Shawn W. Polson

Assistant Professor, Dept. of Computer & Info. Sciences
Assistant Professor, Dept. of Biological Sciences
Coordinator, Bioinformatics Core Facility
Manager, NECC Shared Data Center at UD

Contact

Office: 205F Delaware Biotechnology Institute
Laboratory: 148 Delaware Biotechnology Institute

Mailing address:
Delaware Biotechnology Institute
15 Innovation Way, Rm 205F
University of Delaware
Newark, DE 19711

Phone: (302) 831-3235
Lab: (302)831-4510
FAX: (302) 831-4841

Education

B.S.: Biology (Cell & Molecular)/Computer Science (Minor), University of South Carolina, Aiken SC, Magna Cum Laude (1999)
M.S.: Microbiology & Molecular Medicine, Clemson University, Clemson, SC (2002)
Ph.D.: Marine Biomed. & Environ. Science/Molecular & Cellular Biology & Pathobiology, Medical University of South Carolina, Charleston, SC (2007)
Postdoctoral: University of Delaware, Newark, DE (2008-2010)

Previous Appointments

Faculty, “Genomics for the Non-Genomic Scientist Course”, NOAA’s Coral Reef Conservation Program and National Coral Reef Institute (2008-2009)

Molecular Biologist, NOAA National Ocean Service Center for Environmental Health and Biomolecular Research, JHT (2004-2008)

Sequence Curator.  Marine Genomics Database. Medical University of South Carolina (2004-2008)

Production Editor.  Proceedings of the Eighth Symposium on the Natural History of the Bahamas (1999-2001)

Selected Honors/Awards

• Delaware Biotechnology Institute Symposium, Best Scientific Talk (May 2010)
• Sigma Xi Research Award (November 2006)
• Estuarine Research Federation Travel Award (October 2005)
• NOAA National Ocean Service Certificate of Achievement (July 2004)

Bioinformatics Core

The mission of the CBCB Bioinformatics Core is to, “Provide scientific expertise and core infrastructure support in Bioinformatics and Computational Biology for the Delaware research and education community.”  As the coordinator, I interact with life science researchers to help them define their informatics needs and oversee subsequent collaborative projects, services, and computational access necessary to achieve their research goals. 

Research Interests

My research interests lie at the intersection of genomics and microbial ecology, examining the ways in which microorganisms and viruses affect and are affected by their environments. While I admit a preference for marine research, I also research a broad range of other environments from soils and agriculture to the extreme environments of hot springs and deep sea hydrothermal vents.  The data intensive nature of my research has led me to specialize in bioinformatic aspects, identifying creative solutions to visualize and analyze microbial community data.

Current Projects

• VIROME: Viral Informatics Resource for Metagenome Exploration.  With Eric Wommack (UD) and the CAMERA group (UC-San Diego).  http://virome.dbi.udel.edu
• Role of microorganisms in health and disease of corals.
• Microbial communities of the eastern oyster, Crossostrea virginica.  With Eric Wommack
• Viral assemblages of deep sea hydrothermal vents.  With Eric Wommack, Shannon Williamson, Lisa Zeigler Allen (JCVI), and Craig Cary (Univ of Waikato, NZ)
• Metagenomic analysis of virioplankton from estuarine, coastal, and oceanic environments.  With Shannon Williamson, Lisa Zeigler Allen, and Eric Wommack

Laboratory News Articles

• Undergrad receives research fellowship to study deep-sea viruses
• Researchers to study positive genetic contributions of viruses

Selected Publications

22. Jamindar, S., S.W. Polson, S. Srinivasiah, L. Waidner, and K.E. Wommack. 2012. Evaluation of two approaches for assessing the genetic similarity of virioplankton populations as defined by genome size. Applied and Environmental Microbiology. In press.
21. Lee, C.K.*, C.W. Herbold*, S.W. Polson, K.E. Wommack, S.J. Williamson, I.R. McDonald, S.C. Cary. 2012. Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing. PLoS One. 7(9):e44224. * authors contributed equally
20. Wommack, K.E.*, J. Bhavsar*, S.W. Polson*, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar and D.J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences. In press. * authors contributed equally
19. Wang, Q.*, C.N. Arighi*, B.L. King*, S.W. Polson*, J. Vincent*, C. Chen, H. Huang, B. Kingham, S.T. Page, M.F. Rendino, W.K. Thomas, D.W. Udwary, C.H. Wu, and the North East Bioinformatics Collaborative Curation Team (2011). Community annotation and bioinformatics workforce development in concert – Little skate genome annotation workshops and jamborees. Database, in press. * authors contributed equally
18. Hammond S, Swanberg J, Polson S, Lee KH (2011). Profiling Conserved MicroRNA Expression in Recombinant CHO Cell Lines Using Illumina Sequencing, Biotechnology and Bioengineering. in press.
17. Wommack K.E., S. Srinivasiah, M. Liles, J. Bhavsar, S. Bench, K.E. Williamson, and S.W. Polson. Metagenomic contrasts of viruses in soil and aquatic environments. Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (the “Work”), edited by Frans J. de Bruijn. pp 25-36.
16. Marine, R., S.W. Polson, J. Ravel, G. Hatfull, D. Russell, M. Sullivan, F. Syed, N. Caruccio, M. Dumas, and K.E. Wommack (2011). Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Applied and Environmental Microbiology, 77:8071-8079. [PMC3209006]
15. Dumas, M.D., S.W. Polson, D. Ritter, J. Ravel, J. Gelb Jr., R. Morgan, and K.E. Wommack (2011). Impacts of poultry house environment on poultry litter bacterial community composition. PLOS One, 6(9):e24785 [PMC3174962]
14. Polson, S.W., S.J. Wilhelm, and K.E. Wommack.  Unraveling the viral tapestry: from inside the capsid out.  ISME Journal.  In press.
13. Williamson, K.E., J. Kan, S.W. Polson, S.J. Williamson. Optimizing the Indirect Extraction of Prokaryotic DNA from Soils.  Soil Biology and Biochemistry.  In press.
12. Campbell, B.J., S. W. Polson, T. E. Hanson, M. C. Mack, and E. A. G. Schuur.  2010.  The effect of nutrient deposition on bacterial communities in Arctic tundra soil.  Environmental Microbiology, 12: 1842-1854
11. Schoenfeld, T., M. Liles, K. E. Wommack, S. W. Polson, R. Godiska, and D. Mead. 2009. Functional viral metagenomics and the next generation of molecular tools. Trends in Microbiology.  18: 20-29.
10. Helton, R.R., D.H. Powell, S.C. Cary, S.W. Polson, and K.J. Czymmek. 2009. Observation of Virus-Like Particles in Vascular and Coelomic Hemolymph of Riftia pachyptila. Microscopy and Microanalysis, 15:100-101.
9. Polson, S.W., J.L. Higgins, and C.M. Woodley.  2009.  PCR-based assay for detection of four coral pathogens.  Proceedings of the Eleventh International Coral Reef Symposium.  1: 247-251.
8. Cervino, J., K. Winiarski, S.W. Polson, T. Goreau, and G.W. Smith.  2006.  Identification of bacteria associated with a disease affecting the marine sponge, Ianthella basta, in New Britain, Papua New Guinea.  Marine Ecology Progress Series, 24:139-150.
7. Polson, S.W., M.L. Lundqvist, and C.M. Woodley.  2006.  Systematic approach to a disease investigation: Case example.  Proceedings of the Tenth International Coral Reef Symposium, 1:138-141.
6. Cervino, J.M., M. Littler, D. Littler, S.W. Polson, T.J. Goreau, B. Brooks, G.W. Smith.  2005. Identification of microbes associated with coralline lethal algal disease and its relationship to glacial ice melt (global warming).  Phytopathology, 95(6 suppl): S120-S121.
5. Cervino, J.M., R.L. Hayes, S.W. Polson, S.C. Polson, T.J. Goreau, R.J. Martinez, and G.W. Smith.  2004.  Relationship of Vibrio species infection and elevated temperatures to Yellow Blotch/Band Disease in Caribbean corals.  Applied and Environmental Microbiology, 70:6855-6864.
4. Denner, E.B.M., G. Smith, H.J. Busse, P. Schumann, T. Narzt, S. W. Polson, W. Lubitz and L. L. Richardson.  2003.  Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals.  International Journal of Systematic and Evolutionary Microbiology, 53:1115-1122.
3. Patterson, K.L., J.W. Porter, K.B. Ritchie, S.W. Polson, E. Mueller, E.C. Peters, D.S. Santavy, and G.W. Smith.  2002.  From the Cover: The etiology of white pox, a lethal disease of the Caribbean elkhorn coral, Acropora palmata.  Proceedings of the National Academy of Science, 99(13):8725-8730.
2. Bagwell, C.E., J. La Rocque, G.W. Smith, S.W. Polson, M. Friez, J. Longshore, and C.R. Lovell.  2002.  Molecular diversity of diazotrophs in oligotrophic seagrass bed communities.  FEMS Microbiology Ecology, 39:113-119.
1. Ritchie, K.B., S.W. Polson, and G.W. Smith.  2001.  Microbial Disease Causation in Marine Invertebrates: Problems, Practices, and Future Prospects.  Hydrobiologia.  460:131-139.

Society Memberships

• American Society for Limnology and Oceanography
• American Society for Microbiology
• Association of Biomolecular Resource Facilities
• Coral Disease and Health Consortium
• International Society for Microbial Ecology
• Mensa
• Sigma Xi