| 2025 | "Effects of Riparian Forest Thinning on Resident Salmonid Fishes in Coastal Northern California Catchments" in Freshwater Biology |
| 2025 | "Contemporary evolution of neutral genetic structure in introduced Klamath smallscale suckers (Catostomus rimiculus) recapitulates native patterns" in Conservation Genetics |
| 2021 | "InSTREAM 7: Instream flow assessment and management model for stream trout" in River Research and Applications |
| 2021 | "All Fish, All the Time: A Good General Objective for Fish Passage Projects?" in Fisheries Magazine |
| 2021 | "Recent, small beginnings: genetic analysis suggests Catostomus rimiculus (Klamath smallscale sucker) in the Smith River, California, are introduced" in Journal of Fish Biology |
| 2021 | "Importance of the daily light cycle in population-habitat relations: a simulation study" in Transactions of the American Fisheries Society |
| 2021 | "The distribution of anadromy and residency in steelhead / rainbow trout in the Eel River, northwestern California" in California Fish and Wildlife Journal |
| 2020 | Modeling Populations Of Adaptive Individuals |
| 2020 | "Bridging levels from individuals to communities and ecosystems: Including adaptive behavior and feedbacks in ecological theory and models" in Bulletin of the Ecological Society of America |
| 2020 | "Contingent trade-off decisions with feedbacks in cyclical environments: testing alternative theories" in Behavioral Ecology |
| 2019 | "Predicting impacts of chemicals from organisms to ecosystem service delivery: a case study of endocrine disruptor effects on trout" in Science of the Total Environment |
| 2019 | "California roach (Hesperoleucus symmetricus) in the Eel River of northwestern California: native or introduced?" in Environmental Biology of Fishes |
| 2019 | "Mechanistic simulations predict that thermal and hydrological effects of climate change on Mediterranean trout cannot be offset by adaptive behaviour, evolution, and increased food production" in Science of the Total Environment |
| 2017 | "Axes of fear for stream fish: water depth and distance to cover" in Environmental Biology of Fishes |
| 2017 | "A framework for predicting impacts on ecosystem services from (sub)organismal responses to chemicals" in Environmental Toxicology and Chemistry |
| 2017 | "Response of Steelhead/Rainbow Trout (Oncorhynchus mykiss) populations to debris flows" in Northwest Science |
| 2016 | "Modeling potential river management conflicts between frogs and salmonids" in Canadian Journal of Fisheries and Aquatic Sciences |
| 2016 | "Use of streambed substrate as refuge by Oncorhynchus mykiss during simulated freshets" in Journal of Fish Biology |
| 2016 | "Use of cover for concealment behavior by rainbow trout: influences of cover structure and area" in North American Journal of Fisheries Management. |
| 2015 | "Effects of spatial extent on modeled relations between habitat and anadromous salmonid spawning success" in Transactions of the American Fisheries Society |
| 2015 | "Understanding anadromy as an individual adaptive behaviour: theory and its consequences. In: Sea Trout: Science & Management" in Proceedings of the 2nd International Sea Trout Symposium |
| 2014 | "Effects of streamflow diversion on a fish population: combining empirical data and individual-based models in a site-specific evaluation" in North American Journal of Fisheries Management |
| 2014 | "Feeding modes in stream salmonid population models: is drift feeding the whole story?" in Environmental Biology of Fishes |
| 2014 | "Facultative anadromy in salmonids: linking habitat, individual life history decisions, and population-level consequences" in Canadian Journal of Fisheries and Aquatic Sciences |
| 2013 | "Trait-mediated trophic interactions: is foraging theory keeping up?" in Trends in Ecology and Evolution |
| 2013 | "Contrast of degraded and restored stream habitat using an individual-based salmon model" in North American Journal of Fisheries Management |
| 2013 | "Seasonal and among-stream variation in predator encounter rates for fish prey" in Transactions of the American Fisheries Society |
| 2013 | "Local-scale invasion pathways and small founder numbers in introduced Sacramento pikeminnow (Ptychocheilus grandis)" in Conservation Genetics |
| 2013 | "Seasonal and Among-Stream Variation in Predator Encounter Rates for Fish Prey" in Transactions of the American Fisheries Society |
| 2012 | "Estimating migratory fish distribution from altitude and basin area: a case study in a larger Neotropical river" in Freshwater Biology |
| 2011 | "Estimating Multi-Factor Cumulative Watershed Effects on Fish Populations with an Individual-Based Model" in Fisheries Magazine |
| 2011 | "Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus)" in Ecology and Evolution |
| 2011 | "Historical occurrence of coho salmon (Oncorhynchus kisutch) in streams of the Santa Cruz Mountain region of California: response to an Endangered Species Act petition to delist coho salmon south of San Francisco Bay" in NOAA Technical Memorandum |
| 2011 | "Importance of fish behaviour in modelling conservation problems: food limitation as an example" in Journal of Fish Biology |
| 2011 | "Effects of passage barriers on demographics and stability properties of a virtual trout population" in River Research and Applications |
| 2010 | "Microbial enzyme activity, nutrient uptake and nutrient limitation in forested streams" in Freshwater Biology |
| 2010 | "Carcass Addition Does Not Enhance Juvenile Salmonid Biomass, Growth, or Retention in Six Northwestern California Streams" in North American Journal of Fisheries Management |
| 2009 | "The effect of deposited fine sediment on summer survival and growth of trout in riffles of a small stream" in North American Journal of Fisheries Management |
| 2009 | "Exploring the persistence of stream-dwelling trout populations under alternative real-world turbidity regimes with an individual-based model" in Transactions of the American Fisheries Society |
| 2009 | "InSTREAM: The Individual-Based Stream Trout Research and Environmental Assessment Model" in USDA Forest Service Pacific Southwest Research Station General Technical Report |
| 2009 | "Can remote high-resolution mapping help individual-based fish population models go up-scale?" in AGU Fall Meeting |
| 2008 | "Use of benthic prey by salmonids under turbid conditions in a laboratory stream" in Transactions of the American Fisheries Society |
| 2007 | "Winter feeding success of stream trout under different streamflow and turbidity conditions" in Transactions of the American Fisheries Society |
| 2007 | "Estimating multi-factor cumulative watershed effects on fish populations with an individual-based model" in Fisheries |
| 2006 | "Reduced Streamflow Lowers Dry-Season Growth of Rainbow Trout in a Small Stream" in Transactions of the American Fisheries Society |
| 2005 | "Effects of riparian canopy opening and salmon carcass addition on the abundance and growth of resident salmonids" in Canadian Journal of Fisheries and Aquatic Sciences |
| 2005 | "Tests of theory for diel variation in salmonid feeding activity and habitat use" in Ecology |
| 2005 | "Habitat specific biomass, survival and growth of trout (Oncorhynchus mykiss) during summer in a small coastal stream" in Canadian Journal of Fisheries and Aquatic Sciences |
| 2004 | "An emergent multiple predator effect may enhance biotic resistance in a stream fish assemblage" in Ecology |
| 2003 | "Basin-scale patterns in the drift of embryonic and larval fishes and lamprey ammocoetes in two coastal rivers" in Environmental Biology of Fishes |
