Location: NLS 332 Phone: +1 619 594-4552 Email: vsegurit@sciences.sdsu.edu Victor’s lab blog

Research

Coming soon

Education

Coming soon

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).

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

Tools

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

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 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

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
• 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

Location: GMCS 429 Phone: +1 619 594-3137 Email: sakhter@sciences.sdsu.edu Sajia’s lab blog

Bio

Research

Education

Publications

• Sajia Akhter; Ramy K. Aziz; Robert A. Edwards. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies, 2012 Nucleic Acids Research doi: 10.1093/nar/gks406
• Hedin M, Starrett J, Akhter S, Schönhofer AL, Shultz JW. Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data, 2012 PLoS ONE 7(8): e42888. doi:10.1371/journal.pone.0042888
• Noriko Cassman, Alejandra Prieto-Davó, Kevin Walsh, Genivaldo G. Z. Silva, Florent Angly, Sajia Akhter, Katie Barott, Julia Busch, Tracey McDole, J. Matthew Haggerty, Dana Willner, Gadiel Alarcón, Osvaldo Ulloa, Edward F. DeLong, Bas Dulith, Forest Rohwer, Elizabeth A. Dinsdale. Oxygen minimum zones harbor novel viral communities with low diversity. Environmental Microbiology 2012 [Accepted]
• Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens and Robert Edwards, Accessing the SEED Genome Databases via Web Services API: Tools for Programmers 2010 BMC Bioinformatics 11:319 doi:10.1186/1471-2105-11-319.
• Sajia Akhter, Ipshita Sarkar, Kazi Golam Rabbany, Nahid Akter, Shamim Akhter, Yann Chemin and Honda Kiyoshi, Adapting the LMF Temporal Splining Procedure From Serial to MPI/Linux Clusters, 2007 Journal of Computer Science 3(3): 130-133, Science Publication, New York, USA.

Posters

Location: GMCS 429 Phone: +1 619 594-3137 Email: sakhter@sciences.sdsu.edu Sajia’s lab blog

Bio

Research

Education

Publications

• Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens and Robert Edwards, Accessing the SEED Genome Databases via Web Services API: Tools for Programmers, Accepted in BMC Bioinformatics 2010.
• Sajia Akhter, Ipshita Sarkar, Kazi Golam Rabbany, Nahid Akter, Shamim Akhter, Yann Chemin and Honda Kiyoshi, Adapting the LMF Temporal Splining Procedure From Serial to MPI/Linux Clusters, Journal of Computer Science 3(3): 130-133, 2007, Science Publication, New York, USA.

Posters

Postgraduate Researcher at Edwards Lab (2008-2011) Current location: UCSD Bioengineering 426 Phone: +1 (858) 822 1144 Email: raziz1ATgmailDOTcom Ramy’s section in Edwards Lab Blog on Twitter (azizrk); Scholar; Mendeley; Researcher ID: B-2918-2009 Other blogs: It’s a microbeful world Lost in annotations

Bio (updated on 11/11/11)

Ramy finds it weird to refer to himself in the third person and thinks that bios written in third person—like many other aspects of scientific writing—are pretentious because they are almost always written by the “first person.” Thus, I will write my bio using the first person “I.”

Position

– I am currently a Visiting Scientist at UCSD’s Systems Biology Research Group (AKA Palsson lab). I also hold a tenured Assistant Professor position in the Department of Microbiology, Faculty of Pharmacy, Cairo University (FOPCU).

– I have been in-and-out the Edwards lab between April 2008 and September 2011. During that period, though, my position (or affiliation) and my physical position (location) have changed a few times.  One of the most common questions I get asked is: “where are you exactly working?” The right answer is: online!

• When I joined the lab, I was first appointed as an adjunct faculty member at the Computational Science Research Center of SDSU, a position which I still hold. In July 2008, I was appointed by the University of Chicago as a Research Associate (to work on the NMPDR project while physically at SDSU) then, between July 2009-2011, as a Research Associate at SDSU, instead.

• Between 2008 and 2011, I was also a lecturer (i.e., a tenured junior faculty member involved in teaching and conducting research without taking primary credit for it) in the Department of Microbiology and Immunology at FOPCU. I actually got this position in July 2006. As a lecturer, I taught microbiology and immunology to undergraduate and graduate students between 2006-2008. In addition I started a series of workshops between 2006-2010 on bioinformatics, pharmacogenetics/pharmacogenomics, and gene therapy in FOPCU and in the German University in Cairo (GUC). I also supervised or co-supervised a few undergraduate students and six graduate students (one of whom received her PhD in 2008; two received their MS degrees in 2009 and 2010; while three of them are still–more ore less–working on their master’s projects).

Research

• My main projects at SDSU were to (i) devlop (better) tools and methods for annotating bacteriophage genomes; (ii) annotate phage genomes using the subsystems technology; and (iii) use these tools and annotations for the interpretation of phage genomes and, by extension, microbial genomes, viral, and microbial metagenomes. More details can be found in the Phage Annotation Tools and Methods (PhAnToMe) website.

• My broader research interests are in the evolution of virulence in bacteria (but also in other pathogenic organisms like archaea, unicellular eukaryotes, and Homo sapiens). Because bacterial virulence, like many other bacterial phenotypes, is contributed by bacteriophages, viruses that infect bacteria, I got interested into studying bacteriophages as well. During my PhD project and my first postdoctoral training, I have discovered a variant of a bacterial toxin (streptodornase 1) encoded by a bacteriophage that resides in the genome of the human-restricted pathogen Streptococcus pyogenes (a.k.a. Strep). Strep causes sore throat, pharyngitis, and skin diseases, but can turn into a killer monster (a.k.a. flesh-eating bacteria).

• Finally, I am also interested in several topics that came out of the studies mentioned above. These inclue immunogenetics (how different animals and humans react differently to bacterial infections), reconstructing bacterial virulomes from genomic data, and integrating diverse microarray data to improve the biological relevance of their interpretation.

Education

• PhD in Microbiology and immunology from the University of Tennessee Health Science Center (UTHSC) at Memphis TN (defended December 2004 and officially earned May 2005). Coincidentally, Robert A. Edwards, PhD, was one of my committee members–those who tell you that you are “free to go.”
• BSc in Pharmacy and Pharmaceutical Chemistry from the Faculty of Pharmacy, Cairo University, June 1995.

Office: BIO 231

Lab: BIO 212

Phone: +61 8 8201 3417

Email: robert.edwards@flinders.edu.au

Some photos of 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 at the University of Pennsylvania, Philadelphia, understanding how a leading cause of traveller’s diarrhea (E. coli)causes disease. Dr. Edwards then moved to the University of Illinois, Urbana Champaign to study another food-borne pathogen, Salmonella. These studies merged the nascent area of genomics with traditional microbial genetics to investigate how a particular type of Salmonella became the leading cause of food-borne illness in the United States.

From 2000 to 2004, Dr. Edwards was an Assistant Professor at the University of Tennessee Health Sciences Center in Memphis, TN. Here, Dr. Edwards continued his studies on pathogenic bacteria, notably Salmonella and the bioterrorism weapon Francisella. Dr. Edwards received FBI clearance to work on these bacteria 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 and worked with their team at Argonne National Laboratory. He remains an active software developer for Argonne and the Fellowship, developing open-source software including PERL and Python software for biological analysis and parallel computing that are used by scientists worldwide. Using breakout DNA sequencing technologies, Dr. Edwards’ studies have continually pushed the forefront of both sequencing technology and bioinformatics. His work has been published in leading journals including multiple papers in both Nature and Science.

Dr. Edwards returned to academia in 2007, taking a research and teaching position in the Departments of Computer Science and Biology at San Diego State University where he rose through the ranks to become a Full Professor. He continued to work at the interface of biology and computing.  The National Institutes of Health, the National Science Foundation, the Department of Education, the Department of Defense, the USGS, and private donors funded Dr. Edwards’ research at SDSU, and his work led to breakthroughs in our understanding of how viruses interact with their hosts, and how viruses from around the world carry important genetic information. Dr. Edwards has continued to push current sequencing and bioinformatics technologies, in 2013 took a next-generation sequencing machine to the remote Southern Line Islands to explore metagenomics of coral reefs in real-time. In 2014 Dr. Edwards’ team identified a virus that is present in the intestines of approximately half the people in the world, and in 2019 Dr. Edwards demonstrated the global spread of the virus in a paper that includes collaborators from every continent who collected and sequenced samples. In 2017, Dr. Edwards was elected to the American Academy of Microbiology in recognition of his contributions to the field of microbiology. In 2020, Dr. Edwards took the position of Matthew Flinders Fellow in Bioinformatics at Flinders University, in Adelaide, South Australia, Australia to start the Flinders Accelerator for Microbiome Exploration, to enhance microbiome and metagenome studies in South Australia.

Committed to teaching, Dr. Edwards received the graduate student award for the outstanding educator at the University of Tennessee, the teacher-scholar award and outstanding faculty award four times at San Diego State University. He was Graduate Advisor to the Biological and Medical Informatics Program at SDSU. Rob travels extensively to share his passion for bioinformatics and has taught bioinformatics classes around the US, and in Australia, China, Chile, Europe, Mexico, and North and South America. Dr. Edwards holds a visiting professor position at the Federal University of Rio de Janeiro.

In addition to science and teaching Dr. Edwards is also an advanced scientific SCUBA diver having led teams to study Coral Reefs all over the world. In his spare time, he is an avid international yachtsman, navigating in long-distance offshore races, including navigating the 2019 TransPac race from Los Angeles to Honolulu finishing 4^th out of 89 boats.

Nick Celms

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Nick Celms has been part of the Edwards lab since the Summer of 2008, and works on visualizations of BLAST comparisons. He spent his first two years as an undergraduate at the University of Washington before transferring to San Diego State’s computer science department. Nick is one of SDSU’s first wave of cross-trained students participating in the BioMath program, an emerging NSF priority. Outside the lab, Nick is the Vice President of a student organization called Compassion for African Villages that sends aide to the village of Rundongo, Zimbabwe.

Carny Cheng

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Carny is a Computational Science Masters student. His research focuses mainly on web services providing middleware for scientists to access cyberinfrastructure resources. Carny holds two Bachelors degrees from University of California, San Diego in Computer Engineering and economics. He has spent sometime working in the software industry at Websense, Inc. where he bounced from project to project eventually settling in text classification.

Carny also serves as the lab system administrator. It is advisable to stay on Carny’s good-side if you want your access to the lab’s computing resources.

Kate McNair

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Kate is a …