy of the genus prochlorococcus
• Integration of genomic and proteomic analyses in the classification of the Siphoviridae family
• Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes
• Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype
• GenomePeek - An online tool for prokaryotic genome and metagenome analysis
• Allelic variation contributes to bacterial host specificity
• Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome
• Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
• Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum
• Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data
• Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era
• Applying Shannon's information theory to bacterial and phage genomes and metagenomes
• Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis
• Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data
• Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
• GenomePeek - An online tool for prokaryotic and metagenome analysis
• Microfluidic PCR combined with pyrosequencing for identification of allelic variants with phenotypic associations among targeted Salmonella genes
• SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
• Structure and function of a cyanophage-encoded peptide deformylase
• RAPID RESPONSE: TRANSLATING MULTI-OMICS DATA ON CF EXACERBATIONS IN CLINICALLY RELEVANT TIME FRAMES
• Computational approaches to predict bacteriophage--host relationships
• Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron
• FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation
• FOCUS2: agile and sensitive classification of metagenomics data using a reduced database
• Qudaich: A smart sequence aligner
• Computational Science and Engineering
• GenomePeek—an online tool for prokaryotic genome and metagenome analysis
• Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
• PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
• Quality control and preprocessing of metagenomic datasets
• Viral diversity and dynamics in an infant gut
• The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
• The minimum information about a genome sequence (MIGS) specification
• Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
• Viral and microbial community dynamics in four aquatic environments
• Phylogenetic classification of short environmental DNA fragments
• Bacterial carbon processing by generalist species in the coastal ocean
• Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome
• Insights into antibiotic resistance through metagenomic approaches
• TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
• Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor
• Identification and removal of ribosomal RNA sequences from metatranscriptomes
• Transposases are the most abundant, most ubiquitous genes in nature
• The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
• Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa
• Accessing the SEED genome databases via Web services API: tools for programmers
• Metagenomic analysis of stressed coral holobionts
• PHACTS, a computational approach to classifying the lifestyle of phages
• Viral communities associated with healthy and bleaching corals
• Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing
• MetaBase--the wiki-database of biological databases
• Connecting genotype to phenotype in the era of high-throughput sequencing
• PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
• Functional metagenomic profiling of nine biomes
• Genome sequence of the human pathogen Vibrio cholerae Amazonia
• Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
• Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets
• Fast identification and removal of sequence contamination from genomic and metagenomic datasets
• Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars
• Lysogeny and sporulation in Bacillus isolates from the Gulf of Mexico
• The Microbiome and Virome of CF
• Towards richer descriptions of our collection of genomes and metagenomes
• Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5
• Draft genome sequence of the shrimp pathogen Vibrio harveyi CAIM 1792
• The smallest cells pose the biggest problems: high-performance computing and the analysis of metagenome sequence data
• Genome sequence of the bacterioplanktonic, mixotrophic Vibrio campbellii strain PEL22A, isolated in the Abrolhos Bank
• Genome sequences of the ethanol-tolerant Lactobacillus vini strains LMG 23202T and JP7.8.9
• Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic
• Deviations from Ultrametricity in Phage Protein Distances
• Real-Time Metagenomics
• THE MICROBIOME AND VIROME OF CF: 277★
• Benthic community composition affects O2 availability and variability in a Northern Red Sea fringing reef
• Phage--bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
• MetaBase—the wiki-database of biological databases
• Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases
• Biodiversity and biogeography of phages in modern stromatolites and thrombolites
• Diversification of the Salmonella fimbriae: a model of macro- and microevolution
• Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico
• Erratum
• Experimental and computational assessment of conditionally essential genes in Escherichia coli
• The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
• The RAST Server: rapid annotations using subsystems technology
• Inside or outside: detecting the cellular location of bacterial pathogens
• Evolution of microbial pathogens: Microbial Pathogenesis and Host Response, Cold Spring Harbor Laboratory, NY, USA, 22--26 September 1999
• Community genomics among stratified microbial assemblages in the ocean's interior
• The marine viromes of four oceanic regions
• Viral metagenomics
• Using pyrosequencing to shed light on deep mine microbial ecology
• The Phage Proteomic Tree: a genome-based taxonomy for phage
• Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
• Metagenomic analysis of the microbial community associated with the coral Porites astreoides
• Microbial ecology of four coral atolls in the Northern Line Islands
• Comparative genomics of closely related salmonellae
• Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
• Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences
• An application of statistics to comparative metagenomics
• A role for Salmonella fimbriae in intraperitoneal infections
• The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
• Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis
• A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains
• Fimbrial expression in enteric bacteria: a critical step in intestinal pathogenesis
• Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays
• Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes
• In vitro characterization of the Bacillus subtilis protein tyrosine phosphatase YwqE
• Microbial Genome Sequencing
• Genomic analysis and growth-phase-dependent regulation of the SEF14 fimbriae of Salmonella enterica serovar Enteritidis
• Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality
• Increasing DNA transfer efficiency by temporary inactivation of host restriction
• Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights
• Finding novel genes in bacterial communities isolated from the environment
• Essential genes on metabolic maps
• The importance of complete genome sequences
• Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cienegas, Mexico
• Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil
• Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactis provides insight into its adaptable nature
• Hidden messages within the genetic code
• Eye of newt and toe of frog
• An old dog learns new tricks
• TeraGrid Open Life Science Gateway
• Automated analysis of ARISA data using ADAPT system
• The metagenomics RAST server--a public resource for the automatic phylogenetic and functional analysis of metagenomes
• Random Community Genomics
• The Role of Microbes in the Precipitation of Microbialites in Cuatro Cienegas, Mexico: A Genomic and Stable Isotopic Perspective
• Increasing DNA transfer efficiency by temporary inactivation of host restriction.
• Bacterial select agents and antibiotic resistance genes.
• The National Microbial Pathogen Data Resource
• Eye of newt and toe of frog: Recombinant DNA Principles and Methodologies, edited by James J. Greene and Venigalla B. Rao, and Molecular Biomethods Handbook, edited by Ralph Rapley and John M. Walker
• Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G+C content
• Marine environmental genomics: Unlocking the ocean's secrets
• PhANNs, a fast and accurate tool and web server to classify phage structural proteins
• Nitrogen control in bacteria
• Improved allelic exchange vectors and their use to analyze 987P fimbria gene expression
• Differential regulation of fasA and fasH expression of Escherichia coli 987P fimbriae by environmental cues
• The role of uridylyltransferase in the control of Klebsiella pneumoniae nif gene regulation
• Identification of major and minor chaperone proteins involved in the export of 987P fimbriae
• Tools for Fast Sequence Alignment
• Escherichia coli: Mechanisms of Virulence
• Programmatic Access to the SEED Data Via the Network
• NMPDR-National Microbial Pathogen Data Resource
• Nitrogen control in bacteria.
• Scoring Amino Acid Substitutions In $Φ$hage Genomes
• High-throughput phenotype profiling for bacterial flux-balance model optimization
• Genomics and Bioinformatics: A Practical Course in Sequence Data Analysis
• Search SRA Gateway for Metagenomics Data
• Shannon's Uncertainty and Kullback-Leibler Divergence in Microbial Genome
• Programmed ribosomal frameshifts, and how to find them
• The Promise and Pitfalls of Prophages
• Prophage rates in the human microbiome vary by body site and host health.
• Host Association and Spatial Proximity Shape but Do Not Constrain Population Structure in the Mutualistic Symbiont Xenorhabdus bovienii
• Prophage rates in the human microbiome vary by body site and host health
• Towards the biogeography of butyrate-producing bacteria
• Philympics 2021
• The human gut virome
• Statement in Support of
• Classification Confidence in Exploratory Learning: A User’s Guide
• Compounding Achromobacter Phages for Therapeutic Applications
• Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
• linsalrob/fast-adapter-trimming
• linsalrob/PyFBA
• linsalrob/pyctv
• linsalrob/py_fasta_validator
• linsalrob/primer-trimming
• linsalrob/partie
• linsalrob/PhiSpy
• linsalrob/mgi-adapters
• linsalrob/genbank_to
• linsalrob/atavide_lite
• linsalrob/sam
• linsalrob/fastq-pair
• linsalrob/ComputationalGenomicsManual
• linsalrob/CompareReferences
• linsalrob/atavide
• Prophage Prediction Comparisons
• linsalrob/PPPF
• linsalrob/SearchSRAToolKit
• linsalrob/SearchSRA
• linsalrob/BacterialProteins
• linsalrob/pbj_placer
• linsalrob/partie_hat
• linsalrob/crAssphage
• Surgical Removal of Gut Bacteria Biomass Promotes Weight Gain via Suppression of Energy Expenditure
• Dietary Fat and Carbohydrate Content Modulate Energy Expenditure via Gut Bacteria
• Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome
• Phables
• Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2
• THE MICROBIOME AND VIROME OF CF
• RAPID RESPONSE
• The Role of Microbes in the Precipitation of Microbialites in Cuatro Cienegas, Mexico
• The Biomass and Composition of the Gut Microbiota Modify Anaerobic Metabolism
• Qudaich
• Abolish the order Caudovirales and the families Myoviridae, Siphoviridae and Podoviridae (Caudoviricetes)
• Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy
• Author Correction
• The secret hidden in dust
• Phables: from fragmented assemblies to high-quality bacteriophage genomes
• PRFect: A tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes
• Heat-stressed coral microbiomes are stable and potentially beneficial at the level of taxa and functional genes
• The human gut virome: Composition, colonisation, interactions, and impacts on human health
• Estimating Classification Confidence Using Kernel Densities
• ­ Growth Score : A single metric to define growth in 96-well phenotype assays
• Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes
• Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes
• Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies
• Predicting stop codon reassignment improves functional annotation of bacteriophages
• Prophages: an integral but understudied component of the human microbiome
• The macroecology of butyrate-producing bacteria
• Koverage: Read-coverage analysis for massive (meta)genomics datasets
• How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies
• The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity
• Hybracter
• Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions
• Hecatomb: an integrated software platform for viral metagenomics
• ICP miniseries: ICP – could there be a virus in the works?
• Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples
• ICP – could there be a virus in the works?
• Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages
• Koverage
• Solving genomic puzzles: computational methods for metagenomic binning
• Solving genomic puzzles
• Ecological phage therapy: can bacteriophages help rapidly restore the soil microbiome?
• Prophages
• PRFect
• A novel genus of Pectobacterium bacteriophages display broad host range by targeting several species of Danish soft rot isolates
• Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein.
• Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee
• Temperate gut phages are prevalent, diverse, and predominantly inactive
• Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
• ICP miniseries: ICP--could there be a virus in the works?
• Taxonomy proposal 2021: abolish the order Caudovirales and the families Myoviridae, Siphoviridae and Podoviridae (Caudoviricetes)
• Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee
• Ecological phage therapy
• A globally integrated structure of taxonomy to support biodiversity science and conservation