Category Archives: Current Lab Members

lab members category

About Rob

Robert Edwards – Biography

After receiving his Ph. D. from the University of Sussex, in England studying nitrogen regulation in bacteria, Dr. Edwards moved to the United States to continue his studies. He worked as a Post-Doctoral Researcher with Dr. Dieter Schifferli at the University of Pennsylvania, Philadelphia, understanding the mechanisms and regulation of virulence of enterotoxigenic E. coli, a leading cause of traveler’s diarrhea. Dr. Edwards then moved to the University of Illinois, Urbana Champaign to work with Dr. Stanley Maloy on understanding the virulence of Salmonella. These studies merged the nascent area of genomics with traditional microbial genomics to investigate the virulence of Salmonella enterica serovar Enteritidis, a leading bacterial cause of food-borne illness. During this period, Dr. Edwards began sequencing several Salmonella genomes, and began collaborating on the open-source BioPerl project, to which he remains an active contributor.

From 2000 to 2004, Dr. Edwards was an Assistant Professor at University of Tennessee Health Sciences Center in Memphis, TN. Here, Dr. Edwards continued his studies on pathogenic bacteria, notably Salmonella and the class A Select Agent Francisella. Dr. Edwards was responsible for overseeing the renovation of space into a BSL-3 laboratory, capable of handling Select Agents, and for registering that facility with the CDC. Dr. Edwards received FBI clearance to work on Select Agents, and was invited to the NIH to comment on the use of Select Agents at basic research laboratories.

In 2004, Dr. Edwards moved to the non-profit Fellowship for Interpretation of Genomes to work at the interface of biologists and computer scientists. He remains an active software developer for the Fellowship, and helps guide their development direction through liaisons with microbiological researchers. Using breakout technologies, like pyrosequencing and high throughput bioinformatics analysis, Dr. Edwards’ studies are pushing the forefront of both sequencing technology and bioinformatics. This work was highlighted in three independent publications in Nature at the start of 2008. Dr. Edwards maintains interactions with mathematicians and computer scientists, developing open source software such as the PERL modules for biological analysis and parallel computing he has released to the community through BioPerl and CPAN.

Most recently, Dr. Edwards has returned to academia, and taken a research and teaching position in the Department of Computer Science at San Diego State University. Here he is continuing to work at the interface of biology and computing, but also expanding his research into grid-enabled research and high performance computing. Dr. Edwards has written open-source code for high performance parallel computing that is used worldwide.

Dr. Edwards research is currently funded by the National Science Foundation, and aims to bring high performance computing to the smallest biological organisms – the viruses. Edwards’ research is leading to breakthroughs in our understanding of how viruses interact with their hosts, and how viruses samples from around the world carry important genetic information.

Committed to teaching, Dr. Edwards received the SGAEC award for outstanding educator at the University of Tennessee, teacher-scholar award (2008) and outstanding faculty award (2009) at San Diego State University. He has taught bioinformatics classes around the US, in Brazil, China, Europe, and Mexico. He is funded by the Department of Education to develop joint courses in marine sciences between San Diego and Brazil.

Dr. Edwards maintains strong interactions with biologists, working closely with groups sequencing uncultured microbes (“metagenomes”) from diverse environments such as human samples, oceans, coral reefs, and mines. In addition to bioinformatics analysis Dr. Edwards is also a scientific SCUBA diver having studied both Pacific and Atlantic Coral Reefs, and also enjoys racing sailboats.

Brad Hull

space

 

Location: GMCS 429

Phone: +1 619 742-8541

Email: brad.hull@gmail.com

 

 

Research

Currently working on an upgrade to the BLAST Graphical Output seen on the SEED using HTML5/CSS/Javascript. Past ideas included using Perl/gd, perl/Cairo, and the GWT/Google Viz.

 

Education

Bachelor of Science: Computer Science

SDSU C/O 2009

Daniel Cuevas

space

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