edwardslab

Location: GMCS 429 Phone: +1 619 594-3137 Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it 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

1. Schmieder R and Edwards R: Insights into antibiotic resistance through metagenomic approaches. Future Microbiology 2012, 7:73-89.
2. Schmieder R, Lim YW, Edwards R: Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics 2012, 28:433-435.
3. Li J-W, Schmieder R, Ward RM, Delenick J, Olivares EC, Mittelman D: SEQanswers: An open access community for collaboratively decoding genomes. Bioinformatics 2012.
4. Dwivedi B, Schmieder R, Goldsmith DB, Edwards RA, Breitbart M: PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. BMC Bioinformatics 2012, 13:37.
5. Schmieder R and Edwards R: Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27:863-864.
6. Schmieder R and Edwards R: Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets. PLoS ONE 2011, 6:e17288.
7. Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, Rohwer F, Conrad D: Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J 2011.
8. Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M: Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes. PLoS ONE 2011, 6:e20579.
9. Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, Rainey PB, Schmieder R, Youle M, Conrad D, Rohwer F: Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am. J. Respir. Cell Mol. Biol. 2011.
10. Schmieder R, Lim YW, Rohwer F, Edwards R: TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics 2010, 11:341.
11. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP, Rohwer F, Haynes M: Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A 2010.
12. Thompson FL, Bruce T, Gonzalez A, Cardoso A, Clementino M, Costagliola M, Hozbor C, Otero E, Piccini C, Peressutti S, Schmieder R, Edwards R, Smith M, Takiyama LR, Vieira R, Paranhos R, Artigas LF: Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing. Arch Microbiol 2010.
13. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F: Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE 2009, 4:e7370.
14. Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F: The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput. Biol 2009, 5:e1000593.

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

Tools

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

Awards

• 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 7^th 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

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

• Bioinformatics for metagenomics, Ensenada, Mexico, 2010

• International Human Microbiome Congress (IHMC), Paris, France, 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
• 3^rd 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