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Baker, Peter F. and J. Emil Morhardt. 2001. Survival of chinook salmon smolts in the Sacramento-San Joaquin Delta and Pacific Ocean. In: Brown, Randall L. (ed). Contributions to the biology of central valley salmonids. Fish Bulletin 179. California Department of Fish and Game. Sacramento, California. Vol.2, 163--182. PDF

Bauer, S. and S. Ralph. 2001. Strengthening the use of aquatic habitat indicators in Clean Water Act Programs. Fisheries 26:14-25.

Bauer, S. and S. Ralph. 1999. Aquatic Habitat Indicators and their application to Water Quality Objectives within the Clean Water Act. Idaho Water Resources Research Institute, University of Idaho, and EPA Region 10. EPA 910-R-99-014. Seattle, WA

Bell, E. and W. Duffy. 2007. Previously undocumented two-year freshwater residency of juvenile coho salmon in Prairie Creek, California. Transactions of the American Fisheries Society 136: 996-970. PDF

Bell, E. 2001. Survival, growth and movement of juvenile coho salmon (Oncorhynchus kisutch) over-wintering in alcoves, backwaters, and main channel pools in Prairie Creek, California. Master's thesis. Humboldt State University, Arcata, California.

Bell, E., W. G. Duffy, and T. D. Roelofs. 2001. Fidelity and survival of juvenile coho salmon in response to a flood. Transactions of the American Fisheries Society 130: 450-458. PDF

Braudrick, C. A. and G.E. Grant. 2001. Transport and deposition of large wood debris in streams: A flume experiment. Geomorphology. 41: 263-283.

Caruso, B. S., and P. W. Downs. 2007. Rehabilitation and flood management planning in a steep, boulder-bedded stream. Environmental Management 40: 256-271. PDF

Conquest, L. L., S. C. Ralph, and R. J. Naiman. 1994. Implementation of large-scale stream monitoring efforts: sampling design and data analysis issues. In: Biological Monitoring of Aquatic Systems, S. L. Loeb and A. Spacie (eds.). Lewis Publishers, Boca Raton, Florida.

Conquest, L. L. and S. C. Ralph. 1998. Design considerations for large scale aquatic monitoring efforts. In: Naiman, R. J., R. E. Bilby (eds.), River Ecology and Management: Lessons from the Pacific Coastal Ecoregion. Springer-Verlag, New York.

Cui, Y. 2007. The Unified Gravel-Sand (TUGS) model: simulating sediment transport and gravel/sand grain size distributions in gravel-bedded rivers. Water Resources Research 43: W10436, doi:10.1029/2006WR005330. PDF

Cui, Y. 2007. Examining the dynamics of grain size distributions of gravel/sand deposits in the Sandy River, Oregon with a numerical model. River Research and Applications 23: 732-751. PDF

Cui, Y., G. Parker, C. Braudrick, W. Dietrich, and B. Cluer. 2006. Dam Removal Express Assessment Models (DREAM). Part 1: model development and validation. International Association of Hydraulic Engineering and Research 44: 231-307.

Cui, Y., C. Braudrick, W. Dietrich, B. Cluer, and G. Parker. 2006. Dam Removal Express Assessment Models (DREAM). Part 2: sample runs/ sensitivity tests. International Association of Hydraulic Engineering and Research 44: 308-323.

Cui, Y., Braudrick, B, Dietrich, W.E., Cluer, G., and Parker, G., in preparation, Dam Removal Express Assessment Models (DREAM). Part 2: Sample runs/sensitivity tests, Journal of Hydraulic Research, IAHR. PDF

Cui, Y. and Parker, G. Submitted. Numerical model of sediment pulses and sediment supply disturbances in mountain rivers, Journal of Hydraulic Engineering, ASCE. PDF.

Cui, Y., Parker, G., Braudrick, C., Dietrich, W.E., and Cluer, B. In preparation. Dam Removal Express Assessment Models (DREAM). Part 1: Model development and validation, Journal of Hydraulic Research, IAHR. PDF.

Cui, Y., Parker, G., Lisle, T.E., Gott, J. Hansler-Ball, M.E., Pizzuto, J.E., Allmendinger, N.E., and Reed, J.M. 2003a. Sediment pulses in mountain rivers: 1. Experiments. Water Resources Research, 39(9), 1239, doi: 10.1029/2002WR001803.

Cui, Y., Parker, G., Pizzuto, J., and Lisle, T.E. 2003b. Sediment pulses in mountain rivers: 2. Comparison between experiments and numerical predictions. Water Resources Research, 39(9), 1240, doi: 10.1029/2002WR001805.

Cui, Y. and A.C. Wilcox. in press. Development and Application of Numerical Modeling of Sediment Transport Associated with Dam Removal. in Garcia, M.H., ed., Sedimentation Engineering, ASCE Manual 54 (II), accepted. PDF

Dietrich, W.E., D. Bellugi, and R. Real de Asua. 2001. Validation of the shallow landslide model, SHALSTAB, for forest management. Land Use and Watersheds: Human Influence on Hydrology and Geomorphology in Urban and Forest Areas. American Geophysical Union: Water Science and Application 2: 195-227.

Dietrich, W. E., R. Real de Asua, J. Coyle, B. K. Orr, and M. Trso. 1998. A validation study of the shallow slope stability model, SHALSTAB, in forested lands of northern California. Prepared for Louisiana-Pacific Corporation by Department of Geology and Geophysics, University of California, Berkeley and Stillwater Ecosystem, Watershed & Riverine Sciences, Berkeley, California.

Downs, P. W., and J. D. Stallman. 2005. Sediment budgets as the basis for restoration planning in non-equilibrium environments: Redwood Creek, Marin County, California. Northwest Stream Restoration Design Symposium, Stevenson, Washington.

Downs, P. W., and J. D. Stallman. 2005. Sequential sediment budgets in an ungauged watershed: Redwood Creek, Marin County, California. American Geophysical Union, Fall Meeting, San Francisco, California.

Downs, P.W. 2001. Geomorphological evaluation of river restoration schemes: principles, method, monitoring, assessment, evaluation. Progress?, in Nijland, H.J. and Cals, M.J.R. (eds) River Restoration in Europe: practical approaches, Lelystad, The Netherlands, Institute for Inland Water Management and Waste Water Treatment / RIZA. pp.243-249.

Downs, P.W. and Gregory, K. 2004. River Channel Management: Towards Sustainable Catchment Hydrosystems. Hodder & Stoughton Educational. 256 p. Link to publisher.

Downs, P.W. and Kondolf, G.M. 2002. Post-project appraisals in adaptive management of river channel restoration, Environmental Management, 29, 477-496.

Downs, P.W., Kondolf, G.M. and Skinner, K.S. 2002, in press. Rivers and streams, in Davy, A.J. and Perrow, M.R. (eds.) Handbook of Ecological Restoration, Cambridge, Cambridge University Press.

Downs, P.W. and Priestnall, G. 1999. System design for catchment-scale approaches to studying river channel adjustments using a GIS, International Journal of Geographical Information Systems 13, 3, 247-266.

Downs, P.W. and Priestnall, G. 2003. Modelling catchment processes, for Kondolf, G.M. and Piegay, H. (eds.) Methods in Fluvial Geomorphology, J. Wiley & Sons, pp. 203-228.

Downs, P.W. and Simon, A. 2001. Fluvial geomorphological analysis of the recruitment of large woody debris in Yalobusha river network, central Mississippi, USA, Geomorphology, 37, 65-91.

Downs, P.W. and Thorne, C.R. 1998. Design principles and suitability testing for rehabilitation in a flood defence channel: the River Idle, Nottinghamshire, U.K. Aquatic Conservation: marine and freshwater ecosystems, 8, 17-38.

Downs, P.W. and Thorne, C.R. 2000. Rehabilitation of a lowland river: reconciling flood defence with habitat diversity and geomorphological sustainability, Journal of Environmental Management, 58, 249-268.

Finlay, J.C., Khandwala, S., and M.E. Power. 2002. Spatial Scales of Carbon Flow in a River Food Web. Ecology 83 (7): 1845-1859.

Frissell, C. A. and S. C. Ralph. 1998. Watershed Restoration. In: Naiman, R. J., R. E. Bilby (eds.), River Ecology and Management: Lessons from the Pacific Coastal Ecoregion. Springer-Verlag, New York.

Howald, A.M. and B.K. Orr. 2000. A flora of Valentine Eastern Sierra Reserve. The Herbarium, Museum of Systematics and Ecology (MSE), University of California, Santa Barbara, Publication No. 1, Second Edition (MSE Environmental Report Number 16). PDF

Kramer, S.H., M.Trso, and N.P. Hume. 2001. Timber Harvest and Sediment Loads in Nine Northern California Watersheds Based on Recent Total Maximum Daily Load (TMDL) Studies. Watershed Management Council Networker 10 (1): 1, 17-24. PDF

Kramer, S. H. and R. Klein. 2000. The change in distribution and role of large woody debris in Upper Prairie Creek, a pristine Northern California redwood watershed, after a 10 year flood event. The International Symposium on Large Wood in Rivers, Corvallis, Oregon. October 2000. PDF

Ligon, F.K., A. Rich, G. Rynearson, D. Thornburgh, and W. Trush. 1999. Report of the Scientific Review Panel on California Forest Practice Rules and Salmonid Habitat. Prepared for The Resources Agency of California and the National Marine Fisheries Service. Sacramento, California. PDF

Lisle, T.E., Cui, Y., Parker, G., Pizzuto, J.E. and Dodd, A.M., 2001. The dominance of dispersion in the evolution of bed material waves in gravel bed rivers. Earth Surface Processes and Landforms, 26, 1409-1420

Naiman, R. J., D. G. Lonzarich, T. J. Beechie, and S. C. Ralph. 1992. General principles of classification and the assessment of conservation potential in rivers. In: River Conservation and Management, Boon, Calow and Petts (eds.), John Wiley & Sons Ltd.

Olson & Orr 1999. Combining tree growth, fish and wildlife habitat, mass wasting, sedimentation, and hydrologic models in decision analysis and long-term forest land planning. Forest Ecology and Management 114: 339-348. PDF

Orr, B.K. 1997. Use of a regional watershed analysis approach in long-term forest management planning in California. Watershed Management Council Networker 7(3): 1, 4-6, 13. PDF

Pedersen, D., J. D. Stallman, and M. R. Sloat. 2006. Low elevation aerial photography (LEAP) in riverine settings. HydroVision, Portland, Oregon.

Poole, G. C., C. A. Frissell, and S. C. Ralph. 1997. In-stream habitat unit classification: inadequacies for monitoring and some consequences for management. Journal of the American Water Resources Association 33:879-896.

Ralph, S. C. and G. C. Poole. (2003). Putting monitoring first: Designing accountable ecosystem restoration and management plans. In, Montgomery D. R. , S. Bolton and D. B. Booth (eds.) Restoration of Puget Sound Rivers. University of Washington Press, Seattle, WA.

Ralph, S. C., G. C. Poole, L. L. Conquest, and R. J. Naiman. 1994. Stream channel morphology and woody debris in logged and unlogged basins of Western Washington. Canadian Journal of Fisheries and Aquatic Sciences 51:37-51.

Ralph, S. C., T. Cardoso, G. C. Poole, L. L. Conquest and R. J. Naiman. 1991. Status and trends of instream habitat in forested lands of Washington: The Timber-Fish-Wildlife Ambient Monitoring Project - 1989-1991 Biennial Progress Report. University of Washington, Center for Streamside Studies report to the Washington Department of Natural Resources, Olympia, WA.

Ralph, S. C. 1990. Timber-Fish-Wildlife Stream Ambient Monitoring Field Manual Ver. 2.0. Center for Streamside Studies, University of Washington, Seattle. Report to the TFW Coordinated Monitoring, Evaluation and Research Committee.

Ralph, S. C. 1992. Logging: The Washington State Situation. EPA Journal Vol. 17- 5, Environmental Protection Agency, Washington D.C.

Ralph, S. C. 1977. In the ditch or on the road? An overview on the impacts of highway rights-of-way management on wildlife conservation. Conservation Journal, Vol. 4, No. 3, National Wildlife Federation, Washington D.C.

Ralph, S. C. 1980. Wintering bald eagle census along the main stream Skagit River, Washington, 1979-80. Proceedings of the Washington Bald Eagle Symposium, June 14-15, 1980. Seattle, WA.

Ralph, S. C., W. H. Ryan, and R. LaRock. 1994. Skagit Wild & Scenic River Water Resource Monitoring Plan. Report prepared by Natural Resources Consultants (Seattle) and the Skagit System Cooperative for EPA Region 10 (Seattle) and the USFS, Mt. Baker Snoqualmie National Forest, Lynnwood, WA.

Ralph, S. C. and G. Ruggerone. 1994. Initial water quality assessment of the upper Hood Canal Watershed. Report prepared by Natural Resources Consultants Inc., submitted to the Kitsap County Department of Community Development, Port Orchard, WA.

Ralph, S.C., N.P. Peterson, and C.M. Mendoza. 1994. An inventory of off channel habitat of the lower Chehalis River with applications of remote sensing. Natural Resource Consultants, Inc., Seattle, WA.

Stallman, J. D., R. J. Bowers, N. C. Cabrera, R. Real de Asua, and J. K. Wooster. 2005. Sediment dynamics in the upper McKenzie River basin, central Oregon Cascade Range. American Geophysical Union, Fall Meeting, San Francisco, California.

Stallman, J. D., C. A. Braudrick, D. T. Pedersen, Y. Cui, L. Sklar, W. E. Dietrich, and R. Real de Asua. 2004. Geomorphic effects of boulder placement on gravel capture and retention in a regulated reach of the North Umpqua River, Oregon. American Geophysical Union, Fall Meeting, San Francisco, California.

Stallman, J. D., and K. T. Andrus. 2002. Applying GIS-based residual contouring to landscape evolution studies in the Mendocino triple junction and southern Cascadia forearc regions, northern California. Geological Society of America Cordilleran Section Meeting, Corvallis, Oregon.

Stella, J. C., J. J. Battles, B. K. Orr, and J. R. McBride. 2006, in press. Synchrony of seed dispersal, hydrology, and local climate in a semi-arid river reach in California. Ecosystems.

Stella, J. C. 2005. A field-calibrated model of pioneer riparian tree recruitment for the San Joaquin Basin, CA. Ph.D. Dissertation. University of California, Berkeley, Berkeley, California. PDF

Stella, J. C., J. C. Vick, and B. K. Orr. 2003. Riparian vegetation dynamics on the Merced River. Pages 302-314 in P. M. Faber, editor. California riparian systems: processes and floodplains management, ecology, and restoration. Riparian habitat and floodplains conference proceedings. 12-14 March 2001. The Wilderness Society, Sacramento, California. PDF

Wood, A.L., Simon, A., Downs, P.W., and Thorne, C.R. 2001. Bank-Toe Processes in Incised channels: The Contribution of Apparent Cohesion in Impeding Removal of Failed Cohesive Blocks. Hydrological Processes, 15, 39-61.