All Stories

  1. 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

  2. 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

  3. 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

  4. Standardized bacteriophage purification for personalized phage therapy

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

    Dr Robert A Edwards

  5. 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

  6. 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

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

    Article • Metabolites, April 2020, MDPI AG

    Dr Robert A Edwards

  8. 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

  9. 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

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

    Article • mBio, March 2020, ASM Journals

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • Genes, September 2019, MDPI AG

    Dr Robert A Edwards

  14. 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

  15. 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

  16. 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

  17. 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

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

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

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • mBio, April 2019, ASM Journals

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

  22. Prodigious Prevotella phages

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

    Dr Robert A Edwards

  23. ‘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

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

    Article • February 2019, PeerJ

    Dr Robert A Edwards

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

    Article • February 2019, PeerJ

    Dr Robert A Edwards

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

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

  27. 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

  28. 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

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

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

    Dr Robert A Edwards

  30. Searching the Sequence Read Archive using Jetstream and Wrangler

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

    Dr Robert A Edwards

  31. 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

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

    Article • PeerJ, April 2018, PeerJ

    Dr Robert A Edwards

  33. 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

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

    Article • February 2018, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • January 2018, PeerJ

    Dr Robert A Edwards

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

    Article • January 2018, PeerJ

    Dr Robert A Edwards

  37. 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

  38. Kullback Leibler divergence in complete bacterial and phage genomes

    Article • PeerJ, November 2017, PeerJ

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

  40. Phage Genome Annotation Using the RAST Pipeline

    Article • November 2017, Springer Science + Business Media

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

  41. 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

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

    Article • Nature Methods, October 2017, Springer Science + Business Media

    Dr Robert A Edwards, Dr Nikos C Kyrpides

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

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

    Dr Robert A Edwards

  44. Biological chlorine cycling in the Arctic Coastal Plain

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

    Dr Robert A Edwards

  45. 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

  46. 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

  47. 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

  48. 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

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

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • January 2017, Springer Science + Business Media

    Dr Robert A Edwards

  52. 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

  53. Elucidating genomic gaps using phenotypic profiles

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

    Dr Robert A Edwards

  54. 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

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

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

    Dr Robert A Edwards

  56. Qudaich: A smart sequence aligner

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Dr Robert A Edwards

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

    Article • Frontiers in Microbiology, June 2016, Frontiers

    Dr Robert A Edwards

  58. 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

  59. Global microbialization of coral reefs

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

    Dr Robert A Edwards

  60. Lytic to temperate switching of viral communities

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

    Dr Robert A Edwards

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

    Article • PLoS ONE, February 2016, PLOS

    Dr Robert A Edwards

  62. 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

  63. 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

  64. 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

  65. Allelic variation contributes to bacterial host specificity

    Article • Nature Communications, October 2015, Nature

    Dr Min Yue, Dr Robert A Edwards

  66. 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

  67. 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

  68. 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

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

    Article • PeerJ, June 2015, PeerJ

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • PLoS ONE, June 2015, PLOS

    Dr Robert A Edwards

  72. 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

  73. 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

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

    Article • Virology, March 2015, Elsevier

    Dr Robert A Edwards

  75. 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

  76. 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

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

    Article • October 2014, PeerJ

    Dr Robert A Edwards

  78. Elucidating genomic gaps using phenotypic profiles

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

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

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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

  84. 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, Iruka Okeke

  85. 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

  86. 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

  87. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis

    Article • Genome Announcements, November 2013, ASM Journals

    Dr Robert A Edwards, Karl Klose

  88. Genomic Taxonomy of the Genus Prochlorococcus

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

    Dr Robert A Edwards

  89. 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

  90. 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

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

    Article • Journal of Cystic Fibrosis, March 2013, Elsevier

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

  94. 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

  95. 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

  96. Microbial genomic taxonomy

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

    Dr Robert A Edwards

  97. 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

  98. Multivariate analysis of functional metagenomes

    Article • Frontiers in Genetics, January 2013, Frontiers

    Dr Robert A Edwards

  99. 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

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

    Article • PLoS ONE, October 2012, PLOS

    Dr Robert A Edwards

  101. 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

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

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

    Dr Robert A Edwards

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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

  114. 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

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

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

    Dr Robert A Edwards

  116. Insights into antibiotic resistance through metagenomic approaches

    Article • Future Microbiology, January 2012, Future Medicine

    Dr Robert A Edwards

  117. Identification and removal of ribosomal RNA sequences from metatranscriptomes

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

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • November 2011, Wiley

    Dr Robert A Edwards

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

    Article • November 2011, Wiley

    Dr Robert A Edwards

  121. 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

  122. 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

  123. 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

  124. 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

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

    Article • PLoS ONE, March 2011, PLOS

    Dr Robert A Edwards

  126. Quality control and preprocessing of metagenomic datasets

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

    Dr Robert A Edwards

  127. 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

  128. 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

  129. 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

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

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

    Dr Robert A Edwards

  131. Viral and microbial community dynamics in four aquatic environments

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

    Dr Robert A Edwards

  132. 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

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

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

    Dr Robert A Edwards

  134. 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

  135. Metagenomic analysis of stressed coral holobionts

    Article • Environmental Microbiology, August 2009, Wiley

    Dr Robert A Edwards

  136. Deviations from Ultrametricity in Phage Protein Distances

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

    Dr Robert A Edwards

  137. 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

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

    Article • Environmental Microbiology, January 2009, Wiley

    Dr Robert A Edwards

  139. 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

  140. Erratum: Functional metagenomic profiling of nine biomes

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

    Dr Robert A Edwards

  141. 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

  142. Viral communities associated with healthy and bleaching corals

    Article • Environmental Microbiology, September 2008, Wiley

    Dr Robert A Edwards

  143. 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

  144. 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

  145. 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

  146. 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

  147. Viral diversity and dynamics in an infant gut

    Article • Research in Microbiology, June 2008, Elsevier

    Dr Robert A Edwards

  148. 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

  149. Functional metagenomic profiling of nine biomes

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

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • PLoS ONE, February 2008, PLOS

    Dr Robert A Edwards

  152. Phylogenetic classification of short environmental DNA fragments

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

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

  154. The RAST Server: Rapid Annotations using Subsystems Technology

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

    Dr Robert A Edwards

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

    Article • Environmental Microbiology, November 2007, Wiley

    Dr Robert A Edwards

  156. 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

  157. 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

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

    Article • Oceanography, June 2007, The Oceanography Society

    Dr Robert A Edwards

  159. 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

  160. The Marine Viromes of Four Oceanic Regions

    Article • PLoS Biology, November 2006, PLOS

    Professor curtis A suttle, Dr Robert A Edwards

  161. Essential genes on metabolic maps

    Article • Current Opinion in Biotechnology, October 2006, Elsevier

    Dr Robert A Edwards

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

    Article • Journal of Bacteriology, September 2006, ASM Journals

    Dr Robert A Edwards

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

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

    Dr Robert A Edwards

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

    Article • Ecology Letters, July 2006, Wiley

    Dr Robert A Edwards

  165. 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

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

    Article • Infection and Immunity, January 2006, ASM Journals

    Dr Robert A Edwards

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

    Dr Robert A Edwards

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

    Dr Robert A Edwards

  169. 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

  170. 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

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

    Article • Journal of Bacteriology, July 2005, ASM Journals

    Dr Robert A Edwards

  172. 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

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

    Article • Journal of Bacteriology, May 2005, ASM Journals

    Dr Robert A Edwards

  174. Viral metagenomics

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

    Dr Robert A Edwards

  175. 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

  176. 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

  177. 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

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

    Article • Journal of Bacteriology, August 2002, ASM Journals

    Dr Robert A Edwards

  179. The importance of complete genome sequences

    Article • Trends in Microbiology, May 2002, Elsevier

    Professor Julian Parkhill, Dr Robert A Edwards

  180. Comparative genomics of closely related salmonellae

    Article • Trends in Microbiology, February 2002, Elsevier

    Dr Robert A Edwards

  181. 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

  182. 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

  183. An old dog learns new tricks

    Article • Trends in Microbiology, May 2001, Elsevier

    Dr Robert A Edwards

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

    Article • BioTechniques, February 2001, Future Science

    Dr Robert A Edwards

  185. Evolution of microbial pathogens

    Article • Trends in Genetics, March 2000, Elsevier

    Dr Robert A Edwards

  186. 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

  187. Eye of newt and toe of frog

    Article • Trends in Genetics, June 1999, Elsevier

    Dr Robert A Edwards

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

    Article • BioTechniques, May 1999, Future Science

    Dr Robert A Edwards

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

    Article • Trends in Microbiology, July 1998, Elsevier

    Dr Robert A Edwards

  190. 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

  191. 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

  192. 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

  193. 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

  194. Nitrogen control in bacteria.

    Article • Microbiological Reviews, January 1995, ASM Journals

    Dr Robert A Edwards