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List of works by Robert A Edwards

'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market

scientific article published on 14 March 2019

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage

article

A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains

scientific article

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

scientific article

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

scientific article published in 2023

Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers

scientific article published on 30 July 2019

Aging and Intermittent Fasting Impact on Transcriptional Regulation and Physiological Responses of Adult Drosophila Neuronal and Muscle Tissues

scientific article published on 10 April 2018

Allelic variation contributes to bacterial host specificity.

scientific article

An application of statistics to comparative metagenomics

scientific article published on 20 March 2006

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

scientific article published on 01 January 2020

Applying Shannon's information theory to bacterial and phage genomes and metagenomes

scientific article

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle

scientific article

Bacterial carbon processing by generalist species in the coastal ocean.

scientific article published on 27 January 2008

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data

scientific article

Biodiversity and biogeography of phages in modern stromatolites and thrombolites.

scientific article

Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis.

scientific article

Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing.

scientific article

Combining de novo and reference-guided assembly with scaffold_builder

scientific article

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

scientific article published on 5 August 2014

Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype

scientific article published on 18 June 2015

Computational approaches to predict bacteriophage-host relationships.

scientific article

Connecting genotype to phenotype in the era of high-throughput sequencing.

scientific article published on 21 March 2011

Corrigendum: Allelic variation contributes to bacterial host specificity.

scientific article published on 8 August 2017

Corrigendum: Lytic to temperate switching of viral communities

scientific article

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology

scientific article published on 27 May 2019

Diel population and functional synchrony of microbial communities on coral reefs

scientific article published on 12 April 2019

Differential regulation of fasA and fasH expression of Escherichia coli 987P fimbriae by environmental cues

scientific article published on August 1, 1997

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.

scientific article published on 13 November 2017

Diversification of the Salmonella Fimbriae: A Model of Macro- and Microevolution

scientific article published on June 12, 2012

Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin and Cylindrospermopsin Synthetase Genes.

scientific article published on 5 May 2016

Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis

scientific article published on 7 November 2013

Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792

scientific article published on April 1, 2012

Essential genes on metabolic maps.

scientific article

Experimental and computational assessment of conditionally essential genes in Escherichia coli

scientific article

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

scientific article

Fimbrial expression in enteric bacteria: a critical step in intestinal pathogenesis

scientific article published on 01 July 1998

Finding novel genes in bacterial communities isolated from the environment

article

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

scientific article published on 17 June 2016

Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater

scientific article published on 11 June 2018

Functional metagenomic profiling of nine biomes

scientific article (publication date: 3 April 2008)

Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactis provides insight into its adaptable nature

scientific article published on 01 December 2005

Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G+C content.

scientific article published on May 2004

Genome sequence of the bacterioplanktonic, mixotrophic Vibrio campbellii strain PEL22A, isolated in the Abrolhos Bank.

scientific article

Genome sequence of the human pathogen Vibrio cholerae Amazonia

scientific article published on October 2011

Genome sequences of the ethanol-tolerant Lactobacillus vini strains LMG 23202T and JP7.8.9.

scientific article

Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic

scientific article (publication date: 2012)

GenomePeek-an online tool for prokaryotic genome and metagenome analysis

scientific article published on 16 June 2015

Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum

scientific article published on 3 June 2015

Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes

scientific article published on 05 February 2020

Genomic taxonomy of the genus prochlorococcus.

scientific article

Global microbialization of coral reefs.

scientific article

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

scientific article published on 08 July 2019

Growth Score: a single metric to define growth in 96-well phenotype assays.

scientific article published on 19 April 2018

Identification and removal of ribosomal RNA sequences from metatranscriptomes

scientific article (publication date: February 2012)

Improved allelic exchange vectors and their use to analyze 987P fimbria gene expression

scientific article published on January 30, 1998

In vitro characterization of the Bacillus subtilis protein tyrosine phosphatase YwqE

scientific article

Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality

scientific article published on 01 July 2006

Insights into antibiotic resistance through metagenomic approaches.

scientific article published on January 2012

Integration of genomic and proteomic analyses in the classification of the Siphoviridae family.

scientific article published on 14 November 2014

Kullback Leibler divergence in complete bacterial and phage genomes.

scientific article published on 30 November 2017

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.

scientific article

Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis.

scientific article

Lytic to temperate switching of viral communities

scientific article

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

scientific article

Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data

scientific article

Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa.

scholarly article

Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals.

scientific article published on 15 January 2013

Metagenomic analysis of the microbial community associated with the coral Porites astreoides.

scientific article

Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities

scientific article published on August 28, 2012

Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era.

scientific article

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome.

scientific article published on 16 February 2016

Microbial ecology of four coral atolls in the Northern Line Islands.

scientific article

Microbial genomic taxonomy

scientific article

Microbial taxonomy in the post-genomic era: rebuilding from scratch?

scientific article published on 23 December 2014

Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

scientific article published on 03 March 2020

Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes.

scientific article published in May 2005

Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems

scientific article

MultiPhATE2: code for functional annotation and comparison of phage genomes

scientific article published on 01 May 2021

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.

scientific article published on 8 May 2015

Multivariate analysis of functional metagenomes.

scientific article published on 2 April 2013

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index

scientific article published on 10 December 2020

NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements

scientific article published on 16 September 2019

No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study

scientific article published on 22 June 2021

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.

scientific article published on 28 November 2017

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive

scientific article

PHACTS, a computational approach to classifying the lifestyle of phages

scientific article published on January 11, 2012

PHANOTATE: a novel approach to gene identification in phage genomes

scientific article published on 01 November 2019

PMAnalyzer: a new web interface for bacterial growth curve analysis

scientific article published on 13 February 2017

Perspective on taxonomic classification of uncultivated viruses

PhANNs, a fast and accurate tool and web server to classify phage structural proteins

scientific article published on 02 November 2020

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.

scientific article

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

scientific article

Phylogenetic classification of short environmental DNA fragments

scientific article (publication date: April 2008)

Prodigious Prevotella phages

scientific article published on 01 April 2019

Quality control and preprocessing of metagenomic datasets

scientific article (publication date: 15 March 2011)

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

scientific article

Real time metagenomics: using k-mers to annotate metagenomes

scientific article

Reference-independent comparative metagenomics using cross-assembly: crAss.

scientific article

Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes

scientific article published in Nature Communications

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

scientific article

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

scientific article

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

scientific article

Structure and function of a cyanophage-encoded peptide deformylase

scientific article

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

scientific article

Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis

scientific article

Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

scientific article published on 20 June 2008

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

scientific article

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

scientific article published on 22 January 2018

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

scientific article

The RAST Server: rapid annotations using subsystems technology

scientific article

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

scientific article

The StkSR Two-Component System Influences Colistin Resistance in <i>Acinetobacter baumannii</i>

scientific article published on 08 May 2022

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

scientific article

The minimum information about a genome sequence (MIGS) specification

scientific article

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article

Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

scientific article published on 17 April 2020

Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays.

scientific article published on January 2006

Transposases are the most abundant, most ubiquitous genes in nature.

scientific article

Using viromes to predict novel immune proteins in non-model organisms

scientific article published in August 2016

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes

scientific article published on 08 January 2021

Viral and microbial community dynamics in four aquatic environments.

scientific article

Viral diversity and dynamics in an infant gut.

scientific article