Daniel Cuevas

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Location: GMCS 429

Phone: +1 619 594-3137

Email: dcuevas08@gmail.com

Daniel’s lab blog

 
About Me

I am a graduate student in the Bioinformatics and Medical Informatics department at San Diego State University. I have been working at Edwards Lab since June 2009 but have lived in the beautiful city of San Diego all my life. During my free time I enjoy sitting out in the sun, hanging out at the beach, playing sports, and reading up on new and awesome technologies on the web.

 

Industry Experience
  • Life Technologies – Ion Torrent R&D — Software Engineer / Bioinformatics

 

Education
  • Bachelor of Science in Computer Science. San Diego State University.

 

Research

SEED web services (for Java)

  • The SEED holds many publicly available genome DNA sequences which are annotated based on subsystems and protein functions. It also provides web services to those who are willing to develop applications based on the SEED API. By supplying many methods to obtain these microbial annotations, developers can use, manipulate, and create third party applications to aid their scientific research. My assignment involved learning to use and access the SEED API using the Java programming language. Through this I have written different examples to perform specific functions with the SEED database.

 

RTMg.os

  • OpenSocial Metagenomics (RTMg.os), is an OpenSocial-based application that is part of the RTMg suite of applications. RTMg.os allows the users of social networking sites to share their bioinformatic data and analysis with colleagues and friends. The application stores and retrieves metagenome-annotated data on a server. This allows the user to notify and update their friends about any new annotations that have been acquired, and then display the contents of their data in a tabular format. RTMg.os represents an entirely new way for scientists to collaborate on their data. For information on the entire RTMg project, go here.

 

Rapid Sequence Searching Using A Hashing Technique

  • By implementing a modified data structure to quickly and precisely discover exact nucleotide similarities between several sequenced metagenomes, specific DNA sequences can be analyzed and traced within different environmental regions.

 

Presentations 

Oral presentations:

  • San Diego State University Student Research Symposium (SDSU SRS), San Diego, CA, 2010
  • San Diego State University Student Research Symposium (SDSU SRS), San Diego, CA, 2011

Poster presentations:

  • General meeting of the American Society for Microbiology (ASM), San Diego, CA, 2010
  • San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2010
  • Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2010
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Robert Schmieder

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Location: GMCS 429

Phone: +1 619 594-3137

Email: rschmied@sciences.sdsu.edu

Robert’s lab blog

 

Research

I started in the PhD program in Computational Sciences at SDSU in fall 2008. Since then, I have been working on the development of tools related to metagenomics (genomic analysis of all microorganisms present in a specific habitat) and environmental studies. The Computational Sciences program supports the collaboration between computer scientists and applied sciences, such as Biology. As part of the program, I worked in the laboratory of Dr. Forest Rohwer to extend my training in laboratory methods and now I apply this knowledge to my computational work, analyzing data sets and developing tools for their automatic analysis.

I implemented several programs for the analysis of microbial community samples for the ease of use by biologists, especially those performing specialized analyses in our collaborator’s labs. Additionally, I work on the analysis of metagenomic data from a wide variety of samples including mosquitoes, cystic fibrosis patients, and coral reefs.

 

Education
  • PhD Student (since 2008), Computational Science Research Center, SDSU, San Diego, CA
  • Master of Science in Bioinformatics and Genome Research, 2007 (Bielefeld University, Bielefeld, Germany)
  • Bachelor of Science in Bioinformatics and Genome Research, 2005 (Bielefeld University, Bielefeld, Germany)

More details about my professional and educational background can be found here.

 

Publications

    An up-to-date list of my publications can be found at Google Scholar (http://bit.ly/robpubl).

    wordle could of publications
    My publications in 100 words (Thanks to wordle.net)

     

    Tools

    Some of the tools I developed as part of my research:

    logo_prinseq logo_tagcleaner logo_deconseq logo_riboPicker 
    Awards
    • BiCi Leonardo Melandri Program for Bertinoro Computational Biology 2012
    • Inamori Fellowship, Fall 2011 and Spring 2012
    • First Place in Lavine VentureStart Competition, 2011
    • Travel Grant for International Human Microbiome Congress, 2011
    • Instructionally Related Activities (IRA) Travel Grant, 2010
    • Travel Grant for Human Microbiome Research Conference, 2010
    • Merit Award for poster presentation at 7th annual ACSESS meeting, 2010
    • CGU Fellowship – Math, Fall 2009 and Spring 2010
    • Claremont Graduate University Travel Award for microbial community-profiling project on Curaçao, Netherlands Antilles, 2009
    • California State University Program for Education and Research in Biotechnology (CSUPERB) Travel Grant Award, 2009
    • Instructionally Related Activities (IRA) Travel Grant for ISMB/ECCB 2009
    • Student Travel Grant at Metagenomics 2008
    • German Academic Exchange Service (DAAD) Study Abroad Scholarship, 2007

     

    Presentations

    Oral:

    • Bertinoro Computational Biology Meeting, Bertinoro, Italy, 2012
    • TSRC Cystic Fibrosis Meeting, Telluride, CO, 2011
    • Student Research Symposium (SRS), San Diego, CA, 2010
    • Student Research Symposium (SRS), San Diego, CA, 2009

    Workshop:

    • Bioinformatics for metagenomics, Ensenada, Mexico, 2010

    Poster:

    • International Human Microbiome Congress (IHMC), Paris, France, 2012
    • San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2012
    • Student Research Symposium (SRS), San Diego, CA, 2012
    • Advances in Genome Biology & Technology (AGBT), Marco Island, FL, 2012
    • International Human Microbiome Congress (IHMC), Vancouver, Canada, 2011
    • San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2011
    • Student Research Symposium (SRS), San Diego, CA, 2011
    • Microbiome Studies @ Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii, 2011
    • Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO, 2010
    • Human Microbiome Research Conference, St Louis, MO, 2010
    • General meeting of the American Society for Microbiology (ASM), San Diego, CA, 2010
    • San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2010
    • Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2010
    • Metagenomics, Metadata, and Metaanalysis (M3), Sweden, 2009
    • Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB), Sweden, 2009
    • Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2009
    • San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2009
    • 3rd Annual International Conference on Metagenomics, San Diego, CA, 2008
    • International Coral Reef Symposium (ICRS), Fort Lauderdale, FL, 2008
    • Student Research Symposium (SRS), San Diego, CA, 2008
    • San Diego Microbiology Group (SDMG) All-day meeting, San Diego, CA, 2008
    • Applied Computational Science and Engineering Student Support (ACSESS), San Diego, CA, 2008