|
|
| Vita for Forest Rohwer | | Education |
| University of California San Diego/San Diego State University Joint Doctoral Program in Molecular Biology, 09/92-07/97 advisor: Kathleen McGuire - Doctoral dissertation: Interleukin-2 activation of intracellular signaling pathways: Effects on gene expression, proliferation, and apoptosis, pp. 1-174. 1997.
| | University of Idaho, Letters and Science, 09/91-05/92
| | College of Idaho, BAs in Biology, Chemistry, and History, 09/87-05/91 |
| Professional Experience |
| San Diego State University. Professor. 2009-present
| | San Diego State University. Associate Professor. 2007-2009
| | San Diego State University. Assistant Professor. 2003-2007
| | San Diego State University. Adjunct Assistant Professor. 2001-2003
| | Scripps Institution of Oceanography. Postdoctoral researcher with Dr. Farooq Azam. 1997-2001 |
| Publications |
| Thurber, RV, D Willner-Hall, B Rodriguez-Mueller, C Desnues, RA Edwards, F Angly, E Dinsdale, L Kelly, F Rohwer (2009) Metagenomic analysis of stressed coral holobionts. Environmental Microbiology. 11(5). 1-16. |
|
| Wagner, C, A Salamon, RA Edwards, F Rohwer, P Salamon (2009) Deviations from ultrametricity in phage protein distances. Open Systems & Information Dynamics. 16(1). 1–10. |
|
| Willner, D, R Vega Thurber, F Rohwer (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environmental Microbiology. |
|
| Rohwer, F and RV Thurber (2009) Marine viruses: Manipulating the marine environment. Nature. 459 (7244). 207-212. |
|
| Thurber, BV, M Breitbart, M Haynes, F Rohwer (2009) Laboratory procedures to generate viral metagenomes. Nature Protocols. 4 (4) 470-483. |
|
| Breitbart, M, A Hoare, A Nitti, J Siefert, M Haynes, E Dinsdale, R Edwards, V Souza, F Rohwer, D Hollander (2009) Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico. Environmental Microbiology.11 (1). 16-34. |
|
| Smarr, L, P Gilna, P Papadopoulos, TA DeFanti, G Hidley, J Wooley, EV Armbrust, F Rohwer, E Frost (2009) Building an OptIPlanet collaboratory to support microbial metagenomics. The International Journal of Grid Computing: Theory, Methods, & Applications. 25 (2). 124-131. |
|
| McDaniel L, M Breitbart, J Mobberley, A Long, M Haynes, F Rohwer, JH Paul (2008) Metagenomic analysis of lysogeny in Tampa Bay: Implications for prophage gene expression. PLoS One. 3(9). 1-9. |
 |
| Dinsdale EA, RA Edwards, D Hall, F Angly, M Breitbart, JM Brulc, M Furlan, C Desnues, M Haynes, L Li, L McDaniel, MA Moran , KE Nelson, C Nilsson, R Olson, J Paul, B Rodriguez-Brito, Y Ruan, BK Swan, R Stevens, DL Valentine, RV Thurber, L Wegley, BA White, F Rohwer (2008) Functional metagenomic profiling of nine biomes. Nature. 452. 629-632. > Correction to manuscript published in September 2008.
|
|
| Tringe SG, T Zhang, X Liu, Y Yu, WH Lee, J Yap, F Yao, ST Suan, SK Ing, M Haynes, F Rohwer, CL Wei, P Tan, J Bristow, EM Rubin, Y Ruan (2008) The airborne metagenome in an indoor urban environment. PLoS ONE 3(4): e1862 doi:10.1371/journal.pone.0001862 |
|
| Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature. 452. 340-343. |
|
| Dinsdale, EA, O Pantos, S Smriga, RA Edwards, F Angly, L Wegley, M Hatay, D Hall, E Brown, M Haynes, L Krause, E Sala, SA Sandin, RV Thurber, BL Willis, F Azam, N Knowlton, F Rohwer (2008) Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One. 3(2) e1584. 1-17. |
|
| Sandin, SA, JE Smith, EE DeMartini, EA Dinsdale, SD Donner, AM Friedlander, T Konotchick, M Malay, JE Maragos, D Obura, O Pantos, G Paulay, M Richie, F Rohwer, RE Schroeder, S Walsh, JBC Jackson, N Knowlton, E Sala. (2008) Baselines and degradation of coral reefs in the northern Line Islands. PLoS ONE. 3(2) e1584. 1-11. |
|
| Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant’s gut. Research in Microbiology 159. 367e373. |
|
| Thurber, RLV, Barott, KL, Willner-Hall, D, Liu, H, Rodriguez-Mueller, B, Desnuesa, C, Edwardsa, RA, Haynes, M, Angly, FE, Wegley, L, Rohwer, FL (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proceedings of the National Academy of Sciences, USA. 105 (47). 18413–18418. |
|
| Marhaver KL, RA Edwards, F Rohwer (2008) Viral communities associated with healthy and bleaching corals. Environmental Microbiology. 10 (9). 2277-2286. |
|
| Krause, L, N Diaz, A Goesmann, F Rohwer, S Kelley, RA Edwards, J Stoye (2008) Taxonomic classification of short environmental DNA fragments. Nucleic Acids Research. 36(7):2230-2239. |
|
| Breitbart, M, A Hoare, A Nitti, J Siefert, M Haynes, E Dinsdale, R Edwards, V Souza, F Rohwer, D Hollander (2008; in press) Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico. Environmental Microbiology. |
|
| Dinsdale, E.A. and Rohwer, F, (2008) Dissecting microbial employment. Nature Biotechnology 26:997-998 |
|
| Johnston IS, F Rohwer (2007) Microbial landscapes on the outer tissue surfaces of the reef-building coral Porites compressa. Coral Reefs. 26 (2). 375-383. |
|
| Rosenberg E, CA Kellogg, F Rohwer (2007) Coral microbiology. Oceanography. 20 (2) 114-122. |
|
| Hoffmann KH, B Rodriguez-Brito, M Breitbart, D Bangor, F Angly, B Felts, J Nulton, F Rohwer, P Salamon (2007) Power law rank-abundance models for marine phage communities. FEMS Microbiological Letters 273. 224-228. |
|
| Beman, MJ, KJ Roberts, L Wegley, F Rohwer, CA Francis (2007) Distribution and diversity of archaeal ammonia monooxygenase (amoA) genes associated with corals. Applied and Environmental Microbiology. 73 (17). 5642-5647. |
|
| Fierer, N, M Breitbart, J Nulton, P Salamon, C Lozupone, R Jones, M Robeson, R Edwards, B Felts, S Rayhawk, R Knight, F Rohwer, RB Jackson (2007) Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Applied and Environmental Microbiology. 73 (21). 7059-7066. |
|
| Wegley, L, R Edwards, B Rodriguez-Brito, Hong Liu, F Rohwer (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environmental Microbiology. 9 (11). 2707-2719. |
|
| Kunin, V, S He, F Warnecke, SB Peterson, HG Martin, M Haynes, N Ivanova, LL Blackall, M Breitbart, F Rohwer, KD McMahon, P Hugenholtz (2007) A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research. 18: 293-297. |
|
| Angly F, B Felts, M Breitbart, P Salamon, RA Edwards, C Carlson, AM Chan, M Haynes, S Kelley, H Liu, J Mahaffy, JE Mueller, J Nulton, R Olson, R Parsons, S Rayhawk, CA Suttle, F Rohwer (2006) The marine viromes of four oceanic regions. PLoS Biology. 4 (11). 2121-2131. |
|
| Casas V, J Miyake, H Balsley, J Roarke, S Telles, S Leeds, I Zurita, M Breitbart, D Bartlett, F Azam, F Rohwer (2006) Detection of phage-encoded exotoxins in the environment. FEM Microbiology Letters. 261. 141-149. |
|
| Zhang, T, M Breitbart, WH Lee, J Run, CL Wei, SWL Soh, ML Hibberd, ET Liu, F Rohwer, Y Ruan (2006) RNA viral community in the human gut: Prevalence of plant pathogenic viruses. PLoS Biology. 4 (1). 1-11. |
|
| Yu, Y, M Breitbart, F Rohwer (2006) FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics. 7 (57). 1-9. |
|
| Rodriguez-Brito B, F Rohwer, R Edwards (2006) A statistical approach to compare metagenomes. BMC Bioinformatics. 7 (162). |
|
| Edwards RA, B Rodriguez-Brito, L Wegley, M Haynes, M Breitbart, DM Peterson, MO Saar, S Alexander, EC Alexander, Jr, F Rohwer (2006) Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeological conditions. BMC Genomics. 7 (57). |
|
| Smith JE, M Shaw, RA Edwards, M Hatay, D Obura, O Pantos, E Sala, SA Sandin, S Smriga, F Rohwer (2006) Effects of algae on coral: Algal-mediated, microbe-induced coral mortality. Ecology Letters. 9 (7). 835-845. |
|
| Kline, D, N Kuntz, M Brietbart, N Knowlton, F Rohwer (2006) The unexpected and critical role of elevated organic carbon in coral mortality. Marine Ecology Progress Series. 314. 119-125. |
|
| Wegley L, P Mosier-Boss, S Lieberman, F Rohwer (2006) Rapid enumeration of microbes using bulk fluorescence. Environmental Microbiology. 8 (10). 1775-1782. |
|
| Breitbart, M, R Bhagooli, S Griffin, I Johnston, F Rohwer (2005) Microbial communities associated with skeletal tumors on Porites compressa. FEMS Microbiology Letters. 243. 431-436. |
|
| Hatay, M, N Kuntz, F Rohwer (2005) SPIDERS: A syringe pump system for long-term dosing underwater. Limnology and Oceanography Methods. 3. 38-45 |
|
| Sullivan, MB, M Coleman, P Weigele, F Rohwer, SW Chisholm (2005) Prochlorococcus cyanophage genomes: Phages adapted for infection of open-ocean photosynthetic cells. Public Library of Science (PLoS). 3 (5). 1-17. |
|
| Purdy, A, F Rohwer, R Edwards, F Azam, and DH Bartlett (2005) A glimpse into the expanded genome content of the Vibrio cholerae species through the identification of genes present in environmental strains. Journal of Bacteriology. 187 (9). 2992-3001 |
|
| Paul, JH, SJ Williamson, A Long, D John, A Segall, F Rohwer (2005) The complete genome of phiHSIC, a pseudotemperate marine phage of Listonella pelagia. Applied and Environmental Microbiology. 71 (6). |
|
| Edwards, RA, F Rohwer (2005) Viral Metagenomics. Nature Reviews in Microbiology. 3 (6). 504-510. |
|
| Breitbart, M, F Rohwer (2005) Here a Virus, There a Virus, Everywhere the Same Virus?. Trend in Microbiology. 13 (6). 278-284. |
|
| Kuntz, NM, D Kline, SA Sandin, F Rohwer (2005) Organic carbon and nutrient stressors cause different pathologies and mortality rates in three Caribbean coral species. Marine Ecology Progress Series. 294. 173-180. |
|
| Breitbart, M and F Rohwer (2005) A method for discovering novel DNA viruses in blood. Biotechniques. 39 (5). 729-736. |
|
| Angly, F, B Rodriguez Brito, D Bangor, P McNairnie, M Breitbart, P Salamon, B Felts, J Nulton, J Mahaffy, F Rohwer (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 2005, 6:41 |
|
| Sano, E, S Carlson, L Wegley, F Rohwer (2004) Movement of viruses between biomes. Applied and Environmental Microbiology. 70 (10). 5842-5846. |
|
| Breitbart, M, JH Miyake, F Rohwer (2004) Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiology Letters. 236 (2) 245-252. |
|
| Wegley, L, Y Yu, M Breitbart, V Casas, D Kline, F Rohwer (2004) Coral-associated Archaea. Marine Ecology Progress Series. 273. 89-96. |
|
| Casas, V, D Kline, L Wegley, Y Yu, M Breitbart, F Rohwer (2004) Bacterial communities associated with healthy and white band type I diseased Acroporid corals. Environmental Microbiology. 6(11). 1137-1148. |
|
| Lindell, D, MB Sullivan, ZI Johnson, AC Tolonen, F Rohwer, SW Chisholm (2004) Photosynthesis genes in Prochlorococcus cyanophage. Proceeding of the National Academy of Sciences, USA. 101 (30) 11013-11018. |
|
| Breitbart, M, Wegley, L, Leeds, S, Schoenfeld, T, and F Rohwer (2004) Phage community dynamics in hot springs. Applied and Environmental Microbiology. 70 (30). 1633-1640. |
|
| Breitbart, M, Felts, B, Kelley, S, Mahaffy, JM, Nulton, J, Salamon, P, and F Rohwer (2004) Diversity and population structure of a nearshore marine sediment viral community. Proceedings of the Royal Society B. 271. 565-574. |
|
| Breitbart, M, Hewson, I, Felts, B, Mahaffy, JM, Nulton, J, Salamon, P, and F Rohwer (2003) Metagenomic analyses of an uncultured viral community from human feces. Journal of Bacteriology. 85 (20). 6220-6223. |
|
| Seguritan, V, Feng, I, Rohwer, F, Swift, M, and AM Segall (2003) Genome sequences of two closely related Vibrio parahaemolyticus phages, VP16T and VP16C, that coexist in the same host. Journal of Bacteriology. 185 (21). 6434-6447. |
|
| Mosier-Boss, PA, Lieberman, SH, Andrews, JM, Rohwer, F, Wegley, LE, and M Breitbart (2003) The use of fluorescently-labeled phage in the detection/identification of bacterial species. Applied Spectroscopy. 57 (9). 1138-1144. |
|
| Knowlton, N, and F Rohwer (2003) Microbial mutualisms on coral reefs: The host as a habitat. American Naturalist. 162. S51-S62. |
|
| F Rohwer (2003) Global phage diversity. Cell. 113 (2).141.
> preview for Pedulla et al. (2003) Origins of highly mosaic mycobacteriophage genomes
|
|
| Fung, MM, F Rohwer, KL McGuire (2003) IL-2 activation of a PI3K-dependent STAT3 serine phosphorylation pathway in primary human T-cells. Cellular Signaling. 15. 625-636.
|
|
| HYIP Monitor - Hewson, I, Felts, B, Mahaffy, JM, Nulton, J, Salamon, P, and F Rohwer (2003) Metagenomic analyses of an uncultured viral community from human feces. Journal of Bacteriology. 85 (20). 6220-6223. |
|
| Breitbart, M, P Salamon, B Andresen, J Mahaffy, A Segall, D Mead, F Azam, F Rohwer (2002) Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy USA. 99:14250-14255. |
|
| Rohwer, F, R Edwards (2002) The Phage Proteomic Tree: A genome-based taxonomy system for phage. Journal of Bacteriology. 184 (16). 4529-4535. |
|
| Rohwer, F, V Seguritan, F Azam, and N Knowlton. (2002) Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series. 243. 1-10. |
|
| Hagstrom, A, T Pommier, F Rohwer, K Simu, D Svensson, UL Zweifel (2002) Bio-informatics reveal surprisingly low species richness in marine bacterioplankton. Applied and Environmental Microbiology. 67 (7). 3628-3633. |
|
| Hagstrom, A, T Pommier, F Rohwer, K Simu, D Svensson, UL Zweifel (2002) Bio-informatics reveal surprisingly low species richness in marine bacterioplankton. Applied and Environmental Microbiology. 67 (7). 3628-3633. |
|
| Seguritan, V, F Rohwer (2001) FastGroup: A program to dereplicate libraries of 16S rDNA sequences. BMC Bioinformatics. 2 (9). http://www.biomedcentral.com/browse/biology/ |
|
| Rohwer, F, Seguritan, V, Choi, DH, Segall, A, Azam, F (2001) Production of shotgun libraries using random amplification. BioTechniques. 31 (1). 1-7. |
|
| Rohwer, F, M Breitbart, J Java, F Azam, N Knowlton (2001) Microbial diversity of scleractinian corals. Coral Reefs. 20 (1). 85-95. |
|
| Rohwer, F, AM Segall, G Steward, V Seguritan, M Breitbart, F Wolven, F Azam (2000) The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with non-marine phages. Limnology and Oceanography. 45 (2). 408-418. |
|
| Rohwer, F, F Azam (2000) Direct detection of DNA damage in prokaryotes using TdT-mediated dUTP nick end labeling (TUNEL). Applied and Environmental Microbiology. 66 (3).1001-1006. |
|
| Iacobelli, M, Rohwer, F, P Shanahan, JA Quiroz, KL McGuire (1999) IL-2-mediated cell cycle progression and inhibition of apoptosis does not require NF-kappa B or activating protein-1 activation in primary human T cells. Journal of Immunology. 162 (6). 3308-3014.
|
|
| McGuire, KL, F Rohwer, H Sabzevari, AN Theofilopoulous, MM Fung, K Bower (1999) Signal transduction, cell cycle progression, and gene expression in primary human T cells stimulated with interleukin 2. Research in Developmental Immunology. 1. 149-163. |
|
| Rohwer, F, S Todd, K McGuire (1996) The effect of IL-2 treatment on transcriptional attenuation in proto-oncogenes pim-1 and c-myb in human thymic blast cells. Journal of Immunology. 157 (2). 643-649. |
|
| Rohwer, F, W MacMaster, W Haseltine, C Tsoukas, K McGuire. (1994) Characterization of an IL-2 dependent Human T Cell Leukemia Virus type I (HTLV-I) infected cell line: a system for studying HTLV-I mediated transformation. International Journal of Oncology. 5. 1-7. |
|
| Popular Press | | Kuntz, N, M Breitbart, F Rohwer (2006) The Art of Phage. Microbe. 1(9). 435. |
 |
| Edwards, R, M Breitbart, F Rohwer (2004) Hidden messages within the genetic code. ASM News. 70 (7). 305 |
|
|
|
