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1

Individual-Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: I. Model Description and Baseline Results

Rose, Kenneth A., Kimmerer, Wim J., Edwards, Karen P., Bennett, William A.

Journal:

Transactions of the American Fisheries Society

Year:

2013

Language:

english

File:

PDF, 1.12 MB

english, 2013

2

California's Yolo Bypass: Evidence that flood control Can Be compatible with fisheries, wetlands, wildlife, and agriculture

Sommer, Ted, Harrell, Bill, Nobriga, Matt, Brown, Randall, Moyle, Peter, Kimmerer, Wim, Schemel, Larry

Journal:

Year:

2001

Language:

english

File:

PDF, 1.06 MB

english, 2001

3

Bivalve grazing causes substantial mortality to an estuarine copepod population

Kimmerer, Wim J., Lougee, Laurence

Journal:

Journal of Experimental Marine Biology and Ecology

Year:

2015

Language:

english

File:

PDF, 477 KB

english, 2015

4

Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA

Ted R. Sommer, William C. Harrell, Anke Mueller Solger, Brad Tom, Wim Kimmerer

Journal:

Aquatic Conservation: Marine and Freshwater Ecosystems

Year:

2004

Language:

english

File:

PDF, 247 KB

english, 2004

5

Chronic food limitation of egg production in populations of copepods of the genusAcartiain the San Francisco estuary

Wim J. Kimmerer, Nissa Ferm, Mary Helen Nicolini, Carolina Peñalva

Journal:

Estuaries and Coasts

Year:

2005

Language:

english

File:

PDF, 186 KB

english, 2005

6

Projecting Cumulative Benefits of Multiple River Restoration Projects: An Example from the Sacramento-San Joaquin River System in California

G. Mathias Kondolf, Paul L. Angermeier, Kenneth Cummins, Thomas Dunne, Michael Healey, Wim Kimmerer, Peter B. Moyle, Dennis Murphy, Duncan Patten, Steve Railsback, Denise J. Reed, Robert Spies, Robert

Journal:

Environmental Management

Year:

2008

Language:

english

File:

PDF, 443 KB

english, 2008

7

Managing Water to Protect Fish: A Review of California’s Environmental Water Account, 2001–2005

Larry R. Brown, Wim Kimmerer, Randall Brown

Journal:

Environmental Management

Year:

2009

Language:

english

File:

PDF, 520 KB

english, 2009

8

Is the Response of Estuarine Nekton to Freshwater Flow in the San Francisco Estuary Explained by Variation in Habitat Volume?

Wim J. Kimmerer, Edward S. Gross, Michael L. MacWilliams

Journal:

Estuaries and Coasts

Year:

2009

Language:

english

File:

PDF, 591 KB

english, 2009

9

Short-Term and Interannual Variability in Primary Production in the Low-Salinity Zone of the San Francisco Estuary

Wim J. Kimmerer, Alexander E. Parker, Ulrika E. Lidström, Edward J. Carpenter

Journal:

Estuaries and Coasts

Year:

2012

Language:

english

File:

PDF, 1.00 MB

english, 2012

10

Reevaluating the Generality of an Empirical Model for Light-Limited Primary Production in the San Francisco Estuary

Alexander E. Parker, Wim J. Kimmerer, Ulrika U. Lidström

Journal:

Estuaries and Coasts

Year:

2012

Language:

english

File:

PDF, 540 KB

english, 2012

11

The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

Sommer, Ted, Armor, Chuck, Baxter, Randall, Breuer, Richard, Brown, Larry, Chotkowski, Mike, Culberson, Steve, Feyrer, Fredrick, Gingras, Marty, Herbold, Bruce, Kimmerer, Wim, Mueller-Solger, Anke, No

Journal:

Year:

2007

Language:

english

File:

PDF, 480 KB

english, 2007

12

Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR)

Mac Nally, Ralph, Thomson, James R., Kimmerer, Wim J., Feyrer, Frederick, Newman, Ken B., Sih, Andy, Bennett, William A., Brown, Larry, Fleishman, Erica, Culberson, Steven D., Castillo, Gonzalo

Journal:

Ecological Applications

Year:

2010

Language:

english

File:

PDF, 471 KB

english, 2010

13

Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary

Thomson, James R., Kimmerer, Wim J., Brown, Larry R., Newman, Ken B., Nally, Ralph Mac, Bennett, William A., Feyrer, Frederick, Fleishman, Erica

Journal:

Ecological Applications

Year:

2010

Language:

english

File:

PDF, 875 KB

english, 2010

14

Individual-Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: II. Alternative Baselines and Good versus Bad Years

Rose, Kenneth A., Kimmerer, Wim J., Edwards, Karen P., Bennett, William A.

Journal:

Transactions of the American Fisheries Society

Year:

2013

Language:

english

File:

PDF, 300 KB

english, 2013

15

Phytoplankton Growth Balanced by Clam and Zooplankton Grazing and Net Transport into the Low-Salinity Zone of the San Francisco Estuary

Kimmerer, Wim J., Thompson, Janet K.

Journal:

Estuaries and Coasts

Year:

2014

Language:

english

File:

PDF, 845 KB

english, 2014

16

Chronic Food Limitation of Egg Production in Populations of Copepods of the Genus Acartia in the San Francisco Estuary

Wim J. Kimmerer, Nissa Ferm, Mary Helen Nicolini and Carolina Peñalva

Journal:

Year:

2005

Language:

english

File:

PDF, 2.04 MB

english, 2005

17

Mate Limitation in an Estuarine Population of Copepods

Keun-Hyung Choi and Wim J. Kimmerer

Journal:

Limnology and Oceanography

Year:

2008

Language:

english

File:

PDF, 1.29 MB

english, 2008

18

Plasticity in Vertical Migration by Native and Exotic Estuarine Fishes in a Dynamic Low-Salinity Zone

William A. Bennett, Wim J. Kimmerer and Jon R. Burau

Journal:

Limnology and Oceanography

Year:

2002

Language:

english

File:

PDF, 987 KB

english, 2002

19

Long-Term Changes in Apparent Uptake of Silica in the San Francisco Estuary

Journal:

Limnology and Oceanography

Year:

2005

Language:

english

File:

PDF, 1.43 MB

english, 2005

20

Trophic Links in the Plankton in the Low Salinity Zone of a Large Temperate Estuary: Top-down Effects of Introduced Copepods

York, Joanna K., McManus, George B., Kimmerer, Wim J., Slaughter, Anne M., Ignoffo, Toni R.

Journal:

Estuaries and Coasts

Year:

2014

Language:

english

File:

PDF, 1.88 MB

english, 2014

21

Human-induced biotic invasions and changes in plankton interaction networks

Kratina, Pavel, Mac Nally, Ralph, Kimmerer, Wim J., Thomson, James R., Winder, Monika, Crispo, Erika

Journal:

Journal of Applied Ecology

Year:

2014

Language:

english

File:

PDF, 470 KB

english, 2014

22

Tidal migration and retention of estuarine zooplankton investigated using a particle-tracking model

Kimmerer, Wim J., Gross, Edward S., MacWilliams, Michael L.

Journal:

Limnology and Oceanography

Year:

2014

Language:

english

File:

PDF, 3.95 MB

english, 2014

23

Variability in Length–Weight Relationships Used to Estimate Biomass of Estuarine Fish from Survey Data

Kimmerer, Wim, Avent, Sean R., Bollens, Steven M., Feyrer, Fred, Grimaldo, Lenny F., Moyle, Peter B., Nobriga, Matt, Visintainer, Tammie

Journal:

Transactions of the American Fisheries Society

Year:

2005

Language:

english

File:

PDF, 226 KB

english, 2005

24

Mortality estimates of stage-structured populations must include uncertainty in stage duration and relative abundance

Kimmerer, Wim J.

Journal:

Journal of Plankton Research

Year:

2015

Language:

english

File:

PDF, 562 KB

english, 2015

25

Is the Response of Estuarine Nekton to Freshwater Flow in the San Francisco Estuary Explained by Variation in Habitat Volume?

Wim J. Kimmerer, Edward S. Gross and Michael L. MacWilliams

Journal:

Estuaries and Coasts

Year:

2009

Language:

english

File:

PDF, 2.38 MB

english, 2009

26

Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR)

Ralph Mac Nally, James R. Thomson, Wim J. Kimmerer, Frederick Feyrer, Ken B. Newman, Andy Sih, William A. Bennett, Larry Brown, Erica Fleishman, Steven D. Culberson and Gonzalo Castillo

Journal:

Ecological Applications

Year:

2010

Language:

english

File:

PDF, 2.09 MB

english, 2010

27

Dietary Segregation of Pelagic and Littoral Fish Assemblages in a Highly Modified Tidal Freshwater Estuary

Grimaldo, Lenny F., Stewart, A. Robin, Kimmerer, Wim

Journal:

Marine and Coastal Fisheries Dynamics Management and Ecosystem Science

Year:

2009

Language:

english

File:

PDF, 430 KB

english, 2009

28

Mate limitation in an estuarine population of copepods

Choi, Keun-Hyung, Kimmerer, Wim J.

Journal:

Limnology and Oceanography

Year:

2008

Language:

english

File:

PDF, 397 KB

english, 2008

29

Long-term changes in apparent uptake of silica in the San Francisco estuary

Journal:

Limnology and Oceanography

Year:

2005

Language:

english

File:

PDF, 125 KB

english, 2005

30

Plasticity in vertical migration by native and exotic estuarine fishes in a dynamic low-salinity zone

Bennett, William A., Kimmerer, Wim J., Burau, Jon R.

Journal:

Limnology and Oceanography

Year:

2002

Language:

english

File:

PDF, 942 KB

english, 2002

31

A Bayesian approach to estimating copepod development times from stage frequency data

Kimmerer, Wim, Gould, Alison

Journal:

Limnology and Oceanography Methods

Year:

2010

Language:

english

File:

PDF, 1.05 MB

english, 2010

32

Perils of correlating CUSUM-transformed variables to infer ecological relationships (Breton et al. 2006; Glibert 2010)

Cloern, James E., Jassby, Alan D., Carstensen, Jacob, Bennett, William A., Kimmerer, Wim, Mac Nally, Ralph, Schoellhamer, David H., Winder, Monika

Journal:

Limnology and Oceanography

Year:

2012

Language:

english

File:

PDF, 246 KB

english, 2012

33

[American Society of Civil Engineers Ninth International Conference on Estuarine and Coastal Modeling - Charleston, South Carolina, United States (October 31 -September 2, 2005)] Estuarine and Coastal Modeling (2005) - Simulating Periodic Stratification in the San Francisco Estuary

Gross, Edward S., MacWilliams, Michael L., Kimmerer, Wim

Year:

2006

Language:

english

File:

PDF, 2.13 MB

english, 2006

34

Feeding capabilities and limitations in the nauplii of two pelagic estuarine copepods, Pseudodiaptomus marinus and Oithona davisae

Vogt, Robert A., Ignoffo, Toni R., Sullivan, Lindsay J., Herndon, Julian, Stillman, Jonathon H., Kimmerer, Wim J.

Journal:

Limnology and Oceanography

Year:

2013

Language:

english

File:

PDF, 1.21 MB

english, 2013

35

Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary

James R. Thomson, Wim J. Kimmerer, Larry R. Brown, Ken B. Newman, Ralph Mac Nally, William A. Bennett, Frederick Feyrer and Erica Fleishman

Journal:

Ecological Applications

Year:

2010

Language:

english

File:

PDF, 3.36 MB

english, 2010

36

Prey selection of larval and juvenile planktivorous fish: impacts of introduced prey

Sullivan, Lindsay J., Ignoffo, Toni R., Baskerville-Bridges, Bradd, Ostrach, David J., Kimmerer, Wim J.

Journal:

Environmental Biology of Fishes

Year:

2016

Language:

english

File:

PDF, 501 KB

english, 2016

37

Structure and Flow-Induced Variability of the Subtidal Salinity Field in Northern San Francisco Bay

Monismith, Stephen G., Kimmerer, Wim, Burau, Jon R., Stacey, Mark T.

Journal:

Journal of Physical Oceanography

Year:

2002

Language:

english

File:

PDF, 580 KB

english, 2002

38

The Molecular Ecology of Microcystis sp. Blooms in the San Francisco Estuary Delta

Otten, Timothy G., Paerl, Hans W., Dreher, Theo W., Kimmerer, Wim J., Parker, Alex E.

Journal:

Environmental Microbiology

Year:

2017

Language:

english

File:

PDF, 1.46 MB

english, 2017

39

Effects of freshwater flow and phytoplankton biomass on growth, reproduction, and spatial subsidies of the estuarine copepod Pseudodiaptomus forbesi

Kimmerer, Wim J., Ignoffo, Toni R., Kayfetz, Karen R., Slaughter, Anne M.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.12 MB

english, 2018

40

Individual-Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary III. Effects of Entrainment Mortality and Changes in Prey

Kimmerer, Wim J., Rose, Kenneth A.

Journal:

Transactions of the American Fisheries Society

Year:

2018

Language:

english

File:

PDF, 771 KB

english, 2018

41

Spatial Subsidies and Mortality of an Estuarine Copepod Revealed Using a Box Model

Kimmerer, Wim J., Gross, Edward S., Slaughter, Anne M., Durand, John R.

Journal:

Estuaries and Coasts

Year:

2018

Language:

english

File:

PDF, 1.52 MB

english, 2018

42

In situ ingestion of Microcystis is negatively related to copepod abundance in the upper San Francisco Estuary

Ger, Kemal Ali, Otten, Timothy G., DuMais, Rita, Ignoffo, Toni, Kimmerer, Wim

Journal:

Limnology and Oceanography

Year:

2018

Language:

english

File:

PDF, 581 KB

english, 2018

43

Effect of ocean acidification on the nutritional quality of marine phytoplankton for copepod reproduction

Meyers, Morgan T., Cochlan, William P., Carpenter, Edward J., Kimmerer, Wim J., Melzner, Frank

Journal:

Year:

2019

Language:

english

File:

PDF, 1.22 MB

english, 2019

44

Effect of ocean acidification on the nutritional quality of marine phytoplankton for copepod reproduction

Meyers, Morgan T., Cochlan, William P., Carpenter, Edward J., Kimmerer, Wim J., Melzner, Frank

Journal:

Year:

2019

File:

PDF, 1.22 MB

2019

45

Miczooplankton dynamics in the low salinity zone of the San Francisco Estuary

McManus, George B., York, Joanna K., Kimmerer, Wim J.

Journal:

SIL Proceedings, 1922-2010

Year:

2008

Language:

english

File:

PDF, 879 KB

english, 2008

46

Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses

Kimmerer, Wim J.

Journal:

San Francisco Estuary and Watershed Science

Year:

2004

File:

PDF, 2.09 MB

2004

47

Food Webs of the Delta, Suisun Bay, and Suisun Marsh: An Update on Current Understanding and Possibilities for Management

Brown, Larry, Kimmerer, Wim, Conrad, J. Louise, Lesmeister, Sarah, MuellerâSolger, Anke

Journal:

San Francisco Estuary and Watershed Science

Year:

2016

File:

PDF, 1.43 MB

2016

48

High growth rates of a dominant calanoid copepod in the northern San Francisco Estuary

Owens, Stephanie, Ignoffo, Toni R, Frantzich, Jared, Slaughter, Anne, Kimmerer, Wim

Journal:

Journal of Plankton Research

Year:

2019

File:

PDF, 212.09 MB

2019

49

Fine-Scale Distributions of Zooplankton in the Northern San Francisco Estuary

Kimmerer, Wim, Slaughter, Anne

Journal:

San Francisco Estuary and Watershed Science

Year:

2016

File:

PDF, 1.50 MB

2016

50

The Role of Tidal Marsh Restoration in Fish Management in the San Francisco Estuary

Herbold, Bruce, Baltz, Donald M., Brown, Larry, Grossinger, Robin, Kimmerer, Wim, Lehman, Peggy, Moyle, Peter B., Nobriga, Matt, Simenstad, Charles A.

Journal:

San Francisco Estuary and Watershed Science

Year:

2014

File:

PDF, 192 KB

2014