Dr. Robert A. Edwards, B. Sc. D. Phil
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- Bu səhifədəki naviqasiya:
- Edwards, R.A.
- R.A. Edwards
- Genome Announcements (not peer reviewed)
- Published Meeting Abstracts
- Published Meeting And Book Reviews
- Invited Presentations (Since 2000)
- Teaching: San Diego State University
- University of Tennessee Health Sciences Center
- Trainees: Visting scholars
- Postdoctoral Researchers
- Ph.D. Graduates
- Visting Brazilian Students (Students in my lab only. The exchange welcomed 35 scholars to SDSU)
- Thesis Committee Meetings
- Student Research Projects (since 2011)
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Edwards, R.A. and Dinsdale, E.A. 2007. Marine Environmental Genomics: Unlocking the Ocean’s Secrets. Oceanography. 20:56-61. http://dx.doi.org/10.5670/oceanog.2007.48 2014
journal impact factor: 3.285. Cited by 6. 91.
Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone P, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB. 2007. Metagenomic and small- subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Env. Microbiol. 73:7059–7066. http://dx.doi.org/10.1128/AEM.00358-
Dr. Robert Edwards. Biosketch 07 2014 journal impact factor 3.952. Cited by 248. 92. Wegley, L. g , Edwards, R.A., Rodriguez-Brito, B. g , Liu, H. g , and Rohwer, F. 2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Env. Microbiol. 9:2707-2719. http://dx.doi.org/10.1111/j.1462- 2920.2007.01383.x 2014 journal impact factor: 3.264. Cited by 198. 93. McNeil, L., Reich, C., Aziz, R. p , Disz, T., Cohoon, M., Edwards, R., Gerdes, S., Hwang, K., Kubal, M., Margaryan, G., Olsen, G., Olson, R., Osterman, A., Parrello, B., Vassieva, O., Vonstein, V., Xia, F., Zagnitko, O., Overbeek, R., and Stevens, R. 2007. The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucl. Acids Research 35:D347-353. http://dx.doi.org/10.1093/nar/gkl947 2014 journal impact factor 8.808. Cited by 81. 94. Joyce, A.R. g , Reed, J.L. g , White, A., Edwards, R., Osterman, A., Baba, T., Mori, H., Lesely, S.A., Palsson, B.O., Agarwalla, S. 2006. Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol.. 188:8259-8271. http://dx.doi.org/10.1128/JB.00740-06 2014 journal impact factor 2.688. Cited by 415. 95. Angly, F.E. g , Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H., Mahaffy, J.M., Mueller, J.E., Nulton, J., Olson, R., Parsons, R., Rayhawk, S. g , Suttle, C.A., and Rohwer, F. 2006. The Marine Viromes of Four Oceanic Regions. PLoS Biology. 4:e368. http://dx.doi.org/10.1371/journal.pbio.0040368 2014 journal impact factor: 11.771. Cited by 552. 96. Gerdes, S, Edwards, R.A., Kubal, M. Fonstein, M., Stevens, R., and Osterman, A. 2006. Essential genes on metabolic maps. Curr. Opinion Biotech. 17:448-456. http://dx.doi.org/10.1016/j.copbio.2006.08.006 2014 journal impact factor: 8.035. Cited by 76.
97. Krause, L., g Diaz, N.N., Bartels, D., Edwards, R.A., Pühler, A., Rohwer, F., Meyer, F., and Stoye, J. 2006. Finding Novel Genes in Bacterial Communities Isolated from the Environment. Bioinformatics. 22:e281-9. http://dx.doi.org/10.1093/bioinformatics/btl247
2014 journal impact factor 4.621. Cited by 70. 98. Smith, J.E., Edwards, R.A., Obura, D., Pantos, O. p , Sala, E., Sandin, S.A., Shaw, M., Smriga, S. g , and Rohwer, F. 2006. Indirect effects of algae on coral: algae-mediated, microbe- induced coral mortality. Ecol. Letts. 9: 835. http://dx.doi.org/10.1111/j.1461- 0248.2006.00937.x 2014 journal impact factor: 13.042. Cited by 184. 99.
g , Wegley, L. g , Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander Jr., E.C., and Rohwer, F. 2006. Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeological conditions. BMC Genomics, 7:57. http://dx.doi.org/10.1186/1471-2164-7-57 2014 journal impact factor 4.041. Cited by 377. Cited by 377. 100. Madsen, M. L. g , Nettleton, D., Thacker, E.L., Edwards, R., and Minion, F.C. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect Immun 74: 160-6. http://dx.doi.org/10.1128/IAI.74.1.160-166.2006
2014 journal impact factor: 4.156. Cited by 42. 101. Rodriguez-Brito, B. g , Rohwer, R., and Edwards, R.A. 2006. An application of statistics to comparative metagenomics. BMC Bioinformatics 7:162. http://dx.doi.org/10.1186/1471- 2105-7-162
2014 journal impact factor: 2.672. Cited by 123. 102.
DeLong, E. F., C. M. Preston, T. Mincer, V. Rich, S. J. Hallam, N. U. Frigaard, A. Martinez, M. Page 14 of 30 Dr. Robert Edwards. Biosketch B. Sullivan, R. Edwards, B. R. Brito g , S. W. Chisholm and D. M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496- 503.
http://dx.doi.org/10.1126/science.1120250
2014 journal impact factor: 31.477. Cited by 787.
103. Trotter, M., McAuliffe, O. Callanan, M. Edwards, R. Fitzgerald, G. F. Coffey, A. and Ross, R. P. 2006. Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactis provides insight into its adaptable nature. Gene. 366:189-199. http://dx.doi.org/10.1016/j.gene.2005.09.022
2014 journal impact factor: 2.082. Cited by 18.
104. Overbeek, R., T. Begley, R. M. Butler, J. V. Choudhuri, H. Y. Chuang, M. Cohoon, V. de Crecy- Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E. D. Frank, S. Gerdes, E. M. Glass, A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M. Kubal, N. Larsen, B. Linke, A. C. McHardy, F. Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman, V. Portnoy, G. D. Pusch, D. A. Rodionov, C. Ruckert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko and V. Vonstein 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33: 5691-702. http://dx.doi.org/10.1093/nar/gki866
by 814. 105.
Musumeci, L., C. Bongiorni, L. Tautz, R. A. Edwards, A. Osterman, M. Perego, T. Mustelin and N. Bottini (2005). Low-Molecular-Weight Protein Tyrosine Phosphatases of Bacillus subtilis. J Bacteriol 187: 4945-56. http://dx.doi.org/10.1128/JB.187.14.4945-4956.2005
2014 journal impact factor 2.688. Cited by 31. 106.
Edwards, R.A. and Rohwer, F. 2005. Viral Metagenomics. Nature Rev. Microbiol. 3:504-511. http://dx.doi.org/10.1038/nrmicro1163 2014 journal impact factor: 23.317. Cited by 412. 107.
Aziz, R.K. g , Edwards, R.A., Taylor, W.W., Low, D.E., McGeer, A., and Kotb. M. 2005. Mosaic Prophages with Horizontally Acquired Genes Account for the Emergence and Diversification of the Globally Disseminated M1T1 Clone of Streptococcus pyogenes. J. Bacteriol. 187: 3311-3318. 2014 journal impact factor 2.688. Cited by 82. 108.
Mijakovic, I., Musumeci, L., Tautz, L., Petranovic, D., Edwards, R.A., Jensen, P.R., Mustelin, T., Deutscher, J., and Bottini, N.. In Vitro Characterization of the Bacillus subtilis Protein Tyrosine Phosphatase YwqE. J. Bacteriol. 187: 3384-3390. http://dx.doi.org/10.1128/JB.187.10.3384-3390.2005
Cited by 35. 109.
Purdy A., Rohwer F., Edwards R., Azam F., and Bartlett DH. 2005. A Glimpse into the Expanded Genome Content of Vibrio cholerae through Identification of Genes Present in Environmental Strains. J Bacteriol. 187:2992-3001. http://dx.doi.org/10.1128/JB.187.9.2992-3001.2005
by 46. 110.
Edwards R.A., Breitbart M. g , and Rohwer F.L. 2004. Hidden messages within the genetic code. ASM news. July. 111.
O'Flaherty S., Ross R.P., Edwards R., Meaney W., Fitzgerald G.F., and Coffey A. 2004. Genome of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting Gram-Positive Bacteria with a Low G+C Content. J. Bacteriol. 186:2862-2871. http://dx.doi.org/10.1128/JB.186.9.2862-2871.2004
by 114. Page 15 of 30 Dr. Robert Edwards. Biosketch 112.
Bhattacharyya A, Stilwagen S, Reznik G, Feil H, Feil WS, Anderson I, Bernal A, D'Souza M, Ivanova N, Kapatral V, Larsen N, Los T, Lykidis A, Selkov E Jr, Walunas TL, Purcell A, Edwards RA, Hawkins T, Haselkorn, R, Overbeek R, Kyrpides NC, and Predki PF. 2002 Draft Sequencing and Comparative Genomics of Xylella fastidiosa Strains Reveal Novel Biological Insights. Genome Res. 12:1556-63. http://dx.doi.org/10.1101/gr.370702 2014 journal impact factor: 13.852. Cited by 68. 113. Rohwer, F.L. and Edwards, R.A. 2002. The Phage Proteomic Tree: A Genome-Based Taxonomy for Phage J. Bacteriol. 184:4529-35. http://dx.doi.org/10.1128/JB.184.16.4529- 4535.2002
2014 journal impact factor 2.688. Cited by 339. 114.
Edwards, R.A., G.J. Olsen, and S.R. Maloy. 2002. The importance of complete genome sequences. Trends Microbiol. 10:220. http://dx.doi.org/10.1016/S0966-842X(02)02354-5
2014 journal impact factor: 9.808 115. Edwards, R.A., G.J. Olsen, and S.R. Maloy. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol. 10:94-99. 10.1016/S0966-842X(01)02293-4 2014 journal impact factor: 9.808. Cited by 184. 116.
Townsend, S.M., Kramer, N.E. Edwards, R.A., Baker, S., Hamlin, N., Simmonds, M., Stevens, K., Maloy, S.R., Parkhill, J. And Bäumler, A. J. 2001. Salmonella enterica serotype Typhi possesses a unique repertoire of fimbrial genes. Infect Immun 69:2894-901. http://dx.doi.org/10.1128/IAI.69.5.2894-2901.2001
by 137. 117.
Edwards, R.A. 2001. Microbial Genome Sequencing. ASM News. 67:121. 118.
Edwards, R.A., Matlock, B.C., Heffernan, B.J., and Maloy, S.R. 2001. Genomic Analysis and Growth Phase Dependent Regulation Of The SEF14 Fimbriae of Salmonella enterica Serovar Enteritidis. Microbiology. 147:2705-2715. 2014 journal impact factor: 2.835. Cited by 19.
119. Edwards, R.A. and S.R. Maloy. 2001. Inside or Outside: Determining the location of intracellular pathogens. BioTechniques 30:304-311. 2014 journal impact factor: 2.754. Cited by 4. 120.
Edwards, R.A, D.M. Schifferli, and S.R. Maloy. 2000. A role for Salmonella fimbriae in intraperitoneal infections. Proc. Natl. Acad. Sci USA. 97:1258-1262. http://dx.doi.org/10.1073/pnas.97.3.1258
Reviewed in Trends Microbiol. 8:211. 2014 journal impact factor: 9.809. Cited by 83. 121.
temporary inactivation of host restriction. BioTechniques 26: 892-900. 2014 journal impact factor: 2.754. Cited by 32. 122.
Edwards, R.A., and J.L. Puente. 1998. Fimbrial expression in enteric bacteria: A critical step in intestinal pathogenesis. Trends Microbiol. 6: 282-287. http://dx.doi.org/10.1016/S0966- 842X(98)01288-8
123. Edwards, R.A., L.H. Keller, and D.M. Schifferli. 1998. Improved allelic exchange vectors and their use to analyze 987P fimbria gene expression. Gene 207: 149-157. http://dx.doi.org/10.1016/S0378-1119(97)00619-7
2014 journal impact factor: 2.082. Cited by 276.
124. Edwards, R.A., and D.M. Schifferli. 1997. Differential regulation of fasA and fasH expression of Escherichia coli 987P fimbriae by environmental cues. Mol. Microbiol. 25: 797-809. http://dx.doi.org/10.1046/j.1365-2958.1997.5161875.x
2014 journal impact factor: 5.026. Page 16 of 30 Dr. Robert Edwards. Biosketch Cited by 38. 125.
proteins involved in the export of 987P fimbriae. J. Bacteriol. 178: 3426-3433. 2014 journal impact factor 2.688. Cited by 25. 126.
Merrick, M.J., and R.A. Edwards. 1995. Nitrogen control in bacteria. Microbiol. Mol. Biol. Rev. 59:604-622. 2014 journal impact factor: 15.255. Cited by 564. 127.
impact factor: 2.831. Cited by 43. p Denotes postdoctoral researcher g Denotes graduate student. u Denotes undergraduate student Citations from Google Scholar as of September 1 st , 2014. Journal impact factors from http://www.citefactor.org/
st , 2014.
Genome Announcements (not peer reviewed): 1. Lorenzi AS, Silva GGZ, Lopes FAC, Chia MA, Edwards RA, Bittencourt-Oliveira MC. 2016. Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin and Cylindrospermopsin Synthetase Genes. Genome Announc 4:e00228–16. 2. Calva E, Silva C, Zaidi MB, Sanchez-Flores A, Estrada K, Silva GGZ, Soto-Jiménez LM, Wiesner M, Fernández-Mora M, Edwards RA, Vinuesa P. 2015. Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype. Genome Announc 3:e00663–15. 3. Eppinger Mg , McNair K, Zogaj X, Dinsdale EA, Edwards RA, Klose KE. 2013. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis. Genome Announc. 1. http://dx.doi.org/10.1128/genomeA.00926-13 (No impact factor). Cited by 1
1. R.K. Aziz, Dwivedi, B., Breitbart, M., and Edwards, R.A. 2011 Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets BMC Bioinformatics 12:A9doi:10.1186/1471-2105-12-S7-A9 2. Wu, W., Edwards, R.A., Judson, I. R., Papka, M. E., Thomas, M., and Stevens, R. 2008. TeraGrid Open Life Science Gateway. Proceedings of the 3rd annual TeraGrid Conference, TeraGrid '08. 3. R A Edwards. 2008. The smallest cells pose the biggest problems: high-performance computing and the analysis of metagenome sequence data. J. Phys.: Conf. Ser. 125 012050. http://dx.doi.org/10.1088/1742-6596/125/1/012050
Published Meeting And Book Reviews: Page 17 of 30 Dr. Robert Edwards. Biosketch 1. Farris, L.A. and R.A. Edwards. 2001. An old dog learns new tricks. Trends. Microbiol. 95:243 2. Edwards, R.A., and S.R. Maloy. 2000. Microbial genomics and evolution. Trends Genet 16:115. 3. Edwards, R.A. 2000. Big bugs need little bugs to help them bite. Trends. Microbiol 8:384-385 4. Maloy, S.R., and R.A. Edwards. 1999. Eye of newt and toe of frog. Trends Genet 15:250. 5. Edwards, R.A., and S.R. Maloy. 1998. Examining E. coli. Bioscience 48:323-324. World Wide Web Sites: 1. The Salmonella Source: http://www.salmonella.org/
. Reviewed in Science 2001 293(5532):1019 2. SCUMS: http://scums.sdsu.edu/
3. Edwards Lab: http://edwards.sdsu.edu/research
http://www.phantome.org/
5. The Phage SEED: http://www.phantome.org/PhageSeed/
http://vdm.sdsu.edu/ Major contributions: 1. RAST
http://rast.nmpdr.org/ 2. MG-RAST http://metagenomics.anl.gov/ 3. SEED
http://www.theseed.org/ 4. NMPDR http://www.nmpdr.org/
1. Computational Sciences Research Center, SDSU, 1/2016 2. Translational Research Institute, Brisbane, Australia, 11/2015 3. Federal University of Rio de Janeiro, Brazil 11/2015 4. Univeristy of Queensland, Australia 11/2015 5. Flinders University, Australia 9/2015 6. University of Illinois at Urbana Champaign, 9/2015 7. University of Iowa Medical School, 4/2015 8. Asociacion Mexicana de Microbiología Querétaro, Mexico (two talks) 3/2015 9. JAMS-TOAST, Australian Museum, 2/2015 10. University of New South Wales, 2/2015 11. Sydney Institute of Marine Sciences, 2/2015 12. Flinders University, Adelaide, Australia, 1/2015 13. University of Sao Paulo, Sao Paulo, Brazil, 11/2014 14. University of Sao Paulo, Piricicaba, Brazil, 11/2014 15. Radboud University Medical Center Nijmegen, The Netherlands, 7/2014 16. Viruses of Microbes Meeting, Zurich, Switzerland 7/2014 17. Diponegoro University, Semarang, Indonesia 5/2014 18. Hasanuddin University, Makassar, Indonesia 5/2014 19. Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. 4/2014 20. Computational Sciences Research Center, San Diego 11/2013 21. Lawrence Berkley National Laboratory, 7/2103 Page 18 of 30 Dr. Robert Edwards. Biosketch 22. American Society of Microbiology, Biology of Viruses, San Francisco 7/2013 23. Autonomous University of Mexico, Cuernavaca 4/2013 24. Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. 3/2013 25. Case Western Reserve University Graduate Student invited speaker. Cleveland, OH 3/2013 26. Biolog SRI Conference on Predicting Cell Metabolism and Phenotypes, Menlo Park, CA 3/2013 27. University of California, San Diego. San Diego, CA. 2/2013 28. University of Southern California, Los Angeles, CA. 2/2013 29. LIPI-NSF, Workshop on Dimensions of Biodiversity, Cibinong, Indonesia 2/2013 30. National Science Foundation, Washington DC. 1/2013 31. Southern California Systems Biology Conference, Irvine, CA. 1/2013 32. Congresso Brasileiro de Oceanografia - CBO 2012, Rio de Janeiro, Brazil 11/2012 33. 7th Workshop on Comparative Microbial Genomics and Taxonomy, Rio de Janeiro, Brazil 11/2012
34. Bigelow Laboratory, ME 10/2012 35. Bertinoro Computational Biology Meeting, Bertinoro, Italy, 10/2012 36. International Conference of the IEEE Engineering in Medicine and Biology Society, San Diego, CA 8/2012 37. American Society Microbiology General Meeting, San Francisco, CA 6/2012 38. Roche/454 User Group Meeting, Indianapolis, IN 5/2012 39. International Workshop on Bioinformatics. Cuernavaca, Mexco. 1/2012 40. Instituto de Biotecnología. Cuernavaca, Mexco. 1/2012 41. 6th Workshop on Comparative Microbial Genomics and Taxonomy, Rio de Janeiro, Brazil 10/2011
42. Kavli Foundation Frontiers in Science, National Academy of Sciences, 11/2011 43. Metagenomics Workshop. Florida Branch ASM, 10/2011 44. San Diego State University Research Foundation Inaugural PI Presentation, San Diego 9/2011 45. Ecology and Genomics of Cystic Fibrosis, CO 7/2011 46. Microbial Genomics and Modelling, Park City, UT 7/2011. 47. Life Technologies, 5/2011 48. Computational and Comparative Genomics, Cold Spring Harbor, NY 11/2010 49. Computational Genomics, Cuernavaca, Mexico, 10/2010 50. FIPSE-CAPES directors meeting, Florianopolis, Brazil, 9/2010 51. Molecular Genetics of Bacteria and Phages, Cold Spring Harbor Laboratory, NY, 8/2010 52. 5th Workshop on Comparative Microbial Genomics and Taxonomy, Rio de Janeiro, Brazil 8/2010
53. Advanced Bacterial Genetics Course, Cold Spring Harbor, NY 6/2010 54. American Society for Microbiology, San Diego, CA 5/2010 55. Roche Asia User Group Meeting, Hong Kong, 5/2010 56. Scripps Institution of Oceanography, San Diego, CA 4/2010 57. University of California, Santa Barbara, CA, 4/2010 58. Centro de Investigación Científica y de Educación Superior de Ensenada, BC, Mexico 4/2010 59. First Mexican Congress on Microbiology and Biochemistry, Pachuca, Mexico, 3/2010 60. Bioinformatics Two Day Course, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico 1/2010 61. Rocky 2009, Snowmass, CO, 12/2009 Page 19 of 30 Dr. Robert Edwards. Biosketch 62. Mexican National Congress of Virology, Merida, Mexico, 11/2009 63. University of Florida, Gainsville, FL 10/2009 64. Florida Branch of the American Society for Microbiology, Key West, FL 10/2009 65. Computational Sciences Research Center, San Diego, 9/2009 66. San Diego Consortium for Systems Biology, Salk Institute, San Diego, 8/2009 67. DOE Computing in the Extreme, Chicago IL 8/2009 68. Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 8/2009 69. 4th Workshop on Comparative Microbial Genomics and Taxonomy, Petropolis, Brazil 8/2009 70. C-MORES Workshop on Marine Microbiology, Honolulu, Hawai'i, 5/2009 71. American Society of Microbiology, Philadelphia, PA 5/2009 72. Autonomous University of Mexico, Cuernavaca 03/2009 73. CHI New Genomics Workshop, San Diego, CA 03/2009 74. Collabrx, Palo Alto, CA 03/2009 75. United States Department of Agriculture, Washington DC 02/2009 76. University of California, Santa Barbara 02/2009 77. University of California, Los Angeles 01/2009 78. Rocky Mountain Bioinformatics Meeting, Snowmass, CO 12/2008 79. Roche 454, New Haven, CT 9/2008 80. Scientific Discoveries Through Advanced Computing, Seattle, WA 7/2008 81. International Coral Reef Society Meeting, Fort Lauderdale, FL 7/2008 82. Advanced Bacterial Genetics Course, Cold Spring Harbor, NY 6/2008 83. American Society of Microbiology (ASM), Boston, MA 06/2008 84. Rocky Mountain Bioinformatics Meeting, Snowmass, CO 12/2007 85. US/EU Conference on CyberInfrastructure, Washington, DC 10/2007 86. American Society of Microbiology (ASM), Toronto, Canada 06/2007 87. CHI New Genomics Workshop, San Diego, CA 05/2007 88. Argonne National Labs, Argonne, IL. 03/2007 89. Metagenomics 2006, San Diego, CA 10/2006 90. Joint Genome Institute, Walnut Creek, CA. 09/2006 91. Genome Standard Consortium, Cambridge, England. 09/2006 92. California Metagenomics Workshop, Berkeley, CA. 09/2006 93. ASM/NCBI Genome Annotation Workshop, NIH Bethesda, MD. 08/2006 94. Scientific Committee on Oceanographic Research (SCOR), Vancouver, Canada. 06/2006 95. Scripps Institute of Oceanography 06/2006 96. The Sanger Center, Cambridge, England. 05/2006 97. Society for General Microbiology, Warwick, England. 05/2006 98. San Diego State University Computational Sciences Research Center. 03/2006 99. American Society of Limnology and Oceanography (ASLO), Session Organizer and Chair, HI 02/2006
100. Argonne National Labs, Argonne, IL. 01/2006 101. Analytical Genetics, San Diego, CA. 10/2005 102. Barcode of Life Meeting, Panama. 09/2006 103. American Society of Microbiology (ASM), Session Organizer and Chair. 06/2005 104. San Diego Microbiology Group, San Diego, CA. 05/2005 105. US/EU Conference on Marine Genomics, Bremen, Germany. 05/2005 Page 20 of 30 Dr. Robert Edwards. Biosketch 106.
The Burnham Institute for Medical Research, San Deigo, CA. 07/2004 107.
The New Phage Meeting, Key Biscayne, FL. 06/2004 108.
American Society of Microbiology (ASM), 05/2004 109.
The University of Memphis, Memphis, TN 11/2003 110.
The VA Hospital, Memphis, TN 07/2003 111.
University of Oxford, England, 02/2003 112.
University of Missouri, Columbia, MO 01/2003 113.
San Diego State University, San Diego, CA 11/2002 114.
South East Regional Bioterrorism Workshop, Memphis TN 07/2003 115.
Centre National de la Recherche Scientifique, Gif-sur-Yvette, France,10/2002 116.
Analytical Genetics, Santorini, Greece 10/2002 117.
The University of Sheffield, England 9/2002 118.
American Society of Microbiology (ASM) (session chair), 05/2002 119.
Southern Illinois University, Carbondale, IL 04/2002 120.
Institute of Biotechnology, Cuernavaca, MX 01/2002 121.
Furman College, Greenville, SC 11/2001 122.
Oak Ridge National Laboratory, 10/2001 123.
Molecular Genetics of Bacteria and Phage, Cold Spring Harbor, 09/2001. 124.
Iowa State University, Ames, IA. 04/2001 125.
The Center for Ecology and Hydrology, Oxford University, England, 03/2001 126.
Veterinary School, Autonomous University of Mexico, Mexico, MX 01/2001 127.
Institute of Biotechnology, Cuernavaca, MX 01/2001 128.
Midwest Pathogenesis Meeting, Columbus, OH 10/2000 129.
Molecular Genetics of Bacteria and Phage, Madison, WI, 09/2000. 130.
The VA Hospital, Memphis, TN 07/2000 131.
Salmonella Genomics Meeting, St. Louis MO 04/2000 132.
Midwest Prokaryotic Molecular Biology Meeting, Chicago IL 01/2000 Teaching: San Diego State University: Primary instructor 2014
Fall Programming Problems in Bioinformatics, CS696 2014 Fall
Computational Genomics, CS609 2014
Spring Topics in Comptuational Science, COMP800 2014 Spring
Topics in Global Climate Change, COS696 2014
Spring Web scripting languages, CS547 2014 Spring
Data Structures, CS310 2013
Fall Scientific Data Base Techniques, CS503 2013 Spring
Data Structures, CS310 2013
Spring Web scripting languages, CS547 2012 Fall
CS Advanced Topics: Computational Genomics, CS596 2012
Fall Scientific Data Base Techniques, CS503 Page 21 of 30 Dr. Robert Edwards. Biosketch 2012
Spring Data Structures, CS310 2011 Fall
CS Advanced Topics: Computational Genomics, CS596 2011
Spring Data Structures, CS310 2010 Fall
CS Advanced Topics: Computational Genomics, CS596. This class is being taught in collaboration with Dr. Rosy Guiterrez at the Autonomous University of Mexico, Cuernavaca, Mexico, using the SDSU distance learning technology (video conferencing). 2010 Fall
Computational Sciences Interdisciplinary Approaches, COMP 800 2010
Spring Data Structures, CS310 2009 Fall
Scientific Data Base Techniques, CS503 2009
Spring CS Advanced Topics: Genome Annotation and Analysis, CS696 2009 Spring
Data Structures, CS310 2008
Fall Scientific Data Base Techniques, CS503 2008 Spring
Data Structures, CS310 Guest instructor 2014
Summer Bridges to the Baccalaueate Program 2014 Spring
SDSU/UCSD Integrated Microbiology 2014
Spring Ecological metagenomics, BIO 562 2013 Summer
Bridges to the Baccalaueate Program 2013 Spring SDSU/UCSD Integrated Microbiology 2013
Spring Ecological metagenomics, BIO 562 2012 Spring
Ecological metagenomics, BIO 562 2012 Summer Howard Hughes Program, SDSU 2012 Summer Bridges to the Baccalaueate Program 2011
Fall S-STEM
2011 Summer
Bridges to the Baccalaueate Program 2011 Spring Microbial genetics and physiology BIOL 549 2011
Spring Methods in Bioinformatics CS600 2011 Spring Ecological metagenomics, BIO 562 2010 Summer
Bridges to the Baccalaueate Program 2010
Spring Microbial genetics and physiology BIOL 549 2010 Spring
Ecological metagenomics, BIO 562 2010
Spring Advanced topics in molecular biology, MBIO610 2009 Summer
Bridges to the Baccalaueate Program 2009
Summer Research Experience for Undergraduates 2009 Spring
Advanced topics in computational science COMP 670 2009
Spring Microbial genetics and physiology BIOL 549 2008 Summer
Bridges to the Baccalaueate Program 2008
Spring Microbial genetics and physiology BIOL 549 2007 Summer
Bridges to the Baccalaueate Program 2007
Spring Microbial genetics and physiology BIOL 549 Page 22 of 30 Dr. Robert Edwards. Biosketch University of Tennessee Health Sciences Center: 2004
Molecular Biology, MSCI816 2004
Bioinformatics, MSCI814, course director 2003
Molecular Biology, MSCI816 2002
Bacterial Pathogenesis, MSCI700, course designer and director 2002
Bioinformatics, MSCI814, course director 2002
Molecular Biology, MSCI816 2002
Bioinformatics, MSCI815 2001
Molecular Techniques, MSCI929 Workshops: Instructor 2015
Genomics, Metagenomics, and Viromics, Flinders, Australia (organizer and instructor) 2015
Genomics, Metagenomics, and Viromics, San Diego, CA (organizer and instructor) 2015
High performance computing workshop, San Diego, CA (organizer and instructor) 2015
STEMM: Sequencing Technology Education Using Microbial Metagenomes, San Diego, CA 2015
Tutorial on Omics Analysis and Tools, Sydney, Australia 2015
SIMS Summer Course on Marine Microbial Ecology, Sydney, Australia 2014
2 nd Workshop on analysis of microbial genome sequences and metagenomics, Ensenada, Mexico 2014
STEMM: Sequencing Technology Education Using Microbial Metagenomes, San Diego, CA 2013
Workshop on analysis of microbial genome sequences and metagenomics, La Paz, Mexico 2012
7 th Workshop on Comparative Microbial Genomics and Taxonomy, Rio de Janeiro, Brazil 2012 International Workshop on Bioinformatics, Cuernavaca, Mexico. 2011 6
Workshop on Comparative Microbial Genomics and Taxonomy, Rio de Janeiro, Brazil 2010
5 th Workshop on Comparative Microbial Genomics and Taxonomy, Rio de Janeiro, Brazil 2010 CICESE Two-day course in Bioinformatics and Computational Biology. 2010 Computational Genomics, Cold Spring Harbor Laboratory, NY 2010 Advanced Bacterial Genetics, Cold Spring Harbor Laboratory, NY 2010 UCSB Special Workshop on metagenomics. A two day workshop for 15 students and faculty members of the bioinformatics of metagenomics data. 2010
Microbial genomics and metagenomics workshop, Rio de Janeiro, Brazil. An invited lecturer in a week long workshop on microbial genomics, metagenomics, and taxonomy. 2009 Metagenomics Workshop, Argonne National Laboratory, Argonne IL, 2009 Microbial genomics and metagenomics workshop, Petropolis, Brazil. An invited lecturer in a week long workshop on microbial genomics, metagenomics, and taxonomy. 2009
C-MORES Workshop on Marine Biology. An invited lecturer in this week-long workshop to teach metagenomics and bioinformatics. 2008 Metagenomics Workshop, Argonne National Laboratory, Argonne IL, 2008 Advanced Bacterial Genetics, Cold Spring Harbor Laboratory, NY 2007 Metagenomics Workshop, Argonne National Laboratory, Argonne IL, 2005 Second International Minicourse on Genetics, Genomics, and Epidemiology of Salmonella, Nanning, China. November 2004
First International Minicourse on Genetics, Genomics, and Epidemiology of Salmonella, Page 23 of 30 Dr. Robert Edwards. Biosketch Cuernavaca, Mexico. November Participant 1999
NSF/DOE sponsored participant in the 7th Conference on Small Genomes, Arlington VA 1995
Participant in the Advanced Bacterial Genetics Course, Cold Spring Harbor Laboratory 06/1995
Trainees: Visting scholars Cazares, Adrian (Visiting scholar from CINVESTAV, Mexico City, Mexico) Dutilh, Bas (Visiting scholar from Radboud University Medical Centre, the Netherlands) Fernandes, Lohengrin (Visiting scholar from the Brazilian navy) Paterson, James (Flinders University, Adelaide, Australia) Smith, Renee (Flinders University, Adelaide, Australia) Thompson, Cristiane (Visiting scholar from FIOCRUZ, Brazil) Thompson, Fabiano (Visiting scholar from the Federal University of Rio de Janeiro, Brazil) Postdoctoral Researchers Aziz, Ramy (currently an Assistant Professor, University of Cairo) Frank, Jeremy (currently a Postdoctoral Researcher at Norwegian University of Life Sciences) Matthews, Dave (currently a Head of Technology at Phyllom, Inc) Ph.D. Graduates Schmieder, Robert (currently at Illumina, San Diego) Akhter, Sajia (currently at Stanford University)
Cantu, Adrian Cuevas, Daniel Silva, Genivaldo Bose, Promita Farris, Leigh Seguritan, Victor
Baer, Adam Cheng, Carny Feupe, Stephanie Feudjio Fuyu, David Grant, Matthew Hamel, Kristina
Dr. Robert Edwards. Biosketch Hisakawa, Nao Hull, Brad Kang, Han Suh Liang, Tiff Yujing Levi, Kyle McNair, Kate Naoman, Amna O'Connell, Taylor Park, Songduk Raheema, Julian Robinson, Blaire Sadural, Jeffrey Sanchez, Savannah Smith, Iris Soury, Rima Turner, Nick Williams, Steve Wright, Sheridan
Beacher, Jon Belon, Patrick Benavides, Georgina Blanco, Andres Celms, Nick Comeau, Joey Cuevas, Daniel Dempsey, Michael Garrido, Haydee Goodwin, Josh Hagen, Matthew Hoffman, Josh Hudson, Brian Kamiksisian, Vasken Kassen, Ted Lentz, Palla Li, Jimmy Lin, Joseph Lui, Heqiao Matonis, Ryan Pham, Huy Robinson, Blaire Sadural, Jeffrey Sanchez, Savannah Seitz, Matt Page 25 of 30 Dr. Robert Edwards. Biosketch Smith, Dwaine Steinman, Tracy Tadesse, Ruth Tam, Evan Tosti, Salvatore Turner, Nick Turner, Tyler Vega, Alejandro Wellington-Oguri, Michiyo Westerhoff, David Wright, Sheridan Zhou, Meng
Ballester, Marcela Correia, Guilherme Dias da Silva, Tharles Gambarini, Victor Garza, Daniel Machado, Augustoa Martins, Karen Meirelles, Pedro Monteirocosta, Leonardo Navarrete, Acacio Silva, Jose Aldo Trinidade, Amanda
Baxi, Ankita, AP Biology Research Intern Klimkowsky, Miron High School Summer Studentt St. Bernard, Nashan. McNair Summer Student Davis, Shanita McNair Summer Student Holmes, Stacy McNair Summer Student SDSU Committees: Special Review Panel of the College of Sciences Policy and Planning Committee, 2015 Association of Computing Machinery Faculty Advisor, 2011- Bioinformatics and Medical Informatics Curriculum Committee, 2008- Biotechnology Students Association Faculty Advisor, 2011- Computational Sciences Research Center Advisory Committee, 2007- Page 26 of 30 Dr. Robert Edwards. Biosketch Computer Science Faculty Search Committee, 2014 Dean Maloy five year review. 2013 Diving Safety Committee, 2008- International Committee, 2010- Viromics Institute BioMath position Faculty Search Committee, 2014 Viromics Institute Structural Biology position Faculty Search Committee, 2014
Robert Schmieder CSRC Chair
PhD 11/30/2012 Sajia Akhter CSRC
Chair PhD
08/30/2013 Amna Naoman CS Chair
Msc 11/23/2009 Songduk Park CS Chair Msc 11/30/2009 Matthew Grant CS Chair Msc 12/08/2009 Stephanie Feudjio BMI
Chair Msc
05/01/2011 Kate McNair CSRC Chair
Msc 07/22/2011 Jimmie Dixon CS Chair Msc 08/31/2011 Sheridan Wright CS Chair Msc 11/05/2012 Steven Williams CS Chair Msc 11/21/2012 Andrew Luxner CS Chair Msc 04/18/2013 Tiff Liang BMI
Chair Msc
06/25/2014 Matthew Shaw CS Chair
Msc 12/02/2014 Adriel Carolina BMI
Msc 03/26/2013 Angela DiDomenico Biology
Msc 05/08/2014 Beltran Rodriguez Brito CSRC
PhD 06/09/2009 Ben Knowles Biology
PhD 06/20/2014 Burak Cebecioglu Math
Msc 05/13/2010 Burak Cebecioglu Math
Msc 05/13/2010 Byant Fulk Geology
Msc 05/07/2010 Dave Carlson Biology
Msc 11/21/2013 Dave Carlson Biology
Msc 06/15/2015 Florent Angly CSRC
PhD 06/04/2009 Gauree Bhole CS Msc 05/14/2010 Hoda Sayyadinejad CS Msc
08/28/2014 Jake Minich BMI Msc
05/30/2014 Jordan Satler Biology Msc
05/10/2011 Ketake Raste CS Msc
04/14/2014 Lauryn Keeler BMI Msc
10/04/2013 Lee Ripma Biology Msc
12/02/2013 Lena van der Stapp CSRC Msc
10/14/2011 Mackenzie Mabry Biology Msc
11/26/2013 Martis Cowles Biology* PhD
03/13/2013 Martis Cowles Biology PhD
02/20/2014 Matt Munoz Biology Msc
01/06/2012 Page 27 of 30 Dr. Robert Edwards. Biosketch Nori Cassman BMI Msc
12/16/2013 Paul Fryling BMI Msc
05/08/2013 Pedro Tores BMI Msc
09/10/2013 Pratyusha Uddaraju CS Chair
Msc 10/29/2015 Savannah Sanchez Biology
Msc 02/21/2014 Seena Farzaneh BMI
Msc 04/08/2013 Shashank Sathe BMI
Msc 11/26/2013 Shashank Sathe BMI
Msc 07/10/2015 Sowmya Vijay BMI
Msc 04/16/2014 Srinidhi Balaram CS Msc 04/09/2015 Steve Quistad Biology* PhD
01/31/2013 Steve Quistad Biology PhD
05/01/2015 Veronica Casas Biology PhD
04/22/2011 Wei Wang
CS* PhD
03/13/2014 Wei Wang
CS PhD
03/26/2015 Yan Wei Lim Biology PhD
02/15/2012 Yan Wei Lim Biology* PhD
02/14/2014 Yan Wei Lim Biology* Msc
05/09/2011 * Proposal meeting Student Research Projects (since 2011): Semester Name Class Project Spring 2014 Genivaldo Silva Comp 894 Genivaldo wrote and implemented the FOCUS tool for analysis of metagenomes Spring 2014 Daniel Cuevas Comp 897 Daniel worked on the Viral Dark Matter project, analyzing and modeling the growth of bacteria Spring 2014 David Westerhoff CS 499 David desgined an API for the Viral Dark Matter database to allow computational access ot the data Spring 2014 Ryan Matonis CS 499 Ryan worked on the analysis of Shannon's theory as it applies to DNA sequence analysis Spring 2014 Salvatore Tosti CS 499 Salvatore implemented a complete Python version of the image detection and classification problem for coral reef images
Spring 2014 Ted Kassen CS 499
Ted built a website for analysis of Viral Dark Matter data Spring 2014 Andrew Miller CS 797 Andrew is writing a suffix trie to store genomic data Spring 2013 Sajia Akhter Comp 899 Sajia worked on her PhD thesis Spring 2013 Patrick Belon CS 497
Patrick built an autonomous heart rate measuring device Spring 2013 Heqiao Liu CS 498 HQ designed and implemented the database and website for the Viral Dark Matter project. Spring 2013 Blaire Robinson CS 499 Blaire designed and implemented a microbial database that is used to capture information about how microbes grow Spring 2013 Dwaine Smith CS 499 Dwaine was responsible for adding all the microbe data to the database designed by Blaire.
Dr. Robert Edwards. Biosketch Spring 2013 Haydee Garrido CS 499 Haydee worked on data mining for the Viral Dark Matter Project, implementing different algorithms to explore the raw data. Spring 2013 Jeff Sadural CS 499 Jeff has converted PrinSeq, written by PhD student Rob Schmieder, into C++ code Spring 2013 Tyler Turner CS 499 Tyler wrote and implemented the Prosilica interface for the ATRIS project. Spring 2012 Robert Schmieder Comp 897 Rob worked on his PhD thesis Spring 2012 Sajia Akhter Comp 897 Sajia worked on her PhD thesis Spring 2012 Brian Hudson CS 497
Brian designed and implemented the prosilica interface for the ATRIS software Spring 2012 Heqiao Liu CS 499
HQ designed and implemented the database and website for the Viral Dark Matter project. Spring 2012 Jimmy Li CS 499
Jimmy created a website for automated image analysis, allowing users to upload a set of images and have them analyzed Spring 2012 Michiyo Wellington-Oguri CS 499
Michiyo wrote novel data mining algorithms to identify the host of different kinds of virus Spring 2011 Katelyn McNair Comp 798 Katelyn wrote PHACTS for the comparison of phage genomes Spring 2011 Robert Schmieder Comp 897 Rob worked on his PhD thesis Spring 2011 Sajia Akhter Comp 897 Sajia worked on her PhD thesis Spring 2011 Alf Scotland CS 499 Alf wrote image analysis software to detect the movement of objects in a series of images Spring 2011 Brian Hudson CS 499
Brian designed and implemented the prosilica interface for the ATRIS software Spring 2011 Daniel Cuevas CS 499 Daniel worked on the Viral Dark Matter project, analyzing and modeling the growth of bacteria Fall 2013 Blaire Robinson Bio 499 Blaire designed and implemented a microbial database that is used to capture information about how microbes grow
Fall 2013 Daniel Cuevas Comp 897 Daniel worked on the Viral Dark Matter project, analyzing and modeling the growth of bacteria Fall 2013 David Westerhoff CS 499 David desgined an API for the Viral Dark Matter database to allow computational access ot the data Fall 2013 Patrick Belon CS 499 Patrick built an autonomous heart rate measuring device Fall 2013 Ryan Matonis CS 499 Ryan worked on the analysis of Shannon's theory as it applies to DNA sequence analysis Fall 2013 Ted Kassen CS 499
Ted built a website for analysis of Viral Dark Matter data Fall 2012 Vernon Wages Comp 797 Vernon wrote an image stitching algorithm that can handle thousands of images simultaneously. Fall 2012 Sajia Akhter Comp 897 Sajia worked on her PhD thesis Fall 2012 Robert Schmieder Comp 899 Rob worked on his PhD thesis Fall 2012 Dwaine Smith CS 497 Dwaine was responsible for adding all the microbe data to the database designed by Blaire. Page 29 of 30 Dr. Robert Edwards. Biosketch Fall 2012 Haydee Garrido CS 497 Haydee worked on data mining for the Viral Dark Matter Project, implementing different algorithms to explore the raw data. Fall 2012 Jeff Sadural CS 497 Jeff has converted PrinSeq, written by PhD student Rob Schmieder, into C++ code Fall 2012 Michael Dempsey CS 497 Mike wrote image analysis code in Python using OpenCV to detect movement in images Fall 2012 Tyler Turner CS 497
Tyler wrote and implemented the Prosilica interface for the ATRIS project. Fall 2012 Blaire Robinson CS 499 Blaire designed and implemented a microbial database that is used to capture information about how microbes grow Fall 2012 Daniel Cuevas CS 797
Daniel worked on the Viral Dark Matter project, analyzing and modeling the growth of bacteria Fall 2011 Robert Schmieder Comp 897 Rob worked on his PhD thesis Fall 2011 Sajia Akhter Comp 897 Sajia worked on her PhD thesis Fall 2011 Brian Hudson CS 499
Brian designed and implemented the prosilica interface for the ATRIS software Fall 2011 Jimmy Li
CS 499 Jimmy created a website for automated image analysis, allowing users to upload a set of images and have them analyzed
Fall 2011 Michiyo
Wellington-Oguri CS 499
Michiyo wrote novel data mining algorithms to identify the host of different kinds of virus Fall 2011 Nicholas Turner CS 499 Nick helped design the database for the viral dark matter project
Page 30 of 30 Document Outline
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