Robert A. Edwards Department of Biology San Diego State University Biography Publications Institution JoVE Articles Robert A. Edwards has not added a biography. If you are Robert A. Edwards and would like to personalize this page please email our Author Liaison for assistance. Publications Genomic Comparison of the Closely-Related Salmonella Enterica Serovars Enteritidis, Dublin and Gallinarum PloS One. 2015 | Pubmed ID: 26039056 Multidimensional Metrics for Estimating Phage Abundance, Distribution, Gene Density, and Sequence Coverage in Metagenomes Frontiers in Microbiology. 2015 | Pubmed ID: 26005436 RASTtk: a Modular and Extensible Implementation of the RAST Algorithm for Building Custom Annotation Pipelines and Annotating Batches of Genomes Scientific Reports. 2015 | Pubmed ID: 25666585 Microbial Taxonomy in the Post-genomic Era: Rebuilding from Scratch? Archives of Microbiology. Apr, 2015 | Pubmed ID: 25533848 Sequencing at Sea: Challenges and Experiences in Ion Torrent PGM Sequencing During the 2013 Southern Line Islands Research Expedition PeerJ. 2014 | Pubmed ID: 25177534 Comparative Genomics of 274 Vibrio Cholerae Genomes Reveals Mobile Functions Structuring Three Niche Dimensions BMC Genomics. 2014 | Pubmed ID: 25096633 A Highly Abundant Bacteriophage Discovered in the Unknown Sequences of Human Faecal Metagenomes Nature Communications. 2014 | Pubmed ID: 25058116 Local Genomic Adaptation of Coral Reef-associated Microbiomes to Gradients of Natural Variability and Anthropogenic Stressors Proceedings of the National Academy of Sciences of the United States of America. Jul, 2014 | Pubmed ID: 24982156 FOCUS: an Alignment-free Model to Identify Organisms in Metagenomes Using Non-negative Least Squares PeerJ. 2014 | Pubmed ID: 24949242 Wnt Signaling Directs a Metabolic Program of Glycolysis and Angiogenesis in Colon Cancer The EMBO Journal. Jul, 2014 | Pubmed ID: 24825347 Excited State Photoreaction Between the Indole Side Chain of Tryptophan and Halocompounds Generates New Fluorophores and Unique Modifications Photochemistry and Photobiology. Sep-Oct, 2014 | Pubmed ID: 24738707 Angiogenic Sprouting is Regulated by Endothelial Cell Expression of Slug Journal of Cell Science. May, 2014 | Pubmed ID: 24554431 The Cytokine IL-22 Promotes Pathogen Colonization by Suppressing Related Commensal Bacteria Immunity. Feb, 2014 | Pubmed ID: 24508234 The SEED and the Rapid Annotation of Microbial Genomes Using Subsystems Technology (RAST) Nucleic Acids Research. Jan, 2014 | Pubmed ID: 24293654 Microbial Genomic Taxonomy BMC Genomics. 2013 | Pubmed ID: 24365132 Combining De Novo and Reference-guided Assembly with Scaffold_builder Source Code for Biology and Medicine. 2013 | Pubmed ID: 24267787 Draft Genome Sequence of the Fish Pathogen Piscirickettsia Salmonis Genome Announcements. 2013 | Pubmed ID: 24201203 Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron Cell Host & Microbe. Jul, 2013 | Pubmed ID: 23870311 Circadian Clock Regulates the Host Response to Salmonella Proceedings of the National Academy of Sciences of the United States of America. Jun, 2013 | Pubmed ID: 23716692 Explaining Microbial Phenotypes on a Genomic Scale: GWAS for Microbes Briefings in Functional Genomics. Jul, 2013 | Pubmed ID: 23625995 Multivariate Analysis of Functional Metagenomes Frontiers in Genetics. 2013 | Pubmed ID: 23579547 Structure and Function of a Cyanophage-encoded Peptide Deformylase The ISME Journal. Jun, 2013 | Pubmed ID: 23407310 A Bioinformatic Analysis of Ribonucleotide Reductase Genes in Phage Genomes and Metagenomes BMC Evolutionary Biology. 2013 | Pubmed ID: 23391036 Applying Shannon's Information Theory to Bacterial and Phage Genomes and Metagenomes Scientific Reports. 2013 | Pubmed ID: 23301154 Intracellular Trafficking of the KV1.3 Potassium Channel is Regulated by the Prodomain of a Matrix Metalloprotease The Journal of Biological Chemistry. Mar, 2013 | Pubmed ID: 23300077 SEED Servers: High-performance Access to the SEED Genomes, Annotations, and Metabolic Models PloS One. 2012 | Pubmed ID: 23110173 Reference-independent Comparative Metagenomics Using Cross-assembly: CrAss Bioinformatics (Oxford, England). Dec, 2012 | Pubmed ID: 23074261 Real Time Metagenomics: Using K-mers to Annotate Metagenomes Bioinformatics (Oxford, England). Dec, 2012 | Pubmed ID: 23047562 Metabolic Trajectory of Cellular Differentiation in Small Intestine by Phasor Fluorescence Lifetime Microscopy of NADH Scientific Reports. 2012 | Pubmed ID: 22891156 Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations Among Targeted Salmonella Genes Applied and Environmental Microbiology. Oct, 2012 | Pubmed ID: 22885744 Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux PloS One. 2012 | Pubmed ID: 22848480 Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera Brasiliensis PloS One. 2012 | Pubmed ID: 22768320 Diversification of the Salmonella Fimbriae: a Model of Macro- and Microevolution PloS One. 2012 | Pubmed ID: 22701679 Genome-wide Study of the Defective Sucrose Fermenter Strain of Vibrio Cholerae from the Latin American Cholera Epidemic PloS One. 2012 | Pubmed ID: 22662140 MiR-23a Promotes the Transition from Indolent to Invasive Colorectal Cancer Cancer Discovery. Jun, 2012 | Pubmed ID: 22628407 PhiSpy: a Novel Algorithm for Finding Prophages in Bacterial Genomes That Combines Similarity- and Composition-based Strategies Nucleic Acids Research. Sep, 2012 | Pubmed ID: 22584627 Genome Sequences of the Ethanol-tolerant Lactobacillus Vini Strains LMG 23202T and JP7.8.9 Journal of Bacteriology. Jun, 2012 | Pubmed ID: 22582376 Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio Campbellii Strain PEL22A, Isolated in the Abrolhos Bank Journal of Bacteriology. May, 2012 | Pubmed ID: 22535939 Muscle Sarcomas and Alopecia in A/J Mice Chronically Treated with Nicotine Life Sciences. Nov, 2012 | Pubmed ID: 22521759 Draft Genome Sequence of the Shrimp Pathogen Vibrio Harveyi CAIM 1792 Journal of Bacteriology. Apr, 2012 | Pubmed ID: 22461546 Zinc Sequestration by the Neutrophil Protein Calprotectin Enhances Salmonella Growth in the Inflamed Gut Cell Host & Microbe. Mar, 2012 | Pubmed ID: 22423963 PhiSiGns: an Online Tool to Identify Signature Genes in Phages and Design PCR Primers for Examining Phage Diversity BMC Bioinformatics. 2012 | Pubmed ID: 22385976 TNF-α Induces Up-Regulation of EGFR Expression and Signaling in Human Colonic Myofibroblasts American Journal of Physiology. Gastrointestinal and Liver Physiology. Feb, 2012 | Pubmed ID: 22301110 Characterization of the ELPhiS Prophage from Salmonella Enterica Serovar Enteritidis Strain LK5 Applied and Environmental Microbiology. Jan, 2012 | Pubmed ID: 22247173 PHACTS, a Computational Approach to Classifying the Lifestyle of Phages Bioinformatics (Oxford, England). Jan, 2012 | Pubmed ID: 22238260 Phage-bacteria Relationships and CRISPR Elements Revealed by a Metagenomic Survey of the Rumen Microbiome Environmental Microbiology. Jan, 2012 | Pubmed ID: 22004549 Genome Sequence of the Human Pathogen Vibrio Cholerae Amazonia Journal of Bacteriology. Oct, 2011 | Pubmed ID: 21952545 Cytokine-induced Alterations of α7 Nicotinic Receptor in Colonic CD4 T Cells Mediate Dichotomous Response to Nicotine in Murine Models of Th1/Th17- Versus Th2-mediated Colitis Journal of Immunology (Baltimore, Md. : 1950). Sep, 2011 | Pubmed ID: 21784975 Linking Lipid Metabolism to the Innate Immune Response in Macrophages Through Sterol Regulatory Element Binding Protein-1a Cell Metabolism. May, 2011 | Pubmed ID: 21531336 Mutation of NIMA-related Kinase 1 (NEK1) Leads to Chromosome Instability Molecular Cancer. 2011 | Pubmed ID: 21214959 Accessing the SEED Genome Databases Via Web Services API: Tools for Programmers BMC Bioinformatics. 2010 | Pubmed ID: 20546611 Transposases Are the Most Abundant, Most Ubiquitous Genes in Nature Nucleic Acids Research. Jul, 2010 | Pubmed ID: 20215432 Cancer Research. Feb, 2010 | Pubmed ID: 20145124 Bovine Serum Albumin Glutaraldehyde for Completely Sutureless Laparoscopic Heminephrectomy in a Survival Porcine Model Journal of Endourology / Endourological Society. Mar, 2010 | Pubmed ID: 20059350 Lysogeny and Sporulation in Bacillus Isolates from the Gulf of Mexico Applied and Environmental Microbiology. Feb, 2010 | Pubmed ID: 20008174 The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes PLoS Computational Biology. Dec, 2009 | Pubmed ID: 20011103 Epigenetic Repression of DNA Mismatch Repair by Inflammation and Hypoxia in Inflammatory Bowel Disease-associated Colorectal Cancer Cancer Research. Aug, 2009 | Pubmed ID: 19638594 Metagenomic Analysis of Stressed Coral Holobionts Environmental Microbiology. Aug, 2009 | Pubmed ID: 19397678 Evaluation of the Outcomes of Electrosurgical Induced Bowel Injury Treated with Tissue Glue/sealant Versus Sutured Repair in a Rabbit Model Journal of Endourology / Endourological Society. Mar, 2009 | Pubmed ID: 19275489 The 'buoy' Stent: Evaluation of a Prototype Indwelling Ureteric Stent in a Porcine Model BJU International. Jul, 2009 | Pubmed ID: 19154469 Comparative Study of in Vivo Lymphatic Sealing Capability of the Porcine Thoracic Duct Using Laparoscopic Dissection Devices The Journal of Urology. Jan, 2009 | Pubmed ID: 19010491 Metagenomic Analysis Indicates That Stressors Induce Production of Herpes-like Viruses in the Coral Porites Compressa Proceedings of the National Academy of Sciences of the United States of America. Nov, 2008 | Pubmed ID: 19017800 Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome PloS One. 2008 | Pubmed ID: 18698407 Bone Marrow Stem Cells for Urologic Tissue Engineering World Journal of Urology. Aug, 2008 | Pubmed ID: 18654786 Taxonomic Composition and Gene Content of a Methane-producing Microbial Community Isolated from a Biogas Reactor Journal of Biotechnology. Aug, 2008 | Pubmed ID: 18611419 Viral Diversity and Dynamics in an Infant Gut Research in Microbiology. Jun, 2008 | Pubmed ID: 18541415 Viral Communities Associated with Healthy and Bleaching Corals Environmental Microbiology. Sep, 2008 | Pubmed ID: 18479440 Role for Epithelial Dysregulation in Early-onset Colitis-associated Colon Cancer in Gi2-alpha-/- Mice Inflammatory Bowel Diseases. Jul, 2008 | Pubmed ID: 18340649 Functional Metagenomic Profiling of Nine Biomes Nature. Apr, 2008 | Pubmed ID: 18337718 Comparison of Healing After Cystotomy and Repair with Fibrin Glue and Sutured Closure in the Porcine Model Journal of Endourology / Endourological Society. Jan, 2008 | Pubmed ID: 18315486 Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites Nature. Mar, 2008 | Pubmed ID: 18311127 Microbial Ecology of Four Coral Atolls in the Northern Line Islands PloS One. 2008 | Pubmed ID: 18301735 Phylogenetic Classification of Short Environmental DNA Fragments Nucleic Acids Research. Apr, 2008 | Pubmed ID: 18285365 The RAST Server: Rapid Annotations Using Subsystems Technology BMC Genomics. 2008 | Pubmed ID: 18261238 Bacterial Carbon Processing by Generalist Species in the Coastal Ocean Nature. Feb, 2008 | Pubmed ID: 18223640 Evidence for Differential Roles for NKG2D Receptor Signaling in Innate Host Defense Against Coronavirus-induced Neurological and Liver Disease Journal of Virology. Mar, 2008 | Pubmed ID: 18094157 Metagenomic and Small-subunit RRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil Applied and Environmental Microbiology. Nov, 2007 | Pubmed ID: 17827313 Expression of CXC Chemokine Ligand 10 from the Mouse Hepatitis Virus Genome Results in Protection from Viral-induced Neurological and Liver Disease Journal of Immunology (Baltimore, Md. : 1950). Jul, 2007 | Pubmed ID: 17617609 Development of Indole Chemistry to Label Tryptophan Residues in Protein for Determination of Tryptophan Surface Accessibility Protein Science : a Publication of the Protein Society. Jun, 2007 | Pubmed ID: 17525468 Decreased MAPK- and PGE2-dependent IL-11 Production in Gialpha2-/- Colonic Myofibroblasts American Journal of Physiology. Gastrointestinal and Liver Physiology. Jun, 2007 | Pubmed ID: 17332478 The National Microbial Pathogen Database Resource (NMPDR): a Genomics Platform Based on Subsystem Annotation Nucleic Acids Research. Jan, 2007 | Pubmed ID: 17145713 The Marine Viromes of Four Oceanic Regions PLoS Biology. Nov, 2006 | Pubmed ID: 17090214 Finding Novel Genes in Bacterial Communities Isolated from the Environment Bioinformatics (Oxford, England). Jul, 2006 | Pubmed ID: 16873483 Identification of Trichloroethanol Visualized Proteins from Two-dimensional Polyacrylamide Gels by Mass Spectrometry Analytical Chemistry. Apr, 2006 | Pubmed ID: 16579625 Using Pyrosequencing to Shed Light on Deep Mine Microbial Ecology BMC Genomics. 2006 | Pubmed ID: 16549033 An Application of Statistics to Comparative Metagenomics BMC Bioinformatics. 2006 | Pubmed ID: 16549025 Differential Roles for CXCR3 in CD4+ and CD8+ T Cell Trafficking Following Viral Infection of the CNS European Journal of Immunology. Mar, 2006 | Pubmed ID: 16479546 Low-molecular-weight Protein Tyrosine Phosphatases of Bacillus Subtilis Journal of Bacteriology. Jul, 2005 | Pubmed ID: 15995210 Viral Metagenomics Nature Reviews. Microbiology. Jun, 2005 | Pubmed ID: 15886693 Impaired TGF-beta Responses in Peripheral T Cells of G Alpha I2-/- Mice Journal of Immunology (Baltimore, Md. : 1950). May, 2005 | Pubmed ID: 15879107 In Vitro Characterization of the Bacillus Subtilis Protein Tyrosine Phosphatase YwqE Journal of Bacteriology. May, 2005 | Pubmed ID: 15866923 Mosaic Prophages with Horizontally Acquired Genes Account for the Emergence and Diversification of the Globally Disseminated M1T1 Clone of Streptococcus Pyogenes Journal of Bacteriology. May, 2005 | Pubmed ID: 15866915 Robotic Radical Prostatectomy: a Technique to Reduce PT2 Positive Margins Urology. Dec, 2004 | Pubmed ID: 15596205 Visible Fluorescent Detection of Proteins in Polyacrylamide Gels Without Staining Analytical Biochemistry. Mar, 2004 | Pubmed ID: 14769330 Trp-999 of Beta-galactosidase (Escherichia Coli) is a Key Residue for Binding, Catalysis, and Synthesis of Allolactose, the Natural Lac Operon Inducer Biochemistry. Feb, 2003 | Pubmed ID: 12578395 The Light-induced Reactions of Tryptophan with Halocompounds Photochemistry and Photobiology. Apr, 2002 | Pubmed ID: 12003125 Comparative Genomics of Closely Related Salmonellae Trends in Microbiology. Feb, 2002 | Pubmed ID: 11827811 Visualization of Proteins in Acrylamide Gels Using Ultraviolet Illumination Analytical Biochemistry. Feb, 2002 | Pubmed ID: 11811971 Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins Savannah E. Sanchez1, Daniel A. Cuevas2, Jason E. Rostron1, Tiffany Y. Liang3, Cullen G. Pivaroff1, Matthew R. Haynes1, Jim Nulton4, Ben Felts4, Barbara A. Bailey4, Peter Salamon4, Robert A. Edwards1,5,6, Alex B. Burgin7, Anca M. Segall1, Forest Rohwer1 1Department of Biology, San Diego State University, 2Computational Science Research Center, San Diego State University, 3Bioinformatics and Medical Informatics Research Center, San Diego State University, 4Department of Mathematics and Statistics, San Diego State University, 5Department of Computer Science, San Diego State University, 6Mathematics and Computer Science Division, Argonne National Laboratory, 7SPARC Committee, Broad Institute JoVE 52854 Imunologia e Infecção
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins Savannah E. Sanchez1, Daniel A. Cuevas2, Jason E. Rostron1, Tiffany Y. Liang3, Cullen G. Pivaroff1, Matthew R. Haynes1, Jim Nulton4, Ben Felts4, Barbara A. Bailey4, Peter Salamon4, Robert A. Edwards1,5,6, Alex B. Burgin7, Anca M. Segall1, Forest Rohwer1 1Department of Biology, San Diego State University, 2Computational Science Research Center, San Diego State University, 3Bioinformatics and Medical Informatics Research Center, San Diego State University, 4Department of Mathematics and Statistics, San Diego State University, 5Department of Computer Science, San Diego State University, 6Mathematics and Computer Science Division, Argonne National Laboratory, 7SPARC Committee, Broad Institute JoVE 52854 Imunologia e Infecção