Peer review articles

Zhao, Y.L., K. Wang, H-W. Ackermann, N. Z. Jiao, F. Chen. 2009. Searching for a "hidden" prophage in a marine bacterium. Appl. Environ. Microbiol. (in press)

Short, S., F. Chen, S. Wilhelm. 2009. The Construction and Analysis of Marker Gene Libraries. In: Suttle et al. (eds). Methods in Aquatic Viruses. Limnol. & Oceangr. Methods (in press).

Chen, F., K. Wang, S.J. Huang, H.Y. Cai, M.L. Zhao, N.Z. Jiao, and E. Wommack. 2009. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. Environ. Microbiol. 11: 2884-2892.

Eissler, Y., K. Wang, F. Chen, E. Wommack, W. Coats. 2009. Ultrastructural characterization of the lytic cycle of an intra-nuclear virus infecting the diatom Chaetoceros wighamii (Bacillariophyceae) from Chesapeake Bay, USA. J. Phycol. 45:787-797.

Zhang, Y.Y., N. Jiao, D.R. Colquhoun, R.U. Halden, and F. Chen. 2009. Protein modifications related to phage resistance in a marine roseobacter. Aquatic Microb. Ecol. 55:203-207.

Sparks, W., J. Hough, T. A. Germer, F. Chen, S. DasSarma, et al. 2009. Detection of circular polarization in light scattered from photosynthetic microbes. Proc. Natl. Acad. Sci. 106:7816-7821.

Zhao, Y.L, K. Wang, N.Z, Jiao, and F. Chen. 2009. Genome sequences of two novel phages infecting marine roseobacters. Environ. Microbiol. 11:2055-64.

Zhao, M. R. F. Chen, and N. Z. Jiao. 2009. Niche portioning of flavobacterial proteorhodopsin in the sea. Appl. Environ. Microbiol. 75: 529-533.

Sparks, W. B., J. H. Hough, L. Kolokolova, T. A. Germer, F. Chen, S. DasSarma, P. DasSarma, F. Robb, N. Manset, I.N. Reid F. Duccio Macchetto William Martin. 2009. Circular polarization in scattered light as a possible biomarker. J. Quant. Spectro. Radia. Trans. 110: 1771-1779.

Kan, J., S. E. Evans, F. Chen, M. T. Suzuki. 2008. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat. Microb. Ecol. 51:55-66.

Biers, E. J., K. Wang, C. Pennington, R. Belas, R., F. Chen, and M. A. Moran. 2008. Abundance and expression of gene transfer agent (GTA) genes in marine bacterioplankton. Appl. Environ. Microbiol. 74:2933-2939.

Wang, K. and F. Chen. 2008. Prevalence of highly host-specific cyanophages in the estuarine environment. Environ. Microbiol. 10:300-312 (also cover page).

Mohamed, N. M., E. Cicirelli, J. Kan, F. Chen, F, C. Fuqua, and R. T. Hill. 2008. Diversity and quorum sensing signal production of Proteobacteria associated with marine sponges. Environ. Microbiol. 10:75-86.

Kan, J., M. Suzuki, K. Wang, S. E. Evans, and F. Chen. 2007. High temporal but low spatial heterogeneity of bacterioplankton in the Chesapeake Bay. Appl. Environ. Microbiol. 73:6776-6789.

Jiao, N. Z., Y. Zhang,Y. H. Zeng, P. X. Wang, R. Liu, X. D. Tang, F. Chen, and Q. Li 2007. Deviation in abundance and diversity of aerobic anoxygenic phototrophic bacteria in the ocean. Environ. Microbiol. 9:3091-3099.

Reid, I. N., W. B. Sparks, S. Lubow, M. McGrath, M. Livio, J. Valenti, K.R. Sowers, H.D. Shukla, S. MacAuley, T. Miller, R. Suvanasuthi, R. Belas, A. Colman, F.T. Robb, P. DasSarma, J.A. Müller, J.A. Coker, R. Cavicchioli, F. Chen, S. DasSarma. 2006. Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures. Int. J. Astro. 00 (0): 1-9.

Chen, F., K. Wang, J. Stewart, R. Belas. 2006. Induction of prophages from a marine reseobacterium, Silicibacter sp. TM1040: A genomic approach. Appl. Environ. Microbiol. 72:4995-5001.

Kan, J., B. Crump, K. Wang, and F. Chen. 2006. Bacterioplankton community in Chesapeake Bay: Predictable or random assemblages. Limnol. Oceanogr. 51:2157-2169.

Chen, F., K. Wang, J, Kan, and M. Suzuki, E. Wommack. 2006. Diverse and unique picocyanobacteria found in the Chesapeake Bay. Appl. Environ. Microbiol. 72:2239-2243.

Kan, J., K. Wang, and F. Chen. 2006. Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE). Aquat. Microb. Ecol. 42:7-18.

Kan, J., T. E. Hanson, J. M. Ginter, K. Wang, F. Chen. 2005. Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Systems 1:7.

Bettarel, Y., J. Kan, K. Wang, S. Cooney, K. Williamson, F. Chen, E. Wommack, W. Coats. 2005. Isolation and characterisation of a small nuclear inclusion virus infecting the diatom Chaetoceros c.f. gracilis. Aquat. Microbial. Ecol. 40:103-114.

Lohr, J. E., F. Chen, and R. T. Hill. 2005. Genomic analysis of bacteriophage JL001: Insights into interaction with a sponge-associated alpha-proteobacterium. Appl. Environ. Microbiol. 71: 1598-1609.

Chen, F., K. Wang, J. Kan, D. S. Bachoon, J. Lu, S. Lau, and L. Campbell. 2004. Phylogenetic diversity of Synechococcus in the Chesapeake Bay revealed by ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) large subunit gene (rbcL) sequences. Aquat. Microb. Ecol. 36:153-164.

Kan, J. and F. Chen. 2004. Co-monitoring bacterial and dinoflagellates communities by denaturing gradient gel electrophoresis (DGGE) and SSU rDNA sequencing during a dinoflagellates bloom. Acta Oceanol. Sin. 23:483-492.

Wang, K. and F. Chen. 2004. Genetic diversity and population dynamics of cyanophage communities in the Chesapeake Bay. Aquatic Microbial Ecology 34:105-116, 2004.

Chen, F. and Lu, J. R. 2002. Genomic sequence and evolution of marine cyanophage P60: a new Insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68:2589-2594.

Zhong, Y., F. Chen, J. R. Lu, L. Poorvin, S. Wilhelm, and R. E. Hodson. 2002. Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20. Appl. Environ. Microbiol. 68:1576-1584.

Lau, S. C. K., K. K. W. Mak, F. Chen, and P. Y. Qian. 2002. Bioactivity of bacterial strains isolated from marine biofilms in Hong Kong waters for the induction of larval settlement in the marine polychaete Hydroides elegans. Mar. Ecol. Prog. Ser. 226:301-310.

Bachoon, D., F. Chen, and R. E. Hodson. 2001. RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples. FEMS Microbiol. Lett. 201:127-132.

Lu, J.R., F. Chen, and R. E. Hodson. 2001. Distribution, isolation, host specificity and diversity of marine cyanophages infecting Synechococcus spp. in coastal estuary. Appl. Environ. Microbiol. 67:3285-3290.

Chen, F., J. R. Lu, B. Binder, Y. C., Liu, and R. E. Hodson. 2001. Application of digital image analysis and flow cytometer to enumerate marine viruses stained with SYBR Gold. Appl. Environ. Microbiol. 67:539-545.

Chen, F., B. Binder, R. E. Hodson. 2000. Flow cytometric detection of specific gene expression in prokaryotic cells using in situ RT-PCR. FEMS Microb. Lett. 184:291-295.

Chen, F., W. A. Dustman, and R. E. Hodson. 1999. Detection of toluene dioxygenase gene and gene expression in Pseudomonas putida F1 in a toluene exposed seawater using in situ PCR and hybridization. Hydrobiologia 401:131-138.

Chen, F., J. M. Gonzalez, W. Dustman, M. Moran, and R. Hodson. 1997. In situ reverse transcription: a new molecular approach to study microbial community structure. Appl. Environ. Microbiol. 63:4907-4913.

Chen, F., S. M. Short, and C. A. Suttle. 1996. Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase Genes. Appl. Environ. Microbiol. 62: 2869-2874.

Chen, F., and C. A. Suttle. 1996. Evolutionary relationships among large double-stranded DNA viruses that infect microalgae and other organisms as inferred from DNA polymerase genes. Virology 219:170-178.

Chen, F., S. M. Short and C. A. Suttle. (1996) Sequence analysis indicates high genetic diversity in marine algal virus communities. Eos 76 (3 suppl): OS207.

Chen, F., and C. A. Suttle. 1995. Amplification of DNA polymerase gene fragments from viruses infecting microalgae. Appl. Environ. Microbiol. 61:1274-1278.

Chen, F., and C. A. Suttle. 1995. Nested PCR with three highly degenerate primers for amplification and identification of DNA from related organisms". BioTechniques. 18: 609-612.

Suttle, C. A., and F. Chen. 1992. Mechanisms and rates of decay of marine viruses in seawater. Appl. Environ. Microbiol. 58: 3721-3729.

Chen, F., B. Reid, and C. R. Arnold. 1990. Maturation and spawning of the white shrimp Penaeus vannamei Boore in a recirculating system. Journal of World Aquaculture, 22: 167-172, 1991.

Book Chapters

Jiao, N. Z., C. L. Zhang, F. Chen, J. Kan, and F. Zhang. 2008. Frontiers and Technological Advances in Microbial Processes and Carbon Cycling in the Ocean; pp. 217-267. In: L.P. Mertens (ed), Biological Oceanography Research Trends. Nova Science Publishers, Inc. Hauppauge, NY

Chen, F. and R. E. Hodson. 2001. In situ PCR/RT-PCR coupled with in situ hybridization for detection of functional gene and gene expression in prokaryotic cells. In: J. Paul (ed.) Methods in Marine Microbiology. pp.409-424. Academic Press.

Chen, F., W. A. Dustman, R. E. Hodson. 2000. Application of in situ reverse transcription to estuarine bacterial community analysis. In: C. R. Bell, M. Brylinsky, P. Johnson-Green (ed.), Microbial Biosystems: New Frontiers. Proceedings of the 8th International Symposium on Microbial Ecology. Atlantic Canada Society for Microbial Ecology. Halifax, Canada.

Chen, F. and R. E. Hodson. 1999. Viewing microbes with in situ molecular approaches, a Mini Review. In: H. S. Xu and R. Colwell (ed.), Proceedings in Marine Biotechnology, pp. 300-305, China Ocean Press, Beijing.

Chen, F., W. Dustman, M. A. Moran, and R. E. Hodson. 1998. In situ PCR methodologies for visualization of microscale genetic and taxonomic diversities of prokaryotic communities. ch. 3.3.9. In: A. D. L. Akkermans, J. D. van Elsas, F. J. DeBruijn (ed.), Molecular Microbial Ecology Manual. Kluwer Acadamic Publishers, The Netherland.

Suttle, C. A., A. M. Chan, F. Chen, and D. R. Garza, 1993. Cyanophages and sunlight: a paradox. In: Trends in Microbial Ecology, eds. R. Guerrero & C. Pedros-Alio. pp303-307.

Suttle, C. A., F. Chen, and A. M. Chan. 1992. Marine viruses: decay rates, diversity and ecological implications. In: Nash, C. C. II (ed.) International Marine Biotechnology Conference 'IMBC-91': Short communications of the invited lectures developments in microbiology. W. Brown Co., Dubuque, IA, p. 153-163.

Chen, F., and G. Y. Wang. 1988. Relationship between vertical distribution subsurface chlorophyll a and the seawater stability in the western tropical Pacific Ocean, p. 485-492. In: J. P. Chao and J. A. Young (ed.), Air-Sea Interaction in Tropical Western Pacific, China Ocean Press.

Wang, G. Y., and F. Chen. 1988. Study on ecological structure feature in the western tropical Pacific, p. 493-500. In: J. P. Chao and J. A. Young (ed.), Air-Sea Interaction in Tropical Western Pacific, China Ocean Press.