Author Title Journal Date
1 Patricia M. Glibert Long-Term Changes in Nutrient Loading and Stoichiometry and their relationships with the changes in the food web and dominant pelagic fish species in the San Francisco Estuary, California Reviews in Fisheries Science 


2 Winder, M. and A.D. Jassby Shifts in zooplankton community structure: Implications for food web processes in the Upper San Francisco Estuary. Estuaries and Coasts.


3 Melissa R. Baerwald, Gregg Schumer, Brian Schreier, and Bernie May TaqMan assays for the genetic identification of delta smelt (Hypomesus transpacificus) and wakasagi smelt (Hypomesus nipponensis). Molecular Ecology Resources


4 William J. Miller Revisiting Assumptions that underlie Estimates of Proportional EnTrainment of Delta Smelt by State and Federal Water Diversions from the Sacramento-San Joaquin Delta San Francisco Estuary & Watershed Science


5 Patricia M. Glibert and JoAnn Burkholder Harmful algal blooms and eutrophication: “strategies” for nutrient uptake and growth outside the Redfield comfort zone Chinese Journal of Oceanology and Limnology 


6 Mark N. Maunder and Richard B. Deriso A state–space multistage life cycle model to evaluate population impacts in the presence of density dependence: illustrated with application to delta smelt (Hyposmesus transpacificus) Canadian Journal of Fisheries and Aquatic Sciences


7 Joseph E. Merz, Scott hamilton, Paul S. Berbman, Bradley Cavallo Spatial perspective for delta smelt: a summary of contemporary survey data California Fish and Game


8 Patricia M. Glibert, David Fullerton, Joann M. Burkholder, Jeffery C. Cornwell, Todd M. Kana Ecological Stoichiometry, Biogeochemical Cycling, Invasive Species, and Aquatic Food Webs: San Francisco Estuary and Comparative Systems Reviews in Fisheries Science


9 Resource Management Associates Modeling the Fate and Transport of Nutrients using DSM2: Calibration/Validation Report  


10 William J. Miller, Bryan F. J. Manly, Dennis D. Murphy, David Fullerton, Rob Roy Ramey An Investigation of Factors Affecting the Decline of Delta Smelt (Hypomesus transpacificus) in the Sacramento-San Joaquin Estuary Reviews in Fisheries Science


11 Steven C. Zeug, Paul S. Bergman, Bardley J. Cavallo, Kristopher S. Jones Application of a Life Cycle Simulation Model to Evaluate Impacts of Water Management and Conservation Actions on an Endangered Population of Chinook Salmon Environmental Modeling & Assessing


12 Patricia M. Glibert, J.M. Burkholder, and T.M. Kana Recent advances in understanding of relationships between nutrient availability, forms and stoichiometry and the biogeographical distribution, ecophysiology, and food web effects of pelagic and benthic Prorocentrum spp. Harmful Algae


13 Parker AE, Dugdale RC, Wilkerson FP Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary. Marine Pollution Bulletin


14 Christiane Lancelot, Philippe Grosjean, Ve’ronique Rousseau, Elsa Breton, and Patricia M. Glibert Rejoinder to ‘‘Perils of correlating CUSUM-transformed variables to infer ecological relationships (Breton et al. 2006; Glibert 2010)’’ Limnol. Oceanogr,. 


15 Alexander E. Parker, Victoria E. Hogue, Frances P. Wilkerson, Richard C. Dugdale The effect of inorganic nitrogen speciation on primary production in the San Francisco Estuary Estuarine, Coastal and Shelf Science Apr-12
16 Patricia M. Glibert Ecological stoichiometry and its implications for aquatic ecosystem sustainability Current Opinion in Environmental Sustainability


17 Brian J. Pyper, Steven P. Cramer, Randolph P. Ericksen, Richard M. Sitts Implications of Mark-Selective Fishing for Ocean Harvests and Escapements of Sacramento River Fall Chinook Salmon Populations Marine and Coastal Fisheries: Dynamics, Management,
and Ecosystem Science


18 James Orlando (contributing author) Current Use Pesticides 2012 Pulse of the Delta


19 Melissa R. Baerwald, Gregg Schumer, Brian Schreier, and Bernie May Detection of Threatened Delta Smelt in the Gut Contents of the Invasive Mississippi Silverside in the San Francisco Estuary Using TaqMan Assays Transactions of the American Fisheries Society


20 Patricia M. Glibert, TM Kana, and K Brown. From limitation to excess: the consequences of substrate excess and stoichiometry for phytoplankton physiology, trophodynamics and biogeochemistry, and the implications for modeling. Journal of Marine Systems,


21 Dugdale RC, Wilkerson FP, Parker AE, Marchi A, Taberski K River flow and ammonium discharge determine spring phytoplankton blooms in an urbanized estuary. Estuarine, Coastal and Shelf Science


22 Bradley Cavallo, Joseph Merz, Jose Setka Effects of predator and flow manipulation on Chinook salmon (Oncorhynchus tshawytscha) survival in an imperiled estuary Environmental Biology of Fishes


23 Patricia M. Glibert, Deborah C. Hinkle, Brian Sturgis, Roman V. Jesien Eutrophication of a Maryland/Virginia Coastal Lagoon: a Tipping Point, Ecosystem Changes, and Potential Causes Estuaries and Coasts


24 Dugdale, R.C., Wilkerson, F.P., Parker, A.E. A biogeochemical model of phytoplankton productivity in an urban estuary: the importance of ammonium and freshwater flow Ecological Modeling


25 Fredrick Feyrer, Donald Portz, Darren Odum, Ken B. Newman, Ted Sommer, Dave Contreras, Randall Baxter, Steven B. Slater, Deanna Sereno, Erwin Van Nieuwenhuyse SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the distribution of the Imperiled Delta Smelt PLOS ONE 


26 Joseph E. Merz, Paul S. Bergman, Jenny F. Melgo, and Scott Hamilton Longfin Smelt: spatial dynamics and ontogeny in the San Francisco Estuary, California California Fish and Game 99(30: 122-148; 2013


27 Orlando, J.L., McWayne, Megan, Sanders, Corey, and Hladik, Michelle, Dissolved pesticide concentrations in the Sacramento-San Joaquin Delta and Grizzly Bay, California, 2011–12 U.S. Geological Survey Data Series


28 Dennis Murphy and Scott Hamilton Eastward migration or marsh-ward dispersal: understanding seasonal movements by delta smelt San Francisco Estuary & Watershed Science


29 Valerie Connor Leading Change: The Collaborative Science and Adaptive Management Program San Francisco Estuary & Watershed Science


30 Cornwell, J.C., P.M. Glibert, and M. Owens Nutrient fluxes from the benthic productivity in sediments of the San Francisco Bay Delta Estuaries and Coasts


31 LM Komoroske, RE Connon, BS Cheng, G Castillo, M Hasenbein, J Lindberg, NA Fangue Ontogeny influences sensitivity to climate change stressors in an endangered fish Conservation Biology


32 Patricia M. Glibert, Richard C. Dugdale, Frances Wilkerson, Alexander E. Parker, Jeffrey Alexander, Edmund Antell, Sarah Blaser, Allison Johnson, Jamie Lee, Tricia Lee, Sue Murasko, Shannon Strong Major-but rare- spring blooms in 2014 in San Francisco Bay Delta, California, a result of the long-term drought, increased residence time, and altered nutrient loads and forms Journal of Experimental Marine Biology and Ecology


33 Patricia M. Glibert, Frances P. Wilkerson, Richard C. Dugdale Alexander E. Parker, Jeffrey Alexander, Sarah Blaser, and Susan Murasko Phytoplankton communities from San Francisco Bay Delta respond differently to oxidized and reduced nitrogen substrates– even under conditions that would otherwise suggest nitrogen sufficiency Frontiers in Marine Science


34 James Orlando, Megan McWayne, Corey Sanders, and Michelle Hladik Dissolved Pesticide Concentrations Entering the Sacramento-San Joaquin Delta from the Sacramento and San Joaquin Rivers, California, 2012-13 USGS Data Series 876


35 Bencic, David C.; Biales, Adam D.; Fritsch, Erika; Connon, Richard; Schoenfuss, Heiko; Wang, Rong-Lin; Versteeg, Donald; Naciff, Jorge Real world application of ‘omics endpoints Perspectives: Environmental Toxicology and Chemistry


36 Simone Hasenbein, Sharon P Lawler, Juergen Geist, Richard E. Connon The use of growth and behavioral endpoints to assess the effects of pesticide mixtures upon aquatic organisms Ecotoxicology


37 Simone Hasenbein, Richard E. Connon, Sharon P. Lawler, and Juergen Geist A comparison of the sublethal and lethal toxicity of four pesticides in Hyalella azteca and Chironomus dilutus Environmental Science and Pollution Research


38 Ken M. Jeffries, Susanne M. Brander, Monica T. Britton, Nann A. Fangue, Richard E. Connon Chronic Exposures to Low and High Concentrations of Ibuprofen Elicit Different Gene Response Patterns in a Euryhaline Fish. Environmental Science and Pollution Research Environmental Science and Pollution Research


39 Lindsay Correa, Peter Goodwin, Valerie Connor, & Leo Winternitz Science and Technology As A Guide: Moving from Combat to Collaboration HyrdoLink


40 Adam D. Biales, Erika B. Fritsch, Richard E. Connon In Response: Integration of ‘omics to larger-scale watershed assessments: A mixed government/academic perspective Environmental Toxicology and Chemistry


41 Hasenbein S, Lawler SP, Geist J and Connon RE The use of growth and behavioral endpoints to assess the effects of pesticide mixtures upon aquatic organisms Environmental Toxicology and Chemistry


42 Ken M. Jeffries, Komoroske LM, Truong J, Werner I, Hasenbein M, Hasenbein S, Fangue NA, Connon RE The transcriptome-wide effects of exposure to a pyrethroid pesticide on the critically endangered delta smelt (Hypomesus transpacificus) Environmental Toxicology and Chemistry


43 Hasenbein M, Fangue NA, Geist J, Komoroske LA, Connon RE Physiological stress biomarkers reveal stocking density effects in late larval delta smelt (Hypomesus transpacificus) Journal of Aquaculture


44 S Hasenbein, K Callinan Hoffmann, SP Lawler, RE Connon, LA Deanovic, S Fong, I Werner, AK Miles, SJ Teh, J Geist The comparative toxicity of four pesticides in Hyalella azteca and Chironomus dilutus Environmental Science and Pollution Research


45 LM Komoroske, RE Connon, KM Jeffries, and NA Fangue Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish Molecular Ecology


46 Patricia M. Glibert, Frances P. Wilkerson, Richard C. Dugdale, John A Raven, Christopher L. Dupont, Peter R, Leavitt, Alexander E. Parker, JoAnn M. Burkholder, Todd M. Kana Pluses and minuses of ammonium and nitrate uptake and assimilation by phytoplankton and implications for productivity and community composition, with emphasis on nitrogen enriched conditions Limnology and Oceanography


46 Brown LR, Komoroske LM, Wagner RW, Morgan-King T, Connon RE, May JT, Fangue NA Making climate change projections on management relevant scales: Coupling local-scale models with physiological tolerance forecasts severe habitat contraction for an endangered fish PLoS ONE