Posters

Daniel__ACSESS16

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

Download PDF

Taylor__SRS16

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

Download PDF file

Silva__SRS16

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

Download PDF file

Vito__SRS16

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

Download PDF file

Alex__SRS16

Global and local studies on the evolution of crAssphage

Alejandro Vega, and Rob Edwards

Presented at: Student Presented at: Student Research Symposium (SRS) 2016

Download PDF file

Liu__SRS16

A search engine of genomes sequence for papers

Heqiao Liu, and Rob Edwards

Presented at: Student Presented at: Student Research Symposium (SRS) 2016

Download PDF file

Blaire__SRS16

Genetic and Phenotypic Analysis of Gammaproteobacteria

Blaire Robinson, and Rob Edwards

Presented at: Student Presented at: Student Research Symposium (SRS) 2016

Download PDF file

poster scaffold builderl 2012

Microbial Growth Caracteristic Database Design and Implementation

David Fu, Blaire Robinson, and Rob Edwards

Presented at: Student Presented at: Student Research Symposium (SRS) 2015

Download PDF file (0.3 MB)

poster scaffold builderl 2012

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

Download PDF file (1.5 MB)

 

 poster scaffold builderl 2012

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

Download PDF file (5 MB)

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

Download PDF file (3.49 MB)

poster scaffold builderl 2012

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

Download PDF file (5.46 MB)

poster scaffold builderl 2012

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

Download PDF file (0.15 MB)

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

Download PDF file (0.5 MB)

poster scaffold builderl 2012

Tools for Fast Sequence Alignment

Sajia Akhter, Robert A Edwards

Presented at: Applied Computational Science and Engineering Student Support (ACSESS) 2013

Download PDF file (1.80 MB)

poster

Microbial Database

Blaire Robinson, Dwaine Smith, Daniel Cuevas, Katelyn McNair, Robert Edwards

Presented at: Student Research Symposium (SRS) 2013

Download PDF file (0.4 MB)

poster

FOCUS-A Model to Identify Organisms Present in Metagenomes Based on Codon Usage
Genivaldo G.Z. Silva, Robert A Edwards
Presented at:-San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2013
-Applied Computational Science and Engineering Student Support (ACSESS) 2013

Download PDF file (0.6MB)

poster

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

Download PDF file (1MB)

poster scaffold builderl 2012

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.

Download PDF file (1.52 MB)

poster

Tools for Detecting Macrolide Resistance in the Human Microbiome Robert Schmieder, Yan Wei Lim, Anca Segall, Molly Schmid, and Robert Edwards
Presented at: Advances in Genome Biology & Technology (AGBT) 2012

Download PDF file (1.2 MB)

poster

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

Download PDF file (705 KB)

poster

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

Download PDF file (176 KB)

poster

Tools for Fast Sequence Alignment

Sajia Akhter and Robert Edwards

Presented at: Student Research Symposium (SRS) 2012

Download PDF file (1.3 MB)

poster

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

Download PDF file (4.2 MB)

poster

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

Download PDF file (3.6 MB)

poster

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

Download PDF file (561 KB)

poster

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

Download PDF file (1.5 MB)

poster

Real-Time Metagenomics Analysis

Daniel A. Cuevas, Joshua A. Hoffman and Robert A. Edwards

Presented at: ASM 2010

Download PDF file (980 KB)

poster

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

Download PDF file (1.5 MB)

poster

Identification of Macrolide Resistance Alleles in Environmental Metagenomes

Robert Schmieder, Anca Segall, Molly Schmid and Robert Edwards

Presented at: ASM 2010

Download PDF file (2.7 MB)

poster

Fast Identification and Removal of Sequence Contaminations from Genomic and Metagenomic Datasets

Robert Schmieder and Robert Edwards

Presented at: Human Microbiome Meeting 2010

Download PDF file (1.2 MB)

poster

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

Download PDF file (808 KB)

poster

Phages Without Borders: Distribution of Phage Nucleic Acids in 310 Metagenomes

Ramy K. Aziz, Mya Breitbart and Robert A. Edwards

Presented at: ASM 2010

Download PDF file (1.9 MB)

poster

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

Download PDF file (924 KB)

poster

Predicting Phage Preferences: Lytic vs. Lysogenic Lifestyle from Genomes

Katelyn McNair, Rob Edwards and Barbara Bailey

Presented at: CSHL meeting 2010

Download PDF file (269 KB)

poster

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

Download PDF file (812 KB)

poster

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

Download PDF file (1.6 MB)

poster

Assembler for SOLiD data: by Improving memory management of Velvet assembler

Sajia Akhter and Robert Edwards

Presented at: Rocky Mountain Bioinformatics Conference (Rocky) 2009

Download PDF file (1.0 MB)

poster

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

Download PDF file (940 KB)

poster

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

Download PDF file (3.5 MB)

poster

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

Download