Shawn PolsonShawn 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
(302) 831-3235
Lab:148 Delaware Biotechnology Institute
(302) 831-4510
Fax:(302) 831-4841
Email:polson@dbi.udel.edu

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

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 (2008)
Postdoc   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 Coastal 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

Laboratory News Articles

Publications

More details at: Google Scholar and ResearchGate

39.Crowgey EL, Stabley DL, Chen C, Huang H, Robbins KM, Polson SW, Sol-Church K, Wu CH. An Integrated Approach for Analyzing Clinical Genomic Variant Data from Next Generation Sequencing. J Biomolec Techniq. 2014 Accepted.
38.Manthey AL, Terrel AM, Lachcke SA, Polson SW, Duncan MK. Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis. Genomics Data. 2014. doi: 10.1016/j.gdata.2014.10.015 [link]
37.Sakowski EG, Munsell EV, Hyatt M, Kress W, Williamson SJ, Nasko DJ, Polson SW, Wommack KE. Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses. Proc Natl Acad Sci U S A. 2014 Oct 13. doi: 10.1073/pnas.1401322111 [link]
36.Wilson CA, Brigmon RL, Yeager C, Smith GW, Polson SW. (2014) "Genotypic and Phenotypic Characterization of Aerosolized Bacteria Collected From African Dust Events," Journal of the South Carolina Academy of Science: Vol. 12: Iss. 1, Article 5. [link]
35.Schulz MD, Atay C, Heringer J, Romrig FK, Schwitalla S, Aydin B, Ziegler PK, Varga J, Reindl W, Pommerenke C, Salinas-Riester G, Böck A, Alpert C, Blaut M, Polson SC, Brandl L, Kirchner T, Greten FR, Polson SW, Arkan MC. High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature. 2014 Oct 23;514(7523):508-12. doi: 10.1038/nature13398. Epub 2014 Aug 31. PubMed PMID: 25174708. [link]
34.Wyffels J, L King B, Vincent J, Chen C, Wu CH, Polson SW. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Res. 2014 Aug 12;3:191. doi: 10.12688/f1000research.4996.1. eCollection 2014. PubMed PMID: 25309735; PubMed Central PMCID: PMC4184313. [link]
33.Debruyn JM, Radosevich M, Wommack KE, Polson SW, Hauser LJ, Fawaz MN, Korlach J, Tsai YC. Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum. Genome Announc. 2014 Apr 3;2(2). pii: e00226-14. doi: 10.1128/genomeA.00226-14. PubMed PMID: 24699952; PubMed Central PMCID: PMC3974934. [link]
32.Kalburge SS, Polson SW, Boyd Crotty K, Katz L, Turnsek M, Tarr CL, Martinez-Urtaza J, Boyd EF. Complete Genome Sequence of Vibrio parahaemolyticus Environmental Strain UCM-V493. Genome Announc. 2014 Mar 13;2(2). pii: e00159-14. doi: 10.1128/genomeA.00159-14. PubMed PMID: 24625868; PubMed Central PMCID: PMC3953189. [link]
31.Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E, Polson SW, Wommack KE. Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome. 2014 Jan 30;2(1):3. doi: 10.1186/2049-2618-2-3. PubMed PMID: 24475755; PubMed Central PMCID: PMC3937105. [link]
30.Huang X, Bruce B, Buchan A, Congdon CB, Cramer CL, Jennings SF, Jiang H, Li Z, McClure G, McMullen R, Moore JH, Nanduri B, Peckham J, Perkins A, Polson SW, Rekepalli B, Salem S, Specker J, Wunsch D, Xiong D, Zhang S, Zhao Z. No-boundary thinking in bioinformatics research. BioData Min. 2013 Nov 6;6(1):19. doi: 10.1186/1756-0381-6-19. PubMed PMID: 24192339; PubMed Central PMCID: PMC3827872. [link]
29.Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. ISME J. 2014 Jan;8(1):103-14. doi: 10.1038/ismej.2013.124. Epub 2013 Aug 29. PubMed PMID: 23985748; PubMed Central PMCID: PMC3869006. [link]
28.Campbell BJ, Polson SW, Zeigler Allen L, Williamson SJ, Lee CK, Wommack KE, Cary SC. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities. Front Microbiol. 2013 Jul 24;4:182. doi: 10.3389/fmicb.2013.00182. eCollection 2013. PubMed PMID: 23898323; PubMed Central PMCID: PMC3721025. [link]
27.Srinivasiah S, Lovett J, Polson SW, Bhavsar J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, Wommack KE. Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA. Appl Environ Microbiol. 2013 Sep;79(18):5450-7. doi: 10.1128/AEM.00268-13. Epub 2013 Jun 21. PubMed PMID: 23793630; PubMed Central PMCID: PMC3754152. [link]
26.Jamindar S, Polson SW, Srinivasiah S, Waidner L, Wommack KE. Evaluation of two approaches for assessing the genetic similarity of virioplankton populations as defined by genome size. Appl Environ Microbiol. 2012 Dec;78(24):8773-83. doi: 10.1128/AEM.02432-12. Epub 2012 Oct 12. PubMed PMID: 23064328; PubMed Central PMCID: PMC3502916. [link]
25.Lee CK*, Herbold CW*, Polson SW, Wommack KE, Williamson SJ, McDonald IR, Cary SC. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One. 2012;7(9):e44224. doi: 10.1371/journal.pone.0044224. Epub 2012 Sep 6. PubMed PMID: 22970184; PubMed Central PMCID: PMC3435322. * authors contributed equally [link]
24.Wommack KE*, Bhavsar J*, Polson SW*, Chen J, Dumas M, Srinivasiah S, Furman M, Jamindar S, Nasko DJ. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci. 2012 Jul 30;6(3):427-39. doi: 10.4056/sigs.2945050. Epub 2012 Jul 27. PubMed PMID: 23407591; PubMed Central PMCID: PMC3558967. * authors contributed equally [link]
23.Wang Q*, Arighi CN*, King BL*, Polson SW*, Vincent J*, Chen C, Huang H, Kingham BF, Page ST, Rendino MF, Thomas WK, Udwary DW, Wu CH; North East Bioinformatics Collaborative Curation Team. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford). 2012 Mar 20;2012:bar064. doi: 10.1093/database/bar064. Print 2012. PubMed PMID: 22434832; PubMed Central PMCID: PMC3308154. * authors contributed equally [link]
22.Hammond S, Swanberg JC, Polson SW, Lee KH. Profiling conserved microRNA expression in recombinant CHO cell lines using Illumina sequencing. Biotechnol Bioeng. 2012 Jun;109(6):1371-5. doi: 10.1002/bit.24415. Epub 2012 Jan 23. PubMed PMID: 22189905; PubMed Central PMCID: PMC3330154. [link]
21.Wommack KE, Srinivasiah S, Liles M, Bhavsar J, Bench S, Williamson KE, Polson SW. 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. [link]
20.Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl Environ Microbiol. 2011 Nov;77(22):8071-9. doi: 10.1128/AEM.05610-11. Epub 2011 Sep 23. PubMed PMID: 21948828; PubMed Central PMCID: PMC3209006. [link]
19.Dumas MD, Polson SW, Ritter D, Ravel J, Gelb J Jr, Morgan R, Wommack KE. Impacts of poultry house environment on poultry litter bacterial community composition. PLoS One. 2011;6(9):e24785. doi: 10.1371/journal.pone.0024785. Epub 2011 Sep 16. PubMed PMID: 21949751; PubMed Central PMCID: PMC3174962. [link]
18.Polson SW, Wilhelm SW, Wommack KE. Unraveling the viral tapestry (from inside the capsid out). ISME J. 2011 Feb;5(2):165-8. doi: 10.1038/ismej.2010.81. Epub 2010 Jun 17. Erratum in: ISME J. 2011 Feb;5(2):366. PubMed PMID: 20555364; PubMed Central PMCID: PMC3105704. [link]
17.Williamson KE, Kan J, Polson SW, Williamson SJ. Optimizing the Indirect Extraction of Prokaryotic DNA from Soils. Soil Biology and Biochemistry. 2011 Apr. 43(4):736-748. doi: 10.1016/j.soilbio.2010.04.017 [link]
16.Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EA. The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol. 2010 Jul;12(7):1842-54. doi: 10.1111/j.1462-2920.2010.02189.x. Epub 2010 Mar 7. PubMed PMID: 20236166. [link]
15.Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D. Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol. 2010 Jan;18(1):20-9. doi: 10.1016/j.tim.2009.10.001. Epub 2009 Nov 5. Review. PubMed PMID: 19896852; PubMed Central PMCID: PMC2818347. [link]
14.Helton RR, Powell DH, Cary SC, Polson SW, Czymmek KJ. 2009. Observation of Virus-Like Particles in Vascular and Coelomic Hemolymph of Riftia pachyptila. Microscopy and Microanalysis, 15:100-101.
13.Polson SW, JL Higgins, Woodley CM. 2009. PCR-based assay for detection of four coral pathogens. Proceedings of the Eleventh International Coral Reef Symposium. 1: 247-251. doi: 10.13140/2.1.4058.6248 [link]
12.Cervino J, Winiarski K, Polson SW, Goreau T, Smith GW. 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.
11.Polson SW, Lundqvist ML, Woodley CM. 2006. Systematic approach to a disease investigation: Case example. Proceedings of the Tenth International Coral Reef Symposium, 1:138-141. doi: 10.13140/2.1.4435.4566 [link]
10.Polson SW. Comparative Analysis of Microbial Community Structure Associated with Acroporid Corals During a Disease Outbreak in the Florida Reef Tract. 2007. Ph.D. Thesis. Marine Biomedicine and Environmental Sciences/Molecular and Cellular Biology and Pathobiology, Medical University of South Carolina. 343 pp. doi: 10.13140/2.1.2852.4484 [link]
9.Cervino JM, Littler M, Littler D, Polson SW, Goreau TJ, Brooks B, Smith GW. 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.
8.Cervino JM, Hayes RL, Polson SW, Polson SC, Goreau TJ, Martinez RJ, Smith GW. Relationship of Vibrio species infection and elevated temperatures to yellow blotch/band disease in Caribbean corals. Appl Environ Microbiol. 2004 Nov;70(11):6855-64. PubMed PMID: 15528553; PubMed Central PMCID: PMC525219.
7.Denner EB, Smith GW, Busse HJ, Schumann P, Narzt T, Polson SW, Lubitz W, Richardson LL. Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals. Int J Syst Evol Microbiol. 2003 Jul;53(Pt 4):1115-22. PubMed PMID: 12892136.
6.Patterson KL, Porter JW, Ritchie KB, Polson SW, Mueller E, Peters EC, Santavy DL, Smith GW. The etiology of white pox, a lethal disease of the Caribbean elkhorn coral, Acropora palmata. Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8725-30. Epub 2002 Jun 19. PubMed PMID: 12077296; PubMed Central PMCID: PMC124366.
5.Polson SW. Isolation and characterization of bacteria associated with three coral diseases. 2002. M.S. Thesis. Department of Microbiology and Molecular Medicine, Clemson University. 100 pp.
4.Bagwell CE, Rocque JR, Smith GW, Polson SW, Friez MJ, Longshore JW, Lovell CR. Molecular diversity of diazotrophs in oligotrophic tropical seagrass bed communities. FEMS Microbiol Ecol. 2002 Feb 1;39(2):113-9. doi: 10.1111/j.1574-6941.2002.tb00912.x. PubMed PMID: 19709190. [link]
3.Malmstrøm J, Polson SC, Polson SW, Smith GW, Frisvad JC. A Long-Term Study of Biomass Fluctuations within the Seagrass Communities Surrounding San Salvador Island, Bahamas. Proceedings of the Eighth Symposium on the Natural History of the Bahamas, Editors: Carolyn A. Clark-Simpson, Garriet W. Smith, pp.48-52 [link]
2.Polson SW, Smith GW. A Long-Term Study of Biomass Fluctuations within the Seagrass Communities Surrounding San Salvador Island, Bahamas. Proceedings of the Eighth Symposium on the Natural History of the Bahamas, Publisher: Gerace Research Center, Editors: Carolyn A. Clark-Simpson, Garriet W. Smith, pp.62-67. [link]
1.Ritchie KB, Polson SW, Smith GW. 2001. Microbial Disease Causation in Marine Invertebrates: Problems, Practices, and Future Prospects. Hydrobiologia. 460:131-139. doi: 10.1023/A:1013181718805. [link]

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

 

Center for Bioinformatics & Computational Biology • 15 Innovation Way • Newark, DE 19711 • USA
Phone: 302-831-0161 • E-mail: bioinformatics@udel.edu

Comments | Contact Us | Legal Notices