All Stories

  1. Isolation of mouse midbrain, RNA purification, reverse transcription, and quantitative PCR v2

    Article • August 2026, Springer Science + Business Media

    Dr Robert A Edwards

  2. DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation

    Article • Clinical Microbiology Reviews, August 2026, ASM Journals

    Dr Robert A Edwards

  3. Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny

    Article • Current Protocols, July 2026, Wiley

    Dr Robert A Edwards

  4. Keep it together: Soil core translocation improves establishment of donor‐like microbial communities

    Article • Journal of Applied Ecology, June 2026, Wiley

    Dr Robert A Edwards

  5. Computational prediction resolves thousands of homooligomeric phage protein structures

    Article • May 2026, openRxiv

    Dr Robert A Edwards

  6. Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers

    Article • Nature Communications, May 2026, Springer Science + Business Media

    Dr Robert A Edwards

  7. agtools: A Software Framework to Manipulate Assembly Graphs

    Article • Bioinformatics Advances, May 2026, Oxford University Press (OUP)

    Dr Robert A Edwards

  8. Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease

    Article • Veterinary Microbiology, April 2026, Elsevier

    Dr Robert A Edwards

  9. Baktfold: Sensitive protein functional annotation across the microbial tree of life using structural information

    Article • April 2026, openRxiv

    Dr Robert A Edwards

  10. Interactions of Mucus Monosaccharides and the Epidermal Microbiome in Four Benthic Elasmobranchs

    Article • Environmental Microbiology Reports, March 2026, Wiley

    Dr Robert A Edwards

  11. Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings

    Article • Ecology and Evolution, February 2026, Wiley

    Dr Robert A Edwards

  12. Deciphering the etiology of the 2024 outbreak of undiagnosed febrile illness in Panzi, Democratic Republic of the Congo

    Article • Nature Medicine, February 2026, Springer Science + Business Media

    Dr Robert A Edwards, Dr. Anuj Kumar

  13. Protein structure-informed bacteriophage genome annotation with Phold

    Article • Nucleic Acids Research, January 2026, Oxford University Press (OUP)

    Dr Robert A Edwards

  14. VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

    Article • Nucleic Acids Research, December 2025, Oxford University Press (OUP)

    Dr Robert A Edwards

  15. Author Correction: A roadmap for equitable reuse of public microbiome data

    Article • Nature Microbiology, November 2025, Springer Science + Business Media

    Dr Robert A Edwards, Luis M Rodriguez-R, Professor Konstantinos (Kostas) Kormas

  16. Isolation, engineering and ecology of temperate phages from the human gut

    Article • Nature, October 2025, Springer Science + Business Media

    Dr Robert A Edwards, Prof. Juris A Grasis

  17. Reprogramming resistance: phage-antibiotic synergy targets efflux systems in ESKAPEE pathogens

    Article • mBio, October 2025, ASM Journals

    Dr Robert A Edwards

  18. Central carbon metabolism switching in lytic versus temperate coral reef viral communities

    Article • September 2025, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  19. A roadmap for equitable reuse of public microbiome data

    Article • Nature Microbiology, September 2025, Springer Science + Business Media

    Gareth Trubl, Dr Robert A Edwards, Luis M Rodriguez-R, Professor Konstantinos (Kostas) Kormas

  20. Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan‐Palaeotropical C4 Grass, Themeda triandra

    Article • Plant Cell & Environment, September 2025, Wiley

    Dr Robert A Edwards

  21. Picobirnavirus: how do you find where it’s hiding?

    Article • Critical Reviews in Microbiology, September 2025, Taylor & Francis

    Dr Robert A Edwards

  22. Computational function prediction of bacteria and phage proteins

    Article • Microbiology and Molecular Biology Reviews, August 2025, ASM Journals

    Dr Robert A Edwards

  23. Synteny-aware functional annotation of bacteriophage genomes with Phynteny

    Article • July 2025, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  24. Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins

    Article • July 2025, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  25. Ross River virus genomes from Australia and the Pacific display coincidental and antagonistic codon usage patterns with common vertebrate hosts and a principal vector

    Article • Virology, July 2025, Elsevier

    Dr Robert A Edwards

  26. Strong Host Modulation of Rhizosphere‐to‐Endosphere Microbial Colonisation in Natural Populations of the Pan‐Palaeotropical Keystone Grass Species, Themeda triandra

    Article • Ecology and Evolution, June 2025, Wiley

    Dr Robert A Edwards

  27. Prophages as a source of antimicrobial resistance genes in the human microbiome

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  28. Degraded ecosystem soil and type 2 diabetes gut microbiomes share altered potential metabolism for sugars, lignin and branched-chain fatty acids: a blind spot for global health?

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  29. Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data

    Article • Bioinformatics Advances, December 2024, Oxford University Press (OUP)

    Dr Robert A Edwards

  30. A novel genus of Pectobacterium bacteriophages display broad host range by targeting several species of Danish soft rot isolates

    Article • Virus Research, September 2024, Elsevier

    Dr Robert A Edwards

  31. Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome?

    Article • Ecology and Evolution, August 2024, Wiley

    Dr Robert A Edwards

  32. Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes

    Article • The Science of The Total Environment, August 2024, Elsevier

    Dr Robert A Edwards

  33. Solving genomic puzzles: computational methods for metagenomic binning

    Article • Briefings in Bioinformatics, July 2024, Oxford University Press (OUP)

    Dr Robert A Edwards

  34. ICP – could there be a virus in the works?

    Article • Obstetric Medicine, June 2024, SAGE Publications

    Dr Robert A Edwards

  35. How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

    Article • Microbial Genomics, June 2024, Society for General Microbiology

    Dr Robert A Edwards

  36. Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions

    Article • Microorganisms, May 2024, MDPI AG

    Dr Robert A Edwards

  37. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

    Article • Microbial Genomics, May 2024, Society for General Microbiology

    Dr Robert A Edwards

  38. The macroecology of butyrate‐producing bacteria via metagenomic assessment of butyrate production capacity

    Article • Ecology and Evolution, April 2024, Wiley

    Dr Robert A Edwards

  39. How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

    Article • March 2024, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  40. Koverage: Read-coverage analysis for massive (meta)genomics datasets

    Article • The Journal of Open Source Software, February 2024, The Open Journal

    Dr Robert A Edwards

  41. PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes

    Article • BMC Bioinformatics, February 2024, Springer Science + Business Media

    Peter Salamon, Dr Robert A Edwards

  42. Prophages: an integral but understudied component of the human microbiome

    Article • Microbial Genomics, January 2024, Society for General Microbiology

    Dr Robert A Edwards

  43. Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples

    Article • Microbiology Resource Announcements, January 2024, ASM Journals

    Dr Robert A Edwards

  44. Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages

    Article • ISME Communications, January 2024, Oxford University Press (OUP)

    Dr Robert A Edwards

  45. Hecatomb: an integrated software platform for viral metagenomics

    Article • GigaScience, January 2024, Oxford University Press (OUP)

    Dr Robert A Edwards

  46. Predicting stop codon reassignment improves functional annotation of bacteriophages

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  47. Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  48. A globally integrated structure of taxonomy to support biodiversity science and conservation

    Article • Trends in Ecology & Evolution, December 2023, Elsevier

    Dr Robert A Edwards

  49. Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  50. Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy

    Article • Clinical Infectious Diseases, November 2023, Oxford University Press (OUP)

    Dr Robert A Edwards

  51. The secret hidden in dust: Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework

    Article • Forensic Science International Genetics, November 2023, Elsevier

    Dr Robert A Edwards

  52. Advances and Challenges in Understanding the Virosphere

    Article • October 2023, Cassyni

    Dr Robert A Edwards

  53. Phables: from fragmented assemblies to high-quality bacteriophage genomes

    Article • Bioinformatics, September 2023, Oxford University Press (OUP)

    Dr Robert A Edwards

  54. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

    Article • Microbial Genomics, September 2023, Society for General Microbiology

    Dr Robert A Edwards

  55. Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

    Article • Nature Biotechnology, August 2023, Springer Science + Business Media

    Dr Jens H. Kuhn, Dr Robert A Edwards

  56. Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome

    Article • Scientific Reports, August 2023, Springer Science + Business Media

    Dr Robert A Edwards

  57. Compounding Achromobacter Phages for Therapeutic Applications

    Article • Viruses, July 2023, MDPI AG

    Dr Robert A Edwards

  58. Classification Confidence in Exploratory Learning: A User’s Guide

    Article • Machine Learning and Knowledge Extraction, July 2023, MDPI AG

    Peter Salamon, Dr Robert A Edwards

  59. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

    Article • Nature Biotechnology, July 2023, Springer Science + Business Media

    Dr Jens H. Kuhn, Dr Robert A Edwards

  60. Host Association and Spatial Proximity Shape but Do Not Constrain Population Structure in the Mutualistic Symbiont Xenorhabdus bovienii

    Article • mBio, June 2023, ASM Journals

    Dr Robert A Edwards

  61. Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”

    Article • mBio, June 2023, ASM Journals

    Dr Robert A Edwards, Thomas Tu, Dr Subir Sarker

  62. Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”

    Article • mSphere, June 2023, ASM Journals

    Dr Robert A Edwards, Thomas Tu, Dr Subir Sarker

  63. PRFect: A tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes

    Article • June 2023, Research Square

    Dr Robert A Edwards

  64. Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”

    Article • Journal of Virology, May 2023, ASM Journals

    Dr Robert A Edwards, Thomas Tu, Dr Subir Sarker

  65. The human gut virome: composition, colonization, interactions, and impacts on human health

    Article • Frontiers in Microbiology, May 2023, Frontiers

    Dr Robert A Edwards

  66. Prophage rates in the human microbiome vary by body site and host health

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  67. The Promise and Pitfalls of Prophages

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  68. Programmed ribosomal frameshifts, and how to find them

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  69. Host interactions of novelCrassviralesspecies belonging to multiple families infecting bacterial host,Bacteroides cellulosilyticusWH2

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  70. The utility of dust for forensic intelligence: Exploring collection methods and detection limits for environmental DNA, elemental and mineralogical analyses of dust samples

    Article • Forensic Science International, March 2023, Elsevier

    Dr Robert A Edwards

  71. Heat-stressed coral microbiomes are stable and potentially beneficial at the level of taxa and functional genes

    Article • February 2023, Wiley

    Dr Robert A Edwards

  72. Assessing confidence in classification by machine learning system

    Article • Biophysical Journal, February 2023, Elsevier

    Peter Salamon, Dr Robert A Edwards

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

    Article • Archives of Virology, January 2023, Springer Science + Business Media

    Dr Robert A Edwards

  74. Ten simple rules and a template for creating workflows-as-applications

    Article • PLoS Computational Biology, December 2022, PLOS

    Dr Robert A Edwards

  75. Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome

    Article • October 2022, Research Square

    Dr Robert A Edwards

  76. Towards the biogeography of butyrate-producing bacteria

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  77. The human gut virome: Composition, colonisation, interactions, and impacts on human health

    Article • September 2022, Center for Open Science

    Dr Robert A Edwards

  78. Organizing the bacterial annotation space with amino acid sequence embeddings

    Article • BMC Bioinformatics, September 2022, Springer Science + Business Media

    Dr Robert A Edwards

  79. Ten simple rules and a template for creating workflows-as-applications

    Article • September 2022, Center for Open Science

    Dr Robert A Edwards

  80. Single-cell gene expression links SARS-CoV-2 infection and gut serotonin

    Article • Gut, August 2022, BMJ

    Dr Robert A Edwards

  81. How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research

    Article • Microorganisms, August 2022, MDPI AG

    Dr Robert A Edwards

  82. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

    Article • Microbial Ecology, August 2022, Springer Science + Business Media

    Dr Robert A Edwards

  83. Erratum for Cazares et al., “A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation”

    Article • mSystems, June 2022, ASM Journals

    Dr Robert A Edwards

  84. Hecatomb: An End-to-End Research Platform for Viral Metagenomics

    Article • May 2022, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  85. The StkSR Two-Component System Influences Colistin Resistance in Acinetobacter baumannii

    Article • Microorganisms, May 2022, MDPI AG

    Dr Robert A Edwards

  86. Philympics 2021: Prophage Predictions Perplex Programs

    Article • F1000Research, April 2022, Faculty of 1000, Ltd.

    Dr Robert A Edwards

  87. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

    Article • March 2022, Springer Science + Business Media

    Dr Robert A Edwards

  88. Predicting the capsid architecture of phages from metagenomic data

    Article • Computational and Structural Biotechnology Journal, January 2022, Elsevier

    Dr Robert A Edwards

  89. Perspective on taxonomic classification of uncultivated viruses

    Article • Current Opinion in Virology, December 2021, Elsevier

    Dr Jens H. Kuhn, Dr Robert A Edwards

  90. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

    Article • Archives of Virology, August 2021, Springer Science + Business Media

    Dr Robert A Edwards

  91. Philympics 2021: Prophage Predictions Perplex Programs

    Article • F1000Research, August 2021, Faculty of 1000, Ltd.

    Dr Robert A Edwards

  92. hafeZ: Active prophage identification through read mapping

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Prof. Juris A Grasis, Dr Robert A Edwards

  93. RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content

    Article • Patterns, July 2021, Elsevier

    Dr Robert A Edwards

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

    Article • Pathogens, June 2021, MDPI AG

    Prof Robert Colebunders, Dr Robert A Edwards

  95. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

    Article • June 2021, Springer Science + Business Media

    Dr Robert A Edwards

  96. Philympics 2021: Prophage Predictions Perplex Programs

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  97. Gut Microbiota Represent a Major Thermogenic Biomass

    Article • Function, March 2021, Oxford University Press (OUP)

    Dr Robert A Edwards

  98. MultiPhATE2: code for functional annotation and comparison of phage genomes

    Article • G3 Genes Genomes Genetics, March 2021, Oxford University Press (OUP)

    Dr Robert A Edwards

  99. A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation

    Article • mSystems, February 2021, ASM Journals

    Dr Robert A Edwards

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

    Article • Microorganisms, January 2021, MDPI AG

    Dr Robert A Edwards

  101. NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

    Article • Viruses, December 2020, MDPI AG

    Dr Robert A Edwards

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

    Article • PLoS Computational Biology, November 2020, PLOS

    Dr Robert A Edwards

  103. MultiPhATE2: Code for Functional Annotation and Comparison of Bacteriophage Genomes

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  104. RaFAH: A superior method for virus-host prediction

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  105. Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  106. Latitude and chlorophyll a density drive the distribution of carbohydrate‐active enzymes in the planktonic microbial fraction of the epipelagic zone

    Article • Environmental Microbiology Reports, August 2020, Wiley

    Dr Robert A Edwards

  107. A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes

    Article • mSystems, July 2020, ASM Journals

    Dr Robert A Edwards, Nicholas Shikuma

  108. Standardized bacteriophage purification for personalized phage therapy

    Article • Nature Protocols, July 2020, Springer Science + Business Media

    Dr Robert A Edwards

  109. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge

    Article • Microbiome, June 2020, Springer Science + Business Media

    Dr Robert A Edwards

  110. Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus)

    Article • Meta Gene, June 2020, Elsevier

    Dr Robert A Edwards

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

    Article • Metabolites, April 2020, MDPI AG

    Dr Robert A Edwards

  112. Phage and bacteria diversification through a prophage acquisition ratchet

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  114. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

    Article • Archives of Virology, March 2020, Springer Science + Business Media

    Dr Robert A Edwards

  115. Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents

    Article • Ecology and Evolution, March 2020, Wiley

    Dr Robert A Edwards

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

    Article • mBio, March 2020, ASM Journals

    Dr Robert A Edwards

  117. Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes

    Article • BMC Genomics, February 2020, Springer Science + Business Media

    Dr Robert A Edwards

  118. A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes

    Article • December 2019, Cold Spring Harbor Laboratory Press

    Nicholas Shikuma, Dr Robert A Edwards

  119. Charting the diversity of uncultured viruses of Archaea and Bacteria

    Article • BMC Biology, December 2019, Springer Science + Business Media

    Dr Robert A Edwards

  120. NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements

    Article • Genes, September 2019, MDPI AG

    Dr Robert A Edwards

  121. Genomics to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus)

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • Frontiers in Microbiology, July 2019, Frontiers

    Dr Robert A Edwards

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

    Article • Nature Microbiology, July 2019, Springer Science + Business Media

    Dr Robert A Edwards, Professor Nathaniel J Dominy, Maria Mercedes Zambrano, Professor Lawrence Mugisha

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

    Article • The Journal of Microbiology, May 2019, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Systematic Biology, May 2019, Oxford University Press (OUP)

    Dr Robert A Edwards, Dr Jens H. Kuhn

  126. multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

    Article • Bioinformatics, May 2019, Oxford University Press (OUP)

    Dr Robert A Edwards

  127. PHANOTATE: a novel approach to gene identification in phage genomes

    Article • Bioinformatics, April 2019, Oxford University Press (OUP)

    Dr Robert A Edwards

  128. Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information

    Article • mBio, April 2019, ASM Journals

    Dr Robert A Edwards

  129. Diel population and functional synchrony of microbial communities on coral reefs

    Article • Nature Communications, April 2019, Springer Science + Business Media

    Dr Robert A Edwards

  130. Prodigious Prevotella phages

    Article • Nature Microbiology, March 2019, Springer Science + Business Media

    Dr Robert A Edwards

  131. ‘Genome skimming’ with the MinION hand-held sequencer identifies CITES-listed shark species in India’s exports market

    Article • Scientific Reports, March 2019, Springer Science + Business Media

    Dr Robert A Edwards

  132. PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets

    Article • February 2019, PeerJ

    Dr Robert A Edwards

  133. PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets

    Article • February 2019, PeerJ

    Dr Robert A Edwards

  134. fastq-pair: efficient synchronization of paired-end fastq files

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  135. multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • Nature Communications, January 2019, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • January 2019, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards, Maria Mercedes Zambrano, Professor Lawrence Mugisha

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

    Article • Microbiome, October 2018, Springer Science + Business Media

    Dr Robert A Edwards

  139. Searching the Sequence Read Archive using Jetstream and Wrangler

    Article • July 2018, ACM (Association for Computing Machinery)

    Dr Robert A Edwards

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

    Article • Archives of Microbiology, June 2018, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • PeerJ, April 2018, PeerJ

    Dr Robert A Edwards

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

    Article • International Journal of Molecular Sciences, April 2018, MDPI AG

    Dr Robert A Edwards

  143. THEA: A novel approach to gene identification in phage genomes

    Article • February 2018, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • January 2018, PeerJ

    Dr Robert A Edwards

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

    Article • January 2018, PeerJ

    Dr Robert A Edwards

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

    Article • Archives of Virology, January 2018, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Hanna M Oksanen, Dr Robert A Edwards, Dr Jens H. Kuhn

  147. Kullback Leibler divergence in complete bacterial and phage genomes

    Article • PeerJ, November 2017, PeerJ

    Dr Robert A Edwards

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

    Article • BMC Genomics, November 2017, Springer Science + Business Media

    Dr Robert A Edwards

  149. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Dr Jens H. Kuhn, Dr Robert A Edwards

  150. Phage Genome Annotation Using the RAST Pipeline

    Article • November 2017, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • Nature Microbiology, November 2017, Nature

    Dr Robert A Edwards

  152. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

    Article • Nature Chemical Biology, October 2017, Springer Science + Business Media

    Dr Robert A Edwards, Dr Nikos C Kyrpides

  153. Erratum: Corrigendum: Allelic variation contributes to bacterial host specificity

    Article • Nature Communications, August 2017, Springer Science + Business Media

    Dr Robert A Edwards

  154. Biological chlorine cycling in the Arctic Coastal Plain

    Article • Biodegradation, July 2017, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Nature Communications, July 2017, Nature

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • Frontiers in Microbiology, May 2017, Frontiers

    Dr Robert A Edwards

  157. Variability and host density independence in inductions-based estimates of environmental lysogeny

    Article • Nature Microbiology, April 2017, Nature

    Dr Robert A Edwards, Prof. Juris A Grasis

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

    Article • Bioinformatics, March 2017, Oxford University Press (OUP)

    Dr Robert A Edwards

  159. Prophage genomics reveals patterns in phage genome organization and replication

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  160. PMAnalyzer: a new web interface for bacterial growth curve analysis

    Article • Bioinformatics, February 2017, Oxford University Press (OUP)

    Dr Robert A Edwards

  161. Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

    Article • January 2017, Cold Spring Harbor Laboratory Press

    Dr Nikos C Kyrpides, Dr Robert A Edwards

  162. An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS

    Article • January 2017, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Archives of Virology, December 2016, Springer Science + Business Media

    Dr Robert A Edwards, Prof. Dr. Bas E. Dutilh, Dr Hanna M Oksanen, Dr Jens H. Kuhn

  164. Elucidating genomic gaps using phenotypic profiles

    Article • F1000Research, October 2016, Faculty of 1000, Ltd.

    Dr Robert A Edwards

  165. Poster Session Abstracts

    Article • Pediatric Pulmonology, September 2016, Wiley

    Dr Robert A Edwards

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

    Article • Proceedings of the Royal Society B Biological Sciences, August 2016, Royal Society Publishing

    Dr Robert A Edwards

  167. Erratum: Corrigendum: Lytic to temperate switching of viral communities

    Article • Nature, August 2016, Springer Science + Business Media

    Dr Robert A Edwards

  168. Qudaich: A smart sequence aligner

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • Frontiers in Microbiology, June 2016, Frontiers

    Dr Robert A Edwards

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

    Article • Genome Announcements, May 2016, ASM Journals

    Dr Robert A Edwards

  171. Global microbialization of coral reefs

    Article • Nature Microbiology, April 2016, Springer Science + Business Media

    Dr Robert A Edwards

  172. FOCUS2: agile and sensitive classification of metagenomics data using a reduced database

    Article • March 2016, Cold Spring Harbor Laboratory Press

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  173. Lytic to temperate switching of viral communities

    Article • Nature, March 2016, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • PLOS One, February 2016, PLOS

    Dr Robert A Edwards

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

    Article • Archives of Virology, January 2016, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards, Dr Jens H. Kuhn

  176. Computational approaches to predict bacteriophage–host relationships

    Article • FEMS Microbiology Reviews, December 2015, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  177. Some of the most interesting CASP11 targets through the eyes of their authors

    Article • Proteins Structure Function and Bioinformatics, November 2015, Wiley

    Dr Robert A Edwards

  178. Allelic variation contributes to bacterial host specificity

    Article • Nature Communications, October 2015, Nature

    Dr Min Yue, Dr Robert A Edwards, Prof Min Yue

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

    Article • Bioinformatics, October 2015, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • PLOS One, June 2015, PLOS

    Dr Robert A Edwards

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

    Article • Genome Announcements, June 2015, ASM Journals

    Dr Pablo Vinuesa, Claudia Silva, Dr Robert A Edwards

  182. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    Article • PeerJ, June 2015, PeerJ

    Dr Robert A Edwards

  183. Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

    Article • Journal of Visualized Experiments, June 2015, MyJove Corporation

    Dr Robert A Edwards

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

    Article • PLOS One, June 2015, PLOS

    Dr Robert A Edwards

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

    Article • PLOS One, June 2015, PLOS

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • Frontiers in Microbiology, May 2015, Frontiers

    Dr Robert A Edwards

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

    Article • Virology, March 2015, Elsevier

    Dr Robert A Edwards

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

    Article • Scientific Reports, February 2015, Springer Science + Business Media

    Dr Robert A Edwards

  189. Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

    Article • Archives of Microbiology, December 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Professor Martin Polz, Dr Robert A Edwards

  190. GenomePeek - An online tool for prokaryotic and metagenome analysis

    Article • October 2014, PeerJ

    Dr Robert A Edwards

  191. Elucidating genomic gaps using phenotypic profiles

    Article • F1000Research, September 2014, Faculty of 1000, Ltd.

    Dr Robert A Edwards, DANIEL RIOS GARZA, Daniel A Cuevas

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

    Article • PeerJ, August 2014, PeerJ

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • Nature Communications, July 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • July 2014, PeerJ

    Dr Robert A Edwards

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

    Article • Proceedings of the National Academy of Sciences, June 2014, Proceedings of the National Academy of Sciences

    Dr Robert A Edwards

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

    Article • PeerJ, June 2014, PeerJ

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards, Professor Iruka Okeke

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

    Article • Nucleic Acids Research, November 2013, Oxford University Press (OUP)

    Dr Robert A Edwards

  199. Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis

    Article • Journal of Clinical Microbiology, November 2013, ASM Journals

    Dr Robert A Edwards

  200. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis

    Article • Genome Announcements, November 2013, ASM Journals

    Dr Robert A Edwards, Karl Klose

  201. Genomic Taxonomy of the Genus Prochlorococcus

    Article • Microbial Ecology, August 2013, Springer Science + Business Media

    Dr Robert A Edwards

  202. Mechanistic Model of Rothia mucilaginosa Adaptation toward Persistence in the CF Lung, Based on a Genome Reconstructed from Metagenomic Data

    Article • PLOS One, May 2013, PLOS

    Dr Robert A Edwards

  203. Explaining microbial phenotypes on a genomic scale: GWAS for microbes

    Article • Briefings in Functional Genomics, April 2013, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • Journal of Cystic Fibrosis, March 2013, Elsevier

    Dr Robert A Edwards

  205. Structure and function of a cyanophage-encoded peptide deformylase

    Article • The ISME Journal, February 2013, Springer Science + Business Media

    Dr Robert A Edwards

  206. Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals

    Article • Microbial Ecology, January 2013, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Scientific Reports, January 2013, Springer Science + Business Media

    Dr Robert A Edwards

  208. Combining de novo and reference-guided assembly with scaffold_builder

    Article • Source Code for Biology and Medicine, January 2013, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  209. Microbial genomic taxonomy

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Dr Robert A Edwards

  211. Multivariate analysis of functional metagenomes

    Article • Frontiers in Genetics, January 2013, Frontiers

    Dr Robert A Edwards

  212. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes

    Article • BMC Evolutionary Biology, January 2013, Springer Science + Business Media

    Dr Robert A Edwards

  213. SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

    Article • PLOS One, October 2012, PLOS

    Dr Robert A Edwards

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

    Article • Bioinformatics, October 2012, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  215. Real Time Metagenomics: Using k-mers to annotate metagenomes

    Article • Bioinformatics, October 2012, Oxford University Press (OUP)

    Dr Robert A Edwards

  216. Poster Session Abstracts

    Article • Pediatric Pulmonology, September 2012, Wiley

    Dr Robert A Edwards

  217. Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations among Targeted Salmonella Genes

    Article • Applied and Environmental Microbiology, August 2012, ASM Journals

    Dr Robert A Edwards, Prof Min Yue

  218. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

    Article • PLOS One, July 2012, PLOS

    Jonathan Eisen, Prof. Jonathan A. Eisen, Morgan Langille, Dr Robert A Edwards

  219. Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

    Article • PLOS One, July 2012, PLOS

    Prof. Dr. Bas E. Dutilh, Dr. Gisele Lôbo Hajdu, Dr Robert A Edwards

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

    Article • PLOS One, June 2012, PLOS

    Dr Dieter M Schifferli, Dr Robert A Edwards, Prof Min Yue

  221. Abrolhos Bank Reef Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and Fish Biomass Data

    Article • PLOS One, June 2012, PLOS

    Dr Robert A Edwards

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

    Article • PLOS One, May 2012, PLOS

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

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

    Article • Nucleic Acids Research, May 2012, Oxford University Press (OUP)

    Dr Robert A Edwards

  224. Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9

    Article • Journal of Bacteriology, May 2012, ASM Journals

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  225. Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank

    Article • Journal of Bacteriology, April 2012, ASM Journals

    Dr Robert A Edwards

  226. Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792

    Article • Journal of Bacteriology, March 2012, ASM Journals

    Professor Sonia A. Soto-Rodriguez, Dr Robert A Edwards

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

    Article • BMC Bioinformatics, March 2012, Springer Science + Business Media

    Dr Robert A Edwards

  228. Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis Strain LK5

    Article • Applied and Environmental Microbiology, January 2012, ASM Journals

    Dr Robert A Edwards

  229. PHACTS, a computational approach to classifying the lifestyle of phages

    Article • Bioinformatics, January 2012, Oxford University Press (OUP)

    Dr Robert A Edwards

  230. Insights into antibiotic resistance through metagenomic approaches

    Article • Future Microbiology, January 2012, Future Medicine

    Dr Robert A Edwards

  231. Identification and removal of ribosomal RNA sequences from metatranscriptomes

    Article • Bioinformatics, December 2011, Oxford University Press (OUP)

    Dr Robert A Edwards

  232. MetaBase--the wiki-database of biological databases

    Article • Nucleic Acids Research, December 2011, Oxford University Press (OUP)

    Dr Robert A Edwards

  233. Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites

    Article • November 2011, Wiley

    Dr Robert A Edwards

  234. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

    Article • November 2011, Wiley

    Dr Robert A Edwards

  235. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

    Article • Environmental Microbiology, October 2011, Wiley

    Dr Susannah Green Tringe, Dr Robert A Edwards

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

    Article • Biochimica et Biophysica Acta (BBA) - General Subjects, October 2011, Elsevier

    Dr Robert A Edwards

  237. Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia

    Article • Journal of Bacteriology, September 2011, ASM Journals

    Dr Michel Abanto Marin, Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  238. Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets

    Article • BMC Bioinformatics, August 2011, Springer Science + Business Media

    Dr Robert A Edwards

  239. Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

    Article • PLOS One, March 2011, PLOS

    Dr Robert A Edwards

  240. Quality control and preprocessing of metagenomic datasets

    Article • Bioinformatics, January 2011, Oxford University Press (OUP)

    Dr Robert A Edwards

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

    Article • Archives of Microbiology, November 2010, Springer Science + Business Media

    Dr Robert A Edwards

  242. Chromosomal Rearrangements Formed by rrn Recombination Do Not Improve Replichore Balance in Host-Specific Salmonella enterica Serovars

    Article • PLOS One, October 2010, PLOS

    Dr Robert A Edwards

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

    Article • BMC Bioinformatics, June 2010, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Nucleic Acids Research, March 2010, Oxford University Press (OUP)

    Dr Robert A Edwards

  245. Viral and microbial community dynamics in four aquatic environments

    Article • The ISME Journal, February 2010, Springer Science + Business Media

    Dr Robert A Edwards

  246. Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Dr Robert A Edwards

  247. Lysogeny and Sporulation in Bacillus Isolates from the Gulf of Mexico

    Article • Applied and Environmental Microbiology, December 2009, ASM Journals

    Dr Robert A Edwards

  248. The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

    Article • PLoS Computational Biology, December 2009, PLOS

    Dr Robert A Edwards

  249. Metagenomic analysis of stressed coral holobionts

    Article • Environmental Microbiology, August 2009, Wiley

    Dr Robert A Edwards

  250. Deviations from Ultrametricity in Phage Protein Distances

    Article • Open Systems & Information Dynamics, March 2009, World Scientific Pub Co Pte Lt

    Dr Robert A Edwards

  251. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

    Article • Proceedings of the National Academy of Sciences, February 2009, Proceedings of the National Academy of Sciences

    Dr Robert A Edwards

  252. Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico

    Article • Environmental Microbiology, January 2009, Wiley

    Dr Robert A Edwards

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

    Article • Proceedings of the National Academy of Sciences, November 2008, Proceedings of the National Academy of Sciences

    Dr Robert A Edwards

  254. Erratum: Functional metagenomic profiling of nine biomes

    Article • Nature, October 2008, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • BMC Bioinformatics, September 2008, Springer Science + Business Media

    Dr Robert A Edwards

  256. Viral communities associated with healthy and bleaching corals

    Article • Environmental Microbiology, September 2008, Wiley

    Dr Robert A Edwards

  257. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

    Article • PLOS One, August 2008, PLOS

    Dr Robert A Edwards

  258. Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

    Article • PLOS One, August 2008, PLOS

    Dr Robert A Edwards

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

    Article • Journal of Biotechnology, August 2008, Elsevier

    Dr Robert A Edwards

  260. The smallest cells pose the biggest problems: high-performance computing and the analysis of metagenome sequence data

    Article • Journal of Physics Conference Series, July 2008, Institute of Physics Publishing

    Dr Robert A Edwards

  261. Viral diversity and dynamics in an infant gut

    Article • Research in Microbiology, June 2008, Elsevier

    Dr Robert A Edwards

  262. The minimum information about a genome sequence (MIGS) specification

    Article • Nature Biotechnology, May 2008, Springer Science + Business Media

    Professor Julian Parkhill, Dr Andrew J Spiers, Prof George M Garrity, Dr Robert A Edwards, Dr Nikos C Kyrpides

  263. Functional metagenomic profiling of nine biomes

    Article • Nature, March 2008, Springer Science + Business Media

    Dr Robert A Edwards

  264. Biodiversity and biogeography of phages in modern stromatolites and thrombolites

    Article • Nature, March 2008, Springer Science + Business Media

    Dr Robert A Edwards

  265. Microbial Ecology of Four Coral Atolls in the Northern Line Islands

    Article • PLOS One, February 2008, PLOS

    Dr Robert A Edwards

  266. Phylogenetic classification of short environmental DNA fragments

    Article • Nucleic Acids Research, February 2008, Oxford University Press (OUP)

    Dr Robert A Edwards

  267. Bacterial carbon processing by generalist species in the coastal ocean

    Article • Nature, January 2008, Springer Science + Business Media

    Dr Robert A Edwards

  268. The RAST Server: Rapid Annotations using Subsystems Technology

    Article • BMC Genomics, January 2008, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Environmental Microbiology, November 2007, Wiley

    Dr Robert A Edwards

  270. Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

    Article • Applied and Environmental Microbiology, September 2007, ASM Journals

    Dr Robert A Edwards

  271. Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

    Article • Genome Research, July 2007, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  272. Marine Environmental Genomics: Unlocking the Ocean's Secrets

    Article • Oceanography, June 2007, The Oceanography Society

    Dr Robert A Edwards

  273. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

    Article • Nucleic Acids Research, January 2007, Oxford University Press (OUP)

    Dr Robert A Edwards

  274. The Marine Viromes of Four Oceanic Regions

    Article • PLoS Biology, November 2006, PLOS

    Professor curtis A suttle, Dr Robert A Edwards

  275. Essential genes on metabolic maps

    Article • Current Opinion in Biotechnology, October 2006, Elsevier

    Dr Robert A Edwards

  276. Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli

    Article • Journal of Bacteriology, September 2006, ASM Journals

    Dr Robert A Edwards

  277. Finding novel genes in bacterial communities isolated from the environment

    Article • Bioinformatics, July 2006, Oxford University Press (OUP)

    Dr Robert A Edwards

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

    Article • Ecology Letters, July 2006, Wiley

    Dr Robert A Edwards

  279. Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior

    Article • Science, January 2006, American Association for the Advancement of Science

    Professor Matthew B Sullivan, Dr Robert A Edwards

  280. Transcriptional Profiling of Mycoplasma hyopneumoniae during Heat Shock Using Microarrays

    Article • Infection and Immunity, January 2006, ASM Journals

    Dr Robert A Edwards

  281. Article • BMC Bioinformatics, January 2006, Springer Science + Business Media

    Dr Robert A Edwards

  282. Article • BMC Genomics, January 2006, Springer Science + Business Media

    Dr Robert A Edwards

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

    Article • Gene, January 2006, Elsevier

    Dr Robert A Edwards

  284. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

    Article • Nucleic Acids Research, September 2005, Oxford University Press (OUP)

    Dr Robert A Edwards

  285. Low-Molecular-Weight Protein Tyrosine Phosphatases of Bacillus subtilis

    Article • Journal of Bacteriology, July 2005, ASM Journals

    Dr Robert A Edwards

  286. Mosaic Prophages with Horizontally Acquired Genes Account for the Emergence and Diversification of the Globally Disseminated M1T1 Clone of Streptococcus pyogenes

    Article • Journal of Bacteriology, May 2005, ASM Journals

    Dr Allison McGeer, Dr Robert A Edwards

  287. In Vitro Characterization of the Bacillus subtilis Protein Tyrosine Phosphatase YwqE

    Article • Journal of Bacteriology, May 2005, ASM Journals

    Dr Robert A Edwards

  288. Viral metagenomics

    Article • Nature Reviews Microbiology, May 2005, Springer Science + Business Media

    Dr Robert A Edwards

  289. A Glimpse into the Expanded Genome Content of Vibrio cholerae through Identification of Genes Present in Environmental Strains

    Article • Journal of Bacteriology, May 2005, ASM Journals

    Dr Robert A Edwards

  290. Genome of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting Gram-Positive Bacteria with a Low G+C Content

    Article • Journal of Bacteriology, May 2004, ASM Journals

    Dr Robert A Edwards

  291. Draft Sequencing and Comparative Genomics of Xylella fastidiosa Strains Reveal Novel Biological Insights

    Article • Genome Research, September 2002, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards, Dr Nikos C Kyrpides

  292. The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage

    Article • Journal of Bacteriology, August 2002, ASM Journals

    Dr Robert A Edwards

  293. The importance of complete genome sequences

    Article • Trends in Microbiology, May 2002, Elsevier

    Professor Julian Parkhill, Dr Robert A Edwards

  294. The importance of complete genome sequences

    Article • Trends in Microbiology, May 2002, Elsevier

    Dr Robert A Edwards

  295. Comparative genomics of closely related salmonellae

    Article • Trends in Microbiology, February 2002, Elsevier

    Dr Robert A Edwards

  296. Genomic analysis and growth-phase-dependent regulation of the SEF14 fimbriae of Salmonella enterica serovar Enteritidis

    Article • Microbiology, October 2001, Society for General Microbiology

    Dr Robert A Edwards

  297. Salmonella enterica Serovar Typhi Possesses a Unique Repertoire of Fimbrial Gene Sequences

    Article • Infection and Immunity, May 2001, ASM Journals

    Professor Andreas J Baumler, Dr Robert A Edwards

  298. An old dog learns new tricks

    Article • Trends in Microbiology, May 2001, Elsevier

    Dr Robert A Edwards

  299. Inside or Outside: Detecting the Cellular Location of Bacterial Pathogens

    Article • BioTechniques, February 2001, Future Science

    Dr Robert A Edwards

  300. Evolution of microbial pathogens

    Article • Trends in Genetics, March 2000, Elsevier

    Dr Robert A Edwards

  301. A role for Salmonella fimbriae in intraperitoneal infections

    Article • Proceedings of the National Academy of Sciences, February 2000, Proceedings of the National Academy of Sciences

    Dr Robert A Edwards

  302. Eye of newt and toe of frog

    Article • Trends in Genetics, June 1999, Elsevier

    Dr Robert A Edwards

  303. Increasing DNA Transfer Efficiency by Temporary Inactivation of Host Restriction

    Article • BioTechniques, May 1999, Future Science

    Dr Robert A Edwards

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

    Article • Trends in Microbiology, July 1998, Elsevier

    Dr Robert A Edwards

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

    Article • Gene, January 1998, Elsevier

    Dr Dieter M Schifferli, Dr Robert A Edwards

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

    Article • Molecular Microbiology, August 1997, Wiley

    Dr Dieter M Schifferli, Dr Robert A Edwards

  307. Identification of major and minor chaperone proteins involved in the export of 987P fimbriae.

    Article • Journal of Bacteriology, January 1996, ASM Journals

    Dr Robert A Edwards

  308. Nitrogen control in bacteria

    Article • Microbiological Reviews, December 1995, ASM Journals

    Dr Robert A Edwards

  309. The role of uridylyltransferase in the control ofKlebsiella pneumoniae nif gene regulation

    Article • MGG Molecular & General Genetics, January 1995, Springer Science + Business Media

    Dr Robert A Edwards

  310. Nitrogen control in bacteria.

    Article • Microbiological Reviews, January 1995, ASM Journals

    Dr Robert A Edwards