This is a select list of works produced by the faculty of the USF College of Marine Science. Materials are included when two conditions are satisfied: 1) the creator approves inclusion and 2) the publisher allows the material to be placed in the repository. Please direct questions or requests to expand the list of materials to Jason Boczar.

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Submissions from 2014

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Comparative Metagenomics: Natural Populations of Induced Prophages Demonstrate Highly Unique, Lower Diversity Viral Sequences, Lauren McDaniel, Karyna Rosario, Mya Breitbart, and John Paul

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Assessing Climate Variability Effects on Dengue Incidence in San Juan, Puerto Rico, Pablo Méndez-Lázaro, Frank E. Muller-Karger, Daniel Otis, Matthew J McCarthy, and Marisol Peña-Orellana

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Alteration of Residual Circulation Due to Large-Scale Infrastructure in a Coastal Plain Estuary, Steven D. Meyers, Amanda J. Linville, and Mark E. Luther

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Real‐Time Oceanographic Data: From Safety to Science, Steven D. Meyers, Jeffrey Scudder, and Mark E. Luther

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A Framework for a Marine Biodiversity Observing Network Within Changing Continental Shelf Seascapes, Frank Muller-Karger, Maria Kavanaugh, Enrique Montes, William Balch, and Mya Breitbart

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Spatial Variability of Total Dissolved Copper and Copper Speciation in the Inshore Waters of Bermuda, Véronique Oldham, M. M. Swenson, and Kristen N. Buck

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Comparisons of Different Ensemble Schemes for Glider Data Assimilation on West Florida Shelf, Chudong Pan, Lianyuan Zheng, Robert H. Weisberg, Yonggang Liu, and Chad Lembke

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RNA Viral Metagenome of Whiteflies Leads to the Discovery and Characterization of a Whitefly-Transmitted Carlavirus in North America, Karyna Rosario, Heather Capobianco, Terry Fei Fan Ng, Mya Breitbart, and Jane E. Polston

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A Record of Anthropogenic Effects on Sedimentation in the Manatee River, Florida, Patrick Schwing and Ashanti Johnson

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Characterizing the Deep Sea Benthic Foraminifera Impact and Response to the Deepwater Horizon Blowout in the Northeastern Gulf of Mexico, Patrick Schwing, Isabel Romero, Gregg R. Brooks, David Hastings, Rebecca Larson, and David Hollander

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Characterizing the Impact and Response of Deep Sea Benthic Foraminifera to the Deepwater Horizon Event in the Northeastern Gulf of Mexico, Patrick Schwing, Isabel C. Romero, Gregg Brooks, David W. Hastings, Rebekka Larson, L. M. Reilly, David J. Hollander, and Jeff P. Chanton

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On the Consistency of MODIS Chlorophyll $a$ Products in the Northern South China Sea, S. L. Shang, Q. Dong, Chuanmin M. Hu, G. Lin, Y. H. Li, and S. P. Shang

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A Case Study of Enteric Virus Removal and Insights into the Associated Risk of Water Reuse for Two Wastewater Treatment Pond Systems in Bolivia, E. M. Symonds, M. E. Verbyla, J. O. Lukasik, R. C. Kafle, Mya Breitbart, and J. R. Mihelcic

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Consistency of the Current Global Ocean Observing Systems from an Argo perspective, K. von Schuckmann, J.-B. Sallée, D. Chambers, P.-Y. Le Traon, C. Cabanes, F. Gaillard, S. Speich, and M. Hamon

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Rapid Changes in the Seasonal Sea Level Cycle along the US Gulf Coast from the Late 20th Century, Thomas Wahl, Francisco M. Calafat, and Mark E. Luther

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Stable Isotopes in Fish Eye Lenses as Potential Recorders of Trophic and Geographic History, Amy A. Wallace, David J. Hollander, and Ernst B. Peebles

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Fish eye-lens stable isotopes from the eastern Gulf of Mexico, summer 2013, Amy A. Wallace and Ernst B. Peebles

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Fish Sound Production in the Presence of Harmful Algal Blooms in the Eastern Gulf of Mexico, Carrie C. Wall, Chad Lembke, Chuanmin Hu, and David A. Mann

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Temporal and Spatial Mapping of Red Grouper Epinephelus morio Sound Production, C. C. Wall, P. Simard, M. Lindemuth, Chad Lembke, D. F. Naar, Chuanmin Hu, Brian B. Barnes, Frank E. Muller-Karger, and D. A. Mann

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Why No Red Tide Was Observed on the West Florida Continental Shelf in 2010, Robert H. Weisberg, Lianyuan Zheng, Yonggang Liu, Chad Lembke, Jason M. Lenes, and John J. Walsh

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Gag Grouper Larvae Pathways on the West Florida Shelf, Robert H. Weisberg, Lianyuan Zheng, and Ernst B. Peebles

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Synoptic Volumetric Variations and Flushing of the Tampa Bay Estuary, M. Wilson, Steven D. Meyers, and Mark E. Luther

Submissions from 2013

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Sources of Strong Copper-binding Ligands in Antarctic Peninsula Surface Waters, Randelle Bundy, Katherine Barbeau, and Kristen N. Buck

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A New Method for Precise Determination of Iron, Zinc and Cadmium Stable Isotope Ratios in Seawater by Double-Spike Mass Spectrometry, Tim M. Conway, Angela D. Rosenberg, Jess F. Adkins, and Seth G. John

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High Global Diversity of Cycloviruses Amongst Dragonflies, Anisha Dayaram, Kristen Potter, Angela Moline, Dana Rosenstein, Milen Marinov, John Thomas, Mya Breitbart, Karyna Rosario, Gerardo Argüello-Astorga, and Arvind Varsani

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Molecular and Microscopic Evidence of Viruses in Marine Copepods, Darren Dunlap, Terry Fei Fan Ng, Karyna Rosario, Jorge Barbosa, Anthony Greco, Mya Breitbart, and Ian Hewson

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A Bioinformatic Analysis of Ribonucleotide Reductase Genes in Phage Genomes and Metagenomes, Bhakti Dwivedi, Bingjie Xue, Daniel Lundin, Robert Edwards, and Mya Breitbart

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Metagenomic Identification, Seasonal Dynamics, and Potential Transmission Mechanisms of a Daphnia‐associated Single‐stranded DNA Virus in Two Temperate Lakes, Ian Hewson, Gabriel Ng, WenFang Li, Brenna LaBarre, Isabel Aguirre, Mya Breitbart, and Anthony Greco

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Distinct Iron Isotopic Signatures and Supply from Marine Sediment Dissolution, William B. Homoky, Seth G. John, Tim M. Conway, and Rachel A. Mills

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Gulf of Mexico Hurricane Wave Simulations Using Swan: Bulk Formula-Based Drag Coefficient Sensitivity for Hurricane Ike, Yong Huang, Robert H. Weisberg, Lianyuan Zheng, and Marcel Zijlema

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The Role of Organic Ligands in Iron Cycling and Primary Productivity in the Antarctic Peninsula: A Modeling Study, Mingshun Jiang, Katherine Barbeau, Karen Selph, Christopher Measures, Kristen N. Buck, Farooq Azam, B. Greg Mitchell, and Meng Zhou

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U.S. IOOS Coastal and Ocean Modeling Testbed: Inter-Model Evaluation of Tides, Waves, and Hurricane Surge in the Gulf of Mexico, P. C. Kerr, A. S. Donahue, J. J. Westerink, R. A. Luettich Jr., Lianyuan Zheng, Robert H. Weisberg, and Y. Huang

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Development and Sea Trials of a New Camera-Based Assessment Survey System for Reef Fish Stocks Assessment, Chad Lembke, Alex Silverman, Steven Butcher, Steven Murawski, Sarah Grasty, and Xianpeng Shi

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Sparse Glider Datasets: A Case Study for NoSQL Databases, Michael Lindemuth and Chad Lembke

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Monitoring and Modeling the Deepwater Horizon Oil Spill: a Record Breaking Enterprise, Yonggang Liu, Amy Macfadyen, Zhen-Gang Ji, and Robert H. Weisberg

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Verification of Wave Measurement Systems, Luther Luthe, Guy Meadows, Earle Buckley, Sherryl Gilbert, Heidi Purcell, and Mario Tamburri

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Consideration of a Variable Frequency Energy Conversion System for Marine and Onshore Wind Energy Extraction, Clifford R. Merz

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Metagenomic Identification of a nodavirus and a Circular ssDNA Virus in Semi-purified Viral Nucleic Acids from the Hepatopancreas of Healthy Farfantepenaeus duorarum hrimp, Terry Fei Fan Ng, Shankar Alavandi, Arvind Varsani, Scott Burghart, and Mya Breitbart

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Distinct Lineage of Vesiculovirus from Big Brown Bats, United States, Terry Fei Fan Ng, Cindy Driscoll, Maria Paz Carlos, Algernon Prioleau, Robert Schmieder, Bhakti Dwivedi, Jakk Wong, Yunhee Cha, Steven Head, Mya Breitbart, and Eric Delwart

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Novel Cyclovirus Discovered in the Florida Woods Cockroach Eurycotis floridana (Walker), Marco Padilla-Rodriguez, Karyna Rosario, and Mya Breitbart

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Discovery of a Novel Mastrevirus and Alphasatellite-like Circular DNA in Dragonflies (Epiprocta) from Puerto Rico, Karyna Rosario, Marco Padilla-Rodriguez, Simona Kraberger, Daisy Stainton, Darren Martin, Mya Breitbart, and Arvind Varsani

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Large-Scale Passive Acoustic Monitoring of Fish Sound Production on the West Florida Shelf, Carrie C. Wall, Peter Simard, Chad Lembke, and David A. Mann

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Tracking Subsurface Oil in the Aftermath of the Deepwater Horizon Well Blowout, Robert H. Weisberg, Lianyuan Zheng, and Yonggang Liu

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New Approach to Analysis of Voltammetric Ligand Titration Data Improves Understanding of Metal Speciation in Natural Waters, Mona Wells, Kristen N. Buck, and Sylvia Sander

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Three-Dimensional Structure of a Karenia Brevis Bloom: Observations from Gliders, Satellites, and Field Measurements, Jun Zhao, Chuanmin Hu, Jason M. Lenes, Robert H. Weisberg, Chad Lembke, David C. English, Jennifer Wolny, Lianyuan Zheng, John J. Walsh, and Gary J. Kirkpatrick

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Implications from the Comparisons between Two- and Three-Dimensional Model Simulations of the Hurricane Ike Storm Surge, Lianyuan Zheng, Robert H. Weisberg, Yong Huang, Rick Luettich, Johannes J. Westerink, Patrick C. Kerr, Aaron S. Donahue, Gary Crane, and Linda Akli

Submissions from 2012

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Friction Dominated Exchange in a Florida Estuary, Kimberly D. Arnott, Arnoldo Valle-Levinson University of Florida, and Mark E. Luther

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Marine Viruses: Truth or Dare, Mya Breitbart

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Copper Toxicity in the San Francisco Bay-Delta, Kristen N. Buck

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SCOR Working Group 139: Organic Ligands- A Key Control on Trace Metal Biogeochemistry, Kristen N. Buck, Maeve Lohan, and Sylvia Sander

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The Organic Complexation of Iron and Copper: An Intercomparison of Competitive Ligand Exchange‐adsorptive Cathodic Stripping Voltammetry (CLE‐ACSV) Techniques, Kristen N. Buck, James Moffett, Katherine Barbeau, Randelle Bundy, Yoshiko Kondo, and Jingfeng Wu

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Description and Ecology of a New Middle Ordovician (Llanvirn) Odontopleurid Trilobite from the Builth Inlier of Mid-Wales, with a Review of the Genus Meadowtownella, Tim M. Conway and Joseph P. Botting

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Bacterial Communities Associated with the Ctenophores Mnemiopsis leidyi and Beroe ovata, Camille Daniels and Mya Breitbart

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PhiSiGns: An Online Tool to Identify Signaturegenes in Phages and Design PCR Primers Forexamining Phage Diversity, Bhakti Dwivedi, Robert Schmieder, Dawn Goldsmith, Robert Edwards, and Mya Breitbart

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Detection and Tracking of Ships in Open Sea with Rapidly Moving Buoy-Mounted Camera System, Sergiy Fefilatyev, Dmitry Goldgof, Matthew Shreve, and Chad Lembke

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The Organic Complexation of Iron in the Marine Environment: A Review, Martha Gledhill and Kristen N. Buck

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Benjamin P. Flower (1962–2012), David W. Hastings, Amelia E. Shevenell, and James P. Kennett

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Integrating Observing Systems to Benefit Stakeholders: a Case Study in the Gulf of Mexico, Ann E. Jochens, Matthew K. Howard, Lisa Campbell, Ruth Mullins-Perry, Gary J. Kirkpatrick, Barbara Kirkpatrick, Chris Simoniello, Chuanmin Hu, and Robert H. Weisberg

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Integrating Observing Systems to Benefit Stakeholders: A Case Study in the Gulf of Mexico, Ann E. Jochens, Matthew K. Howard, Lisa Campbell, Ruth Mullins-Perry, Gary Kirkpatrick, Barbara Kirkpatrick, Chris Simoniello, Chuanmin Hu, Robert H. Weisburg, Chad Lembke, Alina Corcoran, Jim Ivey, and Steven H. Wolfe

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Quasi-Lagrangian Drifter Studies of Iron Speciation and Cycling Off Point Conception, California, Andrew King, Kristen N. Buck, and Katherine Barbeau

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A 1-D Simulation Analysis of the Development and Maintenance of the 2001 Red Tide of the Ichthyotoxic Dinoflagellate Karenia Brevis on the West Florida Shelf, Jason M. Lenes, Brian P. Darrow, John J. Walsh, J. K. Jolliff, F. R. Chen, Robert H. Weisberg, and Lianyuan Zheng

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Seasonal Variability on the West Florida Shelf, Yonggang Liu and Robert H. Weisberg

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Comparison of the X-Track Altimetry Estimated Currents with Moored Adcp and Hf Radar Observations on the West Florida Shelf, Yonggang Liu, Robert H. Weisberg, Stefano Vignudelli, Laurent Roblou, and Clifford R. Merz

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Phytoplankton Responses to Atmospheric Metal Deposition in the Coastal and Open-ocean Sargasso Sea, Katherine Mackey, Kristen N. Buck, John Casey, Abigail Cid, Michael Lomas, Yoshiki Sohrin, and Adina Paytan

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Salinity Gradient Power (SGP): A Developmental Roadmap Covering Existing Generation Technologies and Recent Investigative Results into the Feasibility of Bipolar Membrane-Based Salinity Gradient Power Generation, Clifford R. Merz, Wilfrido A. Moreno, Marilyn Barger, and Stephen M. Lipka

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Evolution of the USF/CMS Codar and WERA HF Radar Network, Clifford R. Merz, Robert H. Weisberg, and Yonggang Liu

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Spatially Resolved Genomic, Stable Isotopic, and Lipid Analyses of a Modern Freshwater Microbialite from Cuatro Ciénegas, Mexico, Nitti Nitti, Camille Daniels, Janet Siefert, Valeria Souza, David Hollander, and Mya Breitbart

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Ocean Time-series Reveals Recurring Seasonal Patterns of Virioplankton Dynamics in the Northwestern Sargasso Sea, Rachel Parsons, Mya Breitbart, Michael Lomas, and Craig Carlson

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Diverse Circular ssDNA Viruses Discovered in Dragonflies (Odonata: Epiprocta), Karyna Rosario, Anisha Dayaram, Milen Marinov, Jessica Ware, Simona Kraberger, Daisy Stainton, Mya Breitbart, and Arvind Varsani

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A Field Guide to Eukaryotic Circular Single-stranded DNA Viruses: Insights Gained from Metagenomics, Karyna Rosario, Siobain Duffy, and Mya Breitbart

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A National Glider Network for Sustained Observation of the Coastal Ocean, Daniel L. Rudnick, Rebecca Baltes, Michael Crowley, Oscar Schofield, Craig M. Lee, and Chad Lembke

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Improving Understanding of Organic Metal‐binding Ligands in the Ocean, Sylvia Sander, Kristen N. Buck, and Maeve Lohan

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Shelf-Scale Mapping of Sound Production by Fishes in the Eastern Gulf of Mexico, using Autonomous Glider Technology, Carrie C. Wall, Chad Lembke, and David A. Mann

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A Critique of Alternative Power Generation for Florida by Mechanical and Solar Means, Robert H. Weisberg, Yonggang Liu, Clifford R. Merz, Jyotika I. Virmani, and Lianyuan Zheng

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Modeling the West Florida Coastal Ocean by Downscaling from the Deep Ocean, across the Continental Shelf and into the Estuaries, Lianyuan Zheng and Robert H. Weisberg

Submissions from 2011

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Thermocline Characterisation in the Cariaco Basin: a Modelling Study of the Thermocline Annual Variation and Its Relation with Winds and Chlorophyll-A Concentration, Aida Alvera-Azcarate, Alexander Barth, Robert H. Weisberg, J. J. Castañeda, L. Vandenbulcke, and J. M. Beckers

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Spatial Heterogeneity of Bacterial Communities in the Mucus of Montastraea annularis, Camille Daniels, Amy Zeifman, Kathy Heym, Kim Ritchie, Craig Watson, Ilze Berzins, and Mya Breitbart

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Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity, Dawn Goldsmith, Giuseppe Crosti, Bhakti Dwivedi, Lauren McDaniel, Arvind Varsani, Curtis Suttle, Markus Weinbauer, Ruth-Anne Sandaa, and Mya Breitbart

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Did the Northeastern Gulf of Mexico Become Greener after the Deepwater Horizon Spill?, Chuanmin Hu, Robert H. Weisberg, Yonggang Liu, Lianyuan Zheng, Kendra L. Daly, David C. English, Jun Zhao, and Gabriel A. Vargo

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The Protection and Management of the Sargasso Sea: The Golden Floating Rainforest of the Atlantic Ocean, D.d’A. Laffoley, H.S.J. Roe, M.V. Angel, Ardron Ardron, Bates Bates, Boyd Boyd, Brooke Brooke, and Kristen N. Buck

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Front Matter, Yonggang Liu, Amy Macfadyen, Zhen-Gang Ji, and Robert H. Weisberg

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Introduction to Monitoring and Modeling the Deepwater Horizon Oil Spill, Yonggang Liu, Amy Macfadyen, Zhen-Gang Ji, and Robert H. Weisberg

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A Review of Self-Organizing Map Applications in Meteorology and Oceanography, Yonggang Liu and Robert H. Weisberg

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Evaluation of Trajectory Modeling in Different Dynamic Regions Using Normalized Cumulative Lagrangian Separation, Yonggang Liu and Robert H. Weisberg

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Evolution of the Loop Current System during the Deepwater Horizon Oil Spill Event as Observed with Drifters and Satellites, Yonggang Liu, Robert H. Weisberg, Chuanmin Hu, Charles C. Kovach, and Rolf R. Riethmüller

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Combining Numerical Ocean Circulation Models with Satellite Observations in a Trajectory Forecast System: a Rapid Response to the Deepwater Horizon Oil Spill, Yonggang Liu, Robert H. Weisberg, Chuanmin Hu, and Lianyuan Zheng

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Satellites, Models Combine to Track Deepwater Horizon Oil Spill, Yonggang Liu, Robert H. Weisberg, Chuanmin Hu, and Lianyuan Zheng

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Tracking the Deepwater Horizon Oil Spill: a Modeling Perspective, Yonggang Liu, Robert H. Weisberg, Chuanmin Hu, and Lianyuan Zheng

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Trajectory Forecast as a Rapid Response to the Deepwater Horizon Oil Spill, Yonggang Liu, Robert H. Weisberg, Chuanmin Hu, and Lianyuan Zheng

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Exploring the Diversity of Plant DNA Viruses and Their Satellites Using Vector-Enabled Metagenomics on Whiteflies, Terry Fei Fan Ng, Siobain Duffy, Jane Polston, Elise Bixby, Gary Vallad, and Mya Breitbart

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Metagenomic Identification of a Novel Anellovirus in Pacific Harbor Seal (Phoca vitulina richardsii) Lung Samples and its Detection in Samples from Multiple Years, Terry Fei Fan Ng, Elizabeth Wheeler, Denise Greig, Thomas Waltzek, Frances Gulland, and Mya Breitbart

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Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes, Terry Fei Fan Ng, Dana Willner, Yan Wei Lim, Robert Schmieder, Betty Chau, Christina Nilsson, Simon Anthony, Yijun Ruan, Forest Rohwer, and Mya Breitbart

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Exploring the Viral World Through Metagenomics, Karyna Rosario and Mya Breitbart

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Dragonfly Cyclovirus, a Novel Single-stranded DNA Virus Discovered in Dragonflies (Odonata: Anisoptera), Karyna Rosario, Milen Marinov, Daisy Stainton, Simona Kraberger, Elizabeth Wiltshire, David Collings, Matthew Walters, Darren Martin, Mya Breitbart, and Arvind Varsani

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Comparative Metagenomics of Microbial Traits Within Oceanic Viral Communities, Itai Sharon, Natalia Battchikova, Eva-Mari Aro, Carmela Giglione, Thierry Meinnel, Fabian Glaser, Ron Pinter, Mya Breitbart, Forest Rohwer, and Oded Be ́ja

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A Regional Testbed for Storm Surge and Coastal Inundation Models - an Overview, Y. P. Sheng, Justin R. Davis, Renato Figueiredo, Bin Liu, Huiqing Liu, Rick Luettich, Vladimir A. Paramygin, Robert Weaver, Robert H. Weisberg, Lian Xie, and Lianyuan Zheng

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Holocene Southern Ocean Surface Temperature Variability West of the Antarctic Peninsula, Amelia E. Shevenell, A. E. Ingalls, E. W. Domack, and C. Kelly

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Diversity of Virus–host Systems in Hypersaline Lake Retba, Senegal, Télesphore Sime‐Ngando, Soizick Lucas, Agnès Robin, Kimberly Pause Tucker, Jonathan Colombet, Yvan Bettarel, Elie Desmond, Simonetta Gribaldo, Patrick Forterre, Mya Breitbart, and David Prangishvili

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Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System, Connor Skennerton, Florent Angly, Mya Breitbart, Lauren Bragg, Shaomei He, Katherine McMahon, Philip Hugenholtz, and Gene Tyson

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Closed ranks in Oceanography, LuAnne Thompson, Renellys C. Perez, and Amelia E. Shevenell