Core - Genomics

Sogin, Mitchell L.

Abstract

The Genomics Core Facility will provide access to higher-level bioinformatics capabilities for multiple sequence alignment, and phylogenetic inference or population biology analyses. The faculty and bioinformatics staff of the Bay Paul Center for Comparative Molecular Biology and Evolution has considerable expertise in pure statistics, genome assembly, astrophysical modeling, gene expression, phylogenetics, information management, data acquisition pipelines, and data basing. The combination of this expertise with our advanced computational resources will meet anticipated needs for each of the projects supported by The Woods Hole Center for Oceans and Human Health. Dr. Sogin in consultation with Dr. Andrew McArthur, will advise PIs of individual projects on the use of appropriate computer algorithms. The general approach will be to use CLUSTALX {Jeanmougin, 1998 #27} for the alignment of large data sets. Manual corrections (interactive changes in positioning of gaps) may be used to improve the alignments. The phylogenetic analyses will normally only consider regions where there is confidence in homology of the compared sites.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Institute of Environmental Health Sciences (NIEHS)
• Type: Specialized Center (P50)
• Project #: 5P50ES012742-05
• Application #: 7565990
• Study Section: Special Emphasis Panel (ZES1)
• Budget Start: 2008-01-01
• Budget End: 2008-12-31
• Support Year: 5
• Fiscal Year: 2008
• Total Cost: $95,604

Institution

• Name: Woods Hole Oceanographic Institution
• DUNS #: 001766682
• City: Woods Hole
• State: MA
• Country: United States
• Zip Code: 02543

Publications

Goldstone, Jared V; Sundaramoorthy, Munirathinam; Zhao, Bin et al. (2016) Genetic and structural analyses of cytochrome P450 hydroxylases in sex hormone biosynthesis: Sequential origin and subsequent coevolution. Mol Phylogenet Evol 94:676-687

Halliday, Elizabeth; Ralston, David K; Gast, Rebecca J (2015) Contribution of sand-associated enterococci to dry weather water quality. Environ Sci Technol 49:451-8

Anderson, Donald (2014) HABs in a changing world: a perspective on harmful algal blooms, their impacts, and research and management in a dynamic era of climactic and environmental change. Harmful Algae 2012 (2012) 2012:3-17

Kleindinst, Judith L; Anderson, Donald M; McGillicuddy Jr, Dennis J et al. (2014) Categorizing the severity of paralytic shellfish poisoning outbreaks in the Gulf of Maine for forecasting and management. Deep Sea Res Part 2 Top Stud Oceanogr 103:277-287

Anderson, Donald M; Keafer, Bruce A; Kleindinst, Judith L et al. (2014) Alexandrium fundyense cysts in the Gulf of Maine: long-term time series of abundance and distribution, and linkages to past and future blooms. Deep Sea Res Part 2 Top Stud Oceanogr 103:6-26

McGillicuddy Jr, D J; Townsend, D W; Keafer, B A et al. (2014) Georges Bank: a leaky incubator of Alexandrium fundyense blooms. Deep Sea Res Part 2 Top Stud Oceanogr 103:163-173

Pilskaln, C H; Anderson, D M; McGillicuddy, D J et al. (2014) Spatial and temporal variability of Alexandrium cyst fluxes in the Gulf of Maine: Relationship to seasonal particle export and resuspension. Deep Sea Res Part 2 Top Stud Oceanogr 103:40-54

McGillicuddy Jr, D J; Brosnahan, M L; Couture, D A et al. (2014) A red tide of Alexandrium fundyense in the Gulf of Maine. Deep Sea Res Part 2 Top Stud Oceanogr 103:174-184

Fernandes, Luciano F; Hubbard, Katherine A; Richlen, Mindy L et al. (2014) Diversity and toxicity of the diatom Pseudo-nitzschia Peragallo in the Gulf of Maine, Northwestern Atlantic Ocean. Deep Sea Res Part 2 Top Stud Oceanogr 103:139-162

Halliday, Elizabeth; McLellan, Sandra L; Amaral-Zettler, Linda A et al. (2014) Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations. PLoS One 9:e90815