|
Characterizing Metagenomes Using K-mer Abundance Beverly A Hom and Robert A Edwards Presented at: SDSU Student Research Symposium (SRS) 2017, San Diego, CA
Gap-filling metabolic networks using k-mer distance evidence Taylor G O’Connell, Daniel A Cuevas, and Robert A Edwards Presented at: SDSU Student Research Symposium (SRS) 2017, San Diego, CA
Metabolic model and data-driven exploration linking phenotypes to genotypes Daniel A. Cuevas, Rebecca de Wardt, Dominic Cavalli, Abby Turnlund, Tucker Lopez, Victoria Diaz, Kristen Aguinaldo, Thiago Bruce, Elizabeth Dinsdale, and Robert A. Edwards Presented at: SDSU Student Research Symposium (SRS) 2017, San Diego, CA
From DNA to FBA: how to build your own genome-scale metabolic model Daniel A. Cuevas, Taylor G. O’Connell, Blaire Robinson, Tucker Lopez, Kristen Aguinaldo, Rebecca de Wardt, Rhaya Alkafaji, Thiago Bruce, Elizabeth Dinsdale, and Robert A. Edwards Presented at: SDSU Applied Computational Science and Engineering Student Support meeting (ACSESS) 2016, San Diego, CA
Gap-filling metabolic networks using physicochemical, sequence homology, and functional coupling evidence Taylor O’Connell and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2016
Who is there and what are they doing? Using FOCUS and SUPER-FOCUS for an agile taxonomic and functional analysis of metagenomic big data Genivaldo Silva, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2016
Meta-kaks: a tool to measure natural selection strength on a metagenome Vito A. Cantu, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2016
Global and local studies on the evolution of crAssphage Alejandro Vega, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2016
A search engine of genomes sequence for papers Heqiao Liu, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2016
Genetic and Phenotypic Analysis of Gammaproteobacteria Blaire Robinson, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2016
Phenotyping Diverse Bacteria for Metabolic Network Reconstruction Daniel A Cuevas, Heqiao Liu, Tucker Lopez, Blaire Robinson, Kristen Aguinaldo, Chris Henry, Elizabeth Dinsdale, and Robert A Edwards Presented at: Student Presented at: General Meeting of the American Society for Microbiology (ASM) 2015, New Orleans, LA and SDSU Applied Computational Science and Engineering Student Support meeting (ACSESS) 2015, San Diego, CA
Microbial Growth Caracteristic Database Design and Implementation David Fu, Blaire Robinson, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2015
|
|
Comprehensive Survey of Prophage Genomics and Development of Phage Insertion Site Determination Methods Han S. Kang, Katelyn McNair, Ramy Aziz, and Rob Edwards Presented at: 12th Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2014
|
| Characterization and comparison of prophage integrase genes and core integration sites
Han S. Kang, Katelyn McNair, Ramy Aziz, and Rob Edwards Presented at: Student Presented at: Student Research Symposium (SRS) 2014
|
|
High-throughput phenotype profiling for bacterial flux-balance model optimization Daniel A Cuevas, Daniel Garza, Savannah Sanchez, Jason Rostron, Chris Henry, Anca Segall, Forest Rohwer, and Rob Edwards Presented at: 11th Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2013 and General Meeting of the American Society for Microbiology (ASM) 2014, Boston, MA |
|
Characterizing Unknown Genes Through Metabolomics Tiffany Y. Liang, Savannah Sanchez, Jason Rostron, Jeremy Frank, Daniel Cuevas, Daniel Garza, Anca Segall, Forest Rohwer, Robert Edwards Presented at: 11th Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2013 |
|
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Genivaldo Gueiros Z. Silva and Rob Edwards Presented at: 11th Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2013 |
|
Measuring Growth Quality of Bacteria Using Phenotypic Microarrays Daniel Cuevas, Daniel Garza, Savannah Sanchez, Jason Rostron, Tiff Liang, Anca Segall, Forest Rohwer, Rob Edwards Presented at: San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2013 |
|
Tools for Fast Sequence Alignment Sajia Akhter, Robert A Edwards Presented at: Applied Computational Science and Engineering Student Support (ACSESS) 2013 |
Microbial Database Blaire Robinson, Dwaine Smith, Daniel Cuevas, Katelyn McNair, Robert Edwards Presented at: Student Research Symposium (SRS) 2013 |
FOCUS-A Model to Identify Organisms Present in Metagenomes Based on Codon Usage |
Characterizing Unknown Genes Through Metabolomics Tiffany Y. Liang, Savannah Sanchez, Jason Rostron, Jeremy Frank, Daniel Cuevas, Daniel Garza, Anca Segall, Forest Rohwer, Robert Edwards Presented at: Student Research Symposium (SRS) 2013 Presented at: Applied Computational Science and Engineering Student Support (ACSESS) 2013 |
Scaffold-builder for Combining De Novo and Reference-guided Assembly Genivaldo G. Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Elizabeth A. Dinsdale and Robert A. Edwards. Presented at: 10th Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2012. |
|
Tools for Detecting Macrolide Resistance in the Human Microbiome Robert Schmieder, Yan Wei Lim, Anca Segall, Molly Schmid, and Robert Edwards |
|
Host prediction for viral metagenomes using oligonucleotide profiles Michiyo Wellington-Oguri, Robert Schmieder, Barbara Bailey, Robert A. Edwards, and Bas E. Dutilh Presented at: Student Research Symposium (SRS) 2012 |
|
Database Structure and Visualization Software for Microbial Physiology Data Nicholas Turner, Haquio Liu, Jeremy Frank, and Robert Edwards Presented at: Student Research Symposium (SRS) 2012 |
|
Tools for Fast Sequence Alignment Sajia Akhter and Robert Edwards Presented at: Student Research Symposium (SRS) 2012 |
Tools for Quality Control and Preprocessing of Metagenomic Datasets Robert Schmieder, Yan Wei Lim and Robert Edwards Presented at: Pacific Symposium on Biocomputing (PSB) 2011 |
|
FACIL: fast and accurate genetic code inference and logo Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A.F.T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Hendrik G. Stunnenberg, Marc Strous, Mike S.M. Jetten, Huub J.M. Op den Camp and Martijn A. Huynen Presented at: SDMG All Day Meeting 2011 |
|
Genomic Comparison of Salmonella enterica Serovars Enteritidis and Dublin D. Matthews, R. Schmieder, J. Busch, N. Cassman, M. Doherty, D. Green, B. Matolock, B. Heffernan, G. Olsen, L. Farris, D. Schiffeli, S. Maloy, E. Dinsdale, and R. Edwards Presented at: ASM 2011 |
|
PhiSpy: A novel similarity-independent tool for predicting prophages in microbial genomes Sajia Akhter, Ramy K Aziz, Robert A Edwards Presented at: Evergreeen International Phage Biology Meeting |
Real-Time Metagenomics Analysis Daniel A. Cuevas, Joshua A. Hoffman and Robert A. Edwards Presented at: General Meeting of the American Society for Microbiology (ASM) 2010, San Diego, CA |
|
Investigating the Frequency of Quinolone Resistance Genes in Environmental Samples Sajia Akhter, Anca M. Segall, Molly Schmid and Robert A. Edwards Presented at: ASM 2010 |
|
Identification of Macrolide Resistance Alleles in Environmental Metagenomes Robert Schmieder, Anca Segall, Molly Schmid and Robert Edwards Presented at: ASM 2010 |
|
Fast Identification and Removal of Sequence Contaminations from Genomic and Metagenomic Datasets Robert Schmieder and Robert Edwards Presented at: Human Microbiome Meeting 2010 |
|
PHANTOME: Phage Annotation Tools and Methods Ramy K. Aziz, Brad Hull, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, JP Massar, Matthew Sullivan, Jeff Elhai, Mya Breitbart, Ross Overbeek and Robert A. Edwards Presented at: Institut Pasteur Virus of Microbes meeting 2010 |
|
Phages Without Borders: Distribution of Phage Nucleic Acids in 310 Metagenomes Ramy K. Aziz, Mya Breitbart and Robert A. Edwards Presented at: ASM 2010 |
|
Phage Annotation Tools and Methods Ramy K. Aziz, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, Brad Hull, JP Massar, Mya Breitbart, Matthew Sullivan, Jeff Elhai and Robert A. Edwards Presented at: ASM 2010 |
|
Predicting Phage Preferences: Lytic vs. Lysogenic Lifestyle from Genomes Katelyn McNair, Rob Edwards and Barbara Bailey Presented at: CSHL meeting 2010 |
ADAPTdb/ADAPT – A Framework for the Analysis of ARISA Data Sets Robert Schmieder, Matthew Haynes, Elizabeth Dinsdale, Forest Rohwer, and Robert Edwards Presented at: ISMB/ECCB and M3 2009 |
|
Deviation of amino acid utilization and correlation with G+C composition in bacterial genome Sajia Akhter, Hochul K Lee, Barbara Bailey, Peter Salamon, Robert Edwards Presented at: Applied Computational Science and Engineering Student Support (ACSESS) 2009 |
|
Assembler for SOLiD data: by Improving memory management of Velvet assembler Sajia Akhter and Robert Edwards Presented at: Rocky Mountain Bioinformatics Conference (Rocky) 2009 |
|
Phage Annotation Tools and Methods Ramy K. Aziz, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, JP Massar, Mya Breitbart, Matthew Sullivan, Jeff Elhai and Robert A. Edwards Presented at: Rocky Mountain Bioinformatics Conference (Rocky) 2009 |
Transition in Vibrio spp. correlates with human activity in the Northern Line Islands Robert Schmieder, Tracy McDole, Elizabeth Dinsdale, Matthew Haynes, Forest Rohwer, Robert Edwards Presented at: International Coral Reef Symposium (ICRS) 2008 |
|
|
ADAPTdb/ADAPT – A Framework for the Analysis of ARISA Data Sets Robert Schmieder, Matthew Haynes, Elizabeth Dinsdale, Forest Rohwer, and Robert Edwards Presented at: Metagenomics 2008 |
