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. Molecular & Cellular Biology & Pathobiology
(Marine Biomed. & Environ. Science Conc.)
Medical University of South Carolina, Charleston, SC
2007

Postdoctoral Viral Metagenomics
Department of Plant and Soil Sciences
University of Delaware, Newark, DE
2008-2010

Other Appointments

• Co-Director; Computational Biology, Bioinformatics, & Biomedical Data Science Doctoral Training Program
• Associate Director; Research & Infrastructure; Center for Bioinformatics and Computational Biology
• Program Faculty, Microbiology Program, University of Delaware (2018-present)
• Affiliated Faculty, Data Science Institute, University of Delaware (2018-present)
• Adjunct Associate Professor, Department of Biochemistry and Cell & Molecular Biology, Georgetown University Medical Center (2017-present)
• Affiliated Faculty, Delaware Environmental Institute, University of Delaware (2012-present)
• Affiliated/Graduate Program Faculty, Center for Bioinformatics and Computational Biology, University of Delaware (2012-present)
• Manager, NECC Shared Data Center at the University of Delaware, North East Cyberinfrastructure Consortium (2010-present)

Previous Appointments

• Assistant Professor, Dept. of Computer and Information Sciences, University of Delaware (2010-2017)
• Assistant Professor, Dept. of Biological Sciences, University of Delaware (2010-2017)
• Associate Director, Bioinformatics Network of Delaware, Delaware INBRE (2014-2016)
• Coordinator, Bioinformatics Core Facility, Center for Bioinformatics and Computational Biology, University of Delaware (2010-2015)
• 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

• Role of replicon biochemistry in infection dynamics of viruses
• Connecting Genotype to Phenotype in Microbial Viruses
• Application of Omics Approaches for Optimization of Biopharma Manufacturing Processes
• VIROME: Viral Informatics Resource for Metagenome Exploration.  http://virome.dbi.udel.edu
• MgOl: Metagenomes Online. http://metagenomesonline.org
• Microbial communities of the eastern oyster, Crossostrea virginica.

Laboratory News Articles

• CBB T32, Rachel Keown Fellow: A career path paved with data
• Delaware INBRE/EPSCoR Collaboration: EPSCoR/INBRE cross collaboration on marine viruses and microbes
• Lagrangian Float Cruise: Marine Viruses and Microbes
• Core Supporting COVID Research: NIIMBL Grant will Accelerate COVID-19 Response
• Symposium: Darwin Day Celebration
• DBI Core Facilities: Biotech Powerhouse Wows Congresswoman
• Tessa Jarvis Award: Undergraduate Researchers Compete in Regional Symposium
• Nanofluidics for Viral Ecology: UD teams get millions in NSF funding
• Software Drives Genetic Research: Lima Bean Resistance
• Optimizing Core Facility Operations: Delaware INBRE receives $522,000 award from National Institutes of Health
• Steven Smith Award: Outstanding research scholars
• CBCB in DC: UD Day in DC: Senators, feds, alumni check out latest in research at UD Day in DC
• Gut Microbiome Nature Publication: Researchers find evidence of a link between high fat diets, gut bacteria, and bowel cancer
• NSF VIROME funding: Viral dark matter: UD researchers’ website tracks genetic sequence data from unknown viruses
• Eric Sakowski PNAS Publication: Ancient Gene
• Sam Widmayer, DENIN Scholar: 2013 DENIN Environmental Scholars
• Helen Schmidt, Award: UD science undergraduates excel at annual East Coast competition
• Jessica Chopyk, ASM Fellow: Undergrad receives research fellowship to study deep-sea viruses
• GBMF VIROME Funding: Researchers to study positive genetic contributions of viruses

Society Memberships

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

Publications

More details at: Google Scholar and ResearchGate

1. Kumar M, Tibocha-Bonilla JD, Füssy Z, Lieng C, Schwenck SM, Levesque AV, Al-Bassam MM, Passi A, Neal M, Zuniga C, Kaiyom F, Espinoza JL, Lim H, Polson SW, Allen LZ, Zengler K. Mixotrophic growth of a ubiquitous marine diatom. Sci Adv. 2024 Jul 19;10(29):eado2623. doi: 10.1126/sciadv.ado2623. Epub 2024 Jul 17. PMID: 39018398; PMCID: PMC466952. [link]
2. Harrigan WL, Ferrell BD, Wommack KE, Polson SW, Schreiber ZD, Belcaid M. Improvements in viral gene annotation using large language models and soft alignments. BMC Bioinformatics. 2024 Apr 25;25(1):165. doi: 10.1186/s12859-024-05779-6. PMID: 38664627; PMCID: PMC11046836. [link]
3. Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems. 2023 Dec 21;8(6):e0003823. doi: 10.1128/msystems.00038-23. Epub 2023 Oct 26. PMID: 37882557; PMCID: PMC10734462. [link]
4. Wu LY, Piedade GJ, Moore RM, Harrison AO, Martins AM, Bidle KD, Polson SW, Sakowski EG, Nissimov JI, Dums JT, Ferrell BD, Wommack KE. Ubiquitous, B12-dependent virioplankton utilizing ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean. ISME Commun. 2023 Oct 3;3(1):108. doi: 10.1038/s43705-023-00306-9. PMID: 37789093; PMCID: PMC10547690. [link]
5. Kiledal EA, Shaw M, Polson SW, Maresca JA. Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea. Microbiol Spectr. 2023 Aug 17;11(4):e0511222. doi: 10.1128/spectrum.05112-22. Epub 2023 Jul 5. PMID: 37404173; PMCID: PMC10434110. [link]
6. Remsburg CM, Konrad K, Stepicheva N, Testa M, Lee K, Choe L, Polson S, Bhavsar J, Huang H, Song JL. miR-31-mediated local translation at the mitotic spindle is important for early development. Res Sq [Preprint]. 2023 Jun 14:rs.3.rs-3044775. doi: 10.21203/rs.3.rs-3044775/v1. PMID: 37398341; PMCID: PMC10312921. [link]
7. Whittaker CA, Kucukural A, Gates C, Wilkins OM, Bell GW, Hutchinson JN, Polson SW, Dragon J. Functional Annotation Routines Used by ABRF Bioinformatics Core Facilities – Observations, Comparisons, and Considerations. J Biomol Tech. 2023 Mar 27;34(1):3fc1f5fe.0b74b9db. doi: 10.7171/3fc1f5fe.0b74b9db. PMID: 37089874; PMCID: PMC10121236. [link]
8. Joglekar P, Ferrell BD, Jarvis T, Haramoto K, Place N, Dums JT, Polson SW, Wommack KE, Fuhrmann JJ. Spontaneously Produced Lysogenic Phages Are an Important Component of the Soybean Bradyrhizobium Mobilome. mBio. 2023 Apr 25;14(2):e0029523. doi: 10.1128/mbio.00295-23. Epub 2023 Apr 5. PMID: 37017542; PMCID: PMC10127595.[link]
9. Kugler A, Brigmon RL, Friedman A, Coutelot FM, Polson SW, Seaman JC, Simpson W. Bioremediation of copper in sediments from a constructed wetland ex situ with the novel bacterium Cupriavidus basilensis SRS. Sci Rep. 2022 Oct 21;12(1):17615. doi: 10.1038/s41598-022-20930-0. PMID: 36271237; PMCID: PMC9587019. [link]
10. Keown RA, Dums JT, Brumm PJ, MacDonald J, Mead DA, Ferrell BD, Moore RM, Harrison AO, Polson SW, Wommack KE. Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes. Front Microbiol. 2022 Apr 21;13:858366. doi: 10.3389/fmicb.2022.858366. PMID: 35531281; PMCID: PMC9069017. [link]
11. Zhou N, Keffer JL, Polson SW, Chan CS. Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR. Appl Environ Microbiol. 2022 Jan 25;88(2):e0159521. doi: 10.1128/AEM.01595-21. Epub 2021 Nov 17. PMID: 34788064; PMCID: PMC8788666. [link]
12. Cusick K, Iturbide A, Gautam P, Price A, Polson SW, MacDonald M, Erill I. Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings. PLoS One. 2021 Sep 28;16(9):e0257800. doi: 10.1371/journal.pone.0257800. PMID: 34582496; PMCID: PMC8478169. [link]
13. DeLong JP, Al-Sammak MA, Al-Ameeli ZT, Dunigan DD, Edwards KF, Fuhrmann JJ, Gleghorn JP, Li H, Haramoto K, Harrison AO, Marston MF, Moore RM, Polson SW, Ferrell BD, Salsbery ME, Schvarcz CR, Shirazi J, Steward GF, Van Etten JL, Wommack KE. Towards an integrative view of virus phenotypes. Nat Rev Microbiol. 2022 Feb;20(2):83-94. doi: 10.1038/s41579-021-00612-w. Epub 2021 Sep 14. PMID: 34522049. [link]
14. Leek CC, Soulas JM, Bhattacharya I, Ganji E, Locke RC, Smith MC, Bhavsar JD, Polson SW, Ornitz DM, Killian ML. Deletion of Fibroblast growth factor 9 globally and in skeletal muscle results in enlarged tuberosities at sites of deltoid tendon attachments. Dev Dyn. 2021 Dec;250(12):1778-1795. doi: 10.1002/dvdy.383. Epub 2021 Jun 16. PMID: 34091985; PMCID: PMC8639753. [link]
15. Rosier CL, Polson SW, D’Amico V 3rd, Kan J, Trammell TLE. Urbanization pressures alter tree rhizosphere microbiomes. Sci Rep. 2021 May 3;11(1):9447. doi: 10.1038/s41598-021-88839-8. PMID: 33941814; PMCID: PMC8093231. [link]
16. MacDonald ML, Polson SW, Lee KH. k-mer-Based Metagenomics Tools Provide a Fast and Sensitive Approach for the Detection of Viral Contaminants in Biopharmaceutical and Vaccine Manufacturing Applications Using Next-Generation Sequencing. mSphere. 2021 Apr 21;6(2):e01336-20. doi: 10.1128/mSphere.01336-20. PMID: 33883263; PMCID: PMC8546726. [link]
17. Richards GP, Watson MA, Madison D, Soffer N, Needleman DS, Soroka DS, Uknalis J, Baranzoni GM, Church KM, Polson SW, Elston R, Langdon C, Sulakvelidze A. Bacteriophages against Vibrio coralliilyticus and Vibrio tubiashii: Isolation, Characterization, and Remediation of Larval Oyster Mortalities. Appl Environ Microbiol. 2021 Apr 27;87(10):e00008-21. doi: 10.1128/AEM.00008-21. PMID: 33674441; PMCID: PMC8117752. [link]
18. Tomlinson MJ 4th, Polson SW, Qiu J, Lake JA, Lee W, Abasht B. Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT. Sci Rep. 2021 Feb 17;11(1):3968. doi: 10.1038/s41598-021-83459-8. PMID: 33597613; PMCID: PMC7889858.[link]
19. Sakowski EG, Wommack KE, Polson SW. Oyster Calcifying Fluid Harbors Persistent and Dynamic Autochthonous Bacterial Populations That May Aid in Shell Formation. Mar Ecol Prog Ser. 2020 Oct 29;653:57-75. doi: 10.3354/meps13487. PMID: 33424068; PMCID: PMC7789820. [link]
20. McAllister SM, Vandzura R, Keffer JL, Polson SW, Chan CS. Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents. ISME J. 2021 May;15(5):1271-1286. doi: 10.1038/s41396-020-00849-y. Epub 2020 Dec 17. PMID: 33328652; PMCID: PMC8114936. [link]
21. Ovadia EM, Pradhan L, Sawicki LA, Cowart JE, Huber RE, Polson SW, Chen C, van Golen KL, Ross KE, Wu CH, Kloxin AM. Understanding ER+ Breast Cancer Dormancy Using Bioinspired Synthetic Matrices for Long-Term 3D Culture and Insights into Late Recurrence. Adv Biosyst. 2020 Sep;4(9):e2000119. doi: 10.1002/adbi.202000119. Epub 2020 Jun 30. PMID: 32603024. [link]
22. Barnum CE, Al Saai S, Patel SD, Cheng C, Anand D, Xu X, Dash S, Siddam AD, Glazewski L, Paglione E, Polson SW, Chuma S, Mason RW, Wei S, Batish M, Fowler VM, Lachke SA. The Tudor-domain protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 (HSP27) and lens fiber cell morphology. Hum Mol Genet. 2020 Jul 29;29(12):2076-2097. doi: 10.1093/hmg/ddaa096. PMID: 32420594; PMCID: PMC7390939. [link]
23. Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, Polson SW, Riva A, Settles ML, Thimmapuram J, Levine SS. Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities. J Biomol Tech. 2020 Apr 29:jbt.20-3102-005. doi: 10.7171/jbt.20-3102-005. Epub ahead of print. PMID: 32382253; PMCID: PMC7192196. [link]
24. Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE. Iroki: automatic customization and visualization of phylogenetic trees. PeerJ. 2020 Feb 26;8:e8584. doi: 10.7717/peerj.8584. PMID: 32149022; PMCID: PMC7049256. [link]
25. Joglekar P, Mesa CP, Richards VA, Polson SW, Wommack KE, Fuhrmann JJ. Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.). Syst Appl Microbiol. 2020 Feb 15:126073. doi: 10.1016/j.syapm.2020.126073. Epub ahead of print. PMID: 32139173. [link]
26. Marston MF, Polson SW. Whole-Genome Sequence of the Cyanobacterium Synechococcus sp. Strain WH 8101. Microbiol Resour Announc. 2020 Feb 20;9(8):e01593-19. doi: 10.1128/MRA.01593-19. PMID: 32079636; PMCID: PMC7033273. [link]
27. McAllister SM, Polson SW, Butterfield DA, Glazer BT, Sylvan JB, Chan CS. Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents. mSystems. 2020 Feb 18;5(1):e00553-19. doi: 10.1128/mSystems.00553-19. PMID: 32071158; PMCID: PMC7029218. [link]
28. Cusick KD, Polson SW, Duran G, Hill RT. Multiple Megaplasmids Confer Extremely High Levels of Metal Tolerance in Alteromonas Strains. Appl Environ Microbiol. 2020 Jan 21;86(3):e01831-19. doi: 10.1128/AEM.01831-19. PMID: 31757820. [link]
29. Porto BN, Caixeta ET, Mathioni SM, Vidigal PMP, Zambolim L, Zambolim EM, Donofrio N, Polson SW, Maia TA, Chen C, Adetunji M, Kingham B, Dalio RJD, Resende MLV. Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility. PLoS One. 2019 Apr 18;14(4):e0215598. doi: 10.1371/journal.pone.0215598. eCollection 2019. PubMed PMID: 30998802. [link]
30. Maresca JA, Keffer JL, Hempel PP, Polson SW, Shevchenko O, Bhavsar J, Powell D, Miller KJ, Singh A, Hahn MW. Light Modulates the Physiology of Nonphototrophic Actinobacteria. J Bacteriol. 2019 Apr 24;201(10). pii: e00740-18. doi: 10.1128/JB.00740-18. Print 2019 May 15. PubMed PMID: 30692175. [link]
31. Nasko DJ, Ferrell BD, Moore RM, Bhavsar JD, Polson SW, Wommack KE. CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes. MBio. 2019 Mar 5;10(2). pii: e02651-18. doi: 10.1128/mBio.02651-18. PubMed PMID: 30837341; PubMed Central PMCID: PMC6401485. [link]
32. Harrison AO, Moore RM, Polson SW, Wommack KE. Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton. Front Microbiol. 2019 Feb 5;10:134. doi: 10.3389/fmicb.2019.00134. eCollection 2019. PubMed PMID: 30804913; PubMed Central PMCID: PMC6370689. [link]
33. Hempel P, Keffer JL, Shevchenko O, Henny C, Polson SW, Maresca JA. Complete Genome Sequence of Microbacterium sp. Strain 10M-3C3, Isolated from an Extremely Phosphorus-Poor Lake. Microbiol Resour Announc. 2019 Jan 24;8(4). pii: e01649-18. doi: 10.1128/MRA.01649-18. eCollection 2019 Jan. PubMed PMID: 30701259; PubMed Central PMCID: PMC6346208. [link]
34. Lv M, Zhou Y, Polson SW, Wan LQ, Wang M, Han L, Wang L, Lu XL. Identification of Chondrocyte Genes and Signaling Pathways in Response to Acute Joint Inflammation. Sci Rep. 2019 Jan 14;9(1):93. doi: 10.1038/s41598-018-36500-2. PubMed PMID: 30643177; PubMed Central PMCID: PMC6331554. [link]
35. Richards GP, Needleman DS, Watson MA, Polson SW. Whole-Genome Sequences of Two Pseudoalteromonas piscicida Strains, DE1-A and DE2-A, with Strong Antibacterial Activity against Vibrio vulnificus. Microbiol Resour Announc. 2019 Jan 3;8(1). pii: e01451-18. doi: 10.1128/MRA.01451-18. eCollection 2019 Jan. PubMed PMID: 30637397; PubMed Central PMCID: PMC6318368. [link]
36. Nasko DJ, Chopyk J, Sakowski EG, Ferrell BD, Polson SW, Wommack KE. Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton. Front Microbiol. 2018 Dec 14;9:3053. doi:10.3389/fmicb.2018.03053. eCollection 2018. PubMed PMID: 30619142; PubMed Central PMCID: PMC6302109. [link]
37. Rupp O, MacDonald ML, Li S, Dhiman H, Polson SW, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng. 2018 Apr 28. doi: 10.1002/bit.26722. [Epub ahead of print] PubMed PMID: 29704459.[link]
38. Marine RL, Nasko DJ, Wray J, Polson SW, Wommack KE. Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology. ISME J. 2017 Nov;11(11):2479-2491. doi: 10.1038/ismej.2017.102. Epub 2017 Jul 21. PubMed PMID: 28731469; PubMed Central PMCID: PMC5649160. [link]
39. Manching H, Sengupta S, Hopper KR, Polson SW, Ji Y, Wisser RJ. Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize. G3 (Bethesda). 2017 Jul 5;7(7):2161-2170. doi: 10.1534/g3.117.042036. PubMed PMID: 28526729; PubMed Central PMCID: PMC5499125.[link]
40. Singhal A, Leaman R, Catlett N, Lemberger T, McEntyre J, Polson SW, Xenarios I, Arighi C, Lu Z. Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database (Oxford). 2016 Dec 26;2016. pii:baw161. doi: 10.1093/database/baw161. Print 2016. PubMed PMID: 28025348; PubMed Central PMCID: PMC5199160.[link]
41. Mhora TT, Ernest EG, Wisser RJ, Evans TA, Patzoldt ME, Gregory NF, Westhafer SE, Polson SW, Donofrio NM. Genotyping-by-Sequencing to Predict Resistance to Lima Bean Downy Mildew in a Diversity Panel. Phytopathology. 2016 Oct;106(10):1152-1158. Epub 2016 Aug 22. PubMed PMID: 27546812.[link]
42. Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH; UniProt Consortium. Computational clustering for viral reference proteomes. Bioinformatics. 2016 Feb 26. doi: 10.1093/bioinformatics/btw110 [Epub ahead of print] PubMed PMID: 27153712. [link]
43. Barthold JS, Pugarelli J, MacDonald ML, Ren J, Adetunji MO, Polson SW, Mateson A, Wang Y, Sol-Church K, McCahan SM, Akins RE Jr, Devoto M, Robbins AK. Polygenic inheritance of cryptorchidism susceptibility in the LE/orl rat. Mol Hum Reprod. 2016 Jan;22(1):18-34. doi: 10.1093/molehr/gav060. Epub 2015 Oct 26. PubMed PMID: 26502805; PubMed Central PMCID: PMC4694052. [link]
44. Bishnoi U, Polson SW, Sherrier DJ, Bais HP. Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent. Genome Announc. 2015 Jul 9;3(4). pii: e00696-15. doi:
    10.1128/genomeA.00696-15. PubMed PMID: 26159522; PubMed Central PMCID: PMC4490843.[link]
45. 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 Biomol Tech. 2015 Jan 29. doi: 10.7171/jbt.15-2601-002 [Epub ahead of print] PubMed PMID: 25649353; PubMed Central PMCID: PMC4310222. [link]
46. 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]
47. 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 (From the Cover). Proc Natl Acad Sci U S A. 2014 Oct 13. doi: 10.1073/pnas.1401322111 [link]
48. 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]
49. 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]
50. 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]
51. 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]
52. 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]
53. 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]
54. 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]
55. 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]
56. 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]
57. 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]
58. 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]
59. 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]
60. 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]
61. 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]
62. 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]
63. 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]
64. 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]
65. 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]
66. 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]
67. 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]
68. 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]
69. 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]
70. 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. doi:10.1017/S1431927609096111 [link]
71. 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]
72. 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. doi:10.3354/meps324139 [link]
73. 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]
74. 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]
75. 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. [link]
76. 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. doi: 10.1128/AEM.70.11.6855-6864.2004 PubMed PMID: 15528553; PubMed Central PMCID: PMC525219. [link]
77. 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. doi:10.1099/ijs.0.02359-0 PubMed PMID: 12892136. [link]
78. 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 (From the Cover). 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. doi:10.1073/pnas.092260099 [link]
79. 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.
80. 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]
81. 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]
82. 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]
83. 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]