Institute for Applied Marine Ecology and Monterey Bay National Marine Sanctuary. 2011. Characterizing the Deep: Surveys in the Monterey Bay National Marine Sanctuary 2007-2010. 14pp.

Lindholm, J., A. Knight, and M. Domeier. 2010. Gender-mediated patterns in the movement of California sheephead in the northern Channel Islands (Eastern Pacific). California Department of Fish and Game Journal 96:53-68.

Lindholm, J., and R. Pavia (eds). 2010. Examples of ecosystem-based management in national marine sanctuaries: moving from theory to practice. Marine Sanctuaries Conservation Series ONMS-10-02. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring,MD. 33pp.

Sepulveda, C., A. Knight, N. Nasby-Lucas, M. Domeier. 2010. Fine-scale movements of the swordfish Xiphias gladius in the Southern California Bight. Fisheries Oceanography 19:4, 279–289

Tamsett, A., K. Heinonen, P. Auster and J. Lindholm. In Review. Dynamics of hard substratum communities inside and outside of a fisheries habitat closed area in Stellwagen Bank National Marine Sanctuary (Gulf of Maine, NW Atlantic). Submitted to Marine Sanctuaries Conservation Science Series.

de Marignac, J., J. Hyland, J. Lindholm, D. Kline, and L. Balthis. 2009. A comparison of seafloor habitats and associated benthic fauna in areas open and closed to bottom trawling along the Central California continental shelf. Marine Sanctuaries Conservation Series ONMS-09-02. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD. 44 pp.

Lindholm, J., A. Knight, L. Kaufman and S. Miller. In press (2009). Habitat-mediated signal reception by a passive acoustic receiver array as determined by SCUBA surveys. Proceedings of the American Academy of Underwater Sciences.

Auster, P. and J. Lindholm. 2008. Variation in social foraging by fishes across a coral reef landscape. Proceedings of the 11th International Coral Reef Symposium.

Lindholm, J., M. Kelly, D. Kline and J. de Marignac. 2008. Patterns in the local distribution of the sea whip, Halipteris willemoesi, in an area impacted by mobile fishing gear. Marine Technology Society Journal 42: 64-68.

Auster, P.J., J. Lindholm, M. Plourde, and H. Singh. 2007. Camera configuration and use of AUVs to census mobile fauna. Marine Technology Society Journal 41: 49-52.

Lindholm, J., P.J. Auster, and A. Knight. 2007. Site fidelity and movement of adult Atlantic cod (Gadus morhua) at deep boulder reefs in the western Gulf of Maine. Marine Ecology Progress Series: 342: 239-247.

Lindholm, J., A. Knight, L. Kaufman, and S. Miller. 2006. A pilot study of hogfish (Lachnolaimus maximus Walbaum 1792) movement at the Conch Reef Research Only Area (northern Florida Keys). Marine Sanctuaries Conservation Series NMSP-06-06. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Sanctuary Program, Silver Spring, MD. 14 pp.

Lindholm, J., A. Knight, L. Kaufman and S. Miller. 2006. Site fidelity and movement of the parrotfishes Scarus coeruleus and Scarus taeniopterus at Conch Reef (northern Florida Keys). Caribbean Journal of Science 42: 138-144.

Auster, P.J. and J. Lindholm. 2005. The ecology of fishes on deep boulder reefs in the western Gulf of Maine. p. 91-109 in Proceedings of the American Academy of Underwater Sciences. Connecticut Sea Grant, Groton.

Lindholm, J., L. Kaufman, S. Miller, A. Wagschal & M. Newville. 2005. Movement of Ocyurus chrysurus Bloch 1790 and Mycteroperca bonaci Poey 1860 in the northern Florida Keys National Marine Sanctuary as determined by acoustic telemetry. Marine Sanctuaries Conservation Series MSD-05-4. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Marine Sanctuaries Division, Silver Spring, MD. 17 pp.

Lindholm, J. (ed). 2005. Special Issue: Acoustic Tracking of Marine Fishes and the Design of Marine Protected Areas. Marine Technology Society Journal, Volume 39, No. 1.

Lindholm, J., S. Fangman, L. Kaufman and S. Miller. 2005. In situ tagging and tracking of coral reef fishes from the Aquarius undersea laboratory. Marine Technology Society Journal 39: 68-73.

Lindholm, J., P. Auster and P. Valentine. 2004. Role of a large marine protected area for conserving landscape attributes of sand habitats on Georges Bank (Northwest Atlantic). Marine Ecology Progress Series 269:61-68

Auster, P., J. Lindholm, and P. Valentine. 2003. Primary and secondary habitats of juvenile Acadian redfish (Sebastes fasciatus). Environmental Biology of Fishes 68: 381-389.

Lindholm, J. (ed.). 2003. Special Issue: Science, Technology and Management in the US National Marine Sanctuary Program. Marine Technology Society Journal. Vol. 37, No. 1.

Lindholm, J. and P. Auster. 2003. Site utilization by Atlantic cod (Gadus morhua) in off-shore gravel habitat as determined by acoustic telemetry: implications for the design of marine protected areas. Marine Technology Society Journal 37: 27-34.

Auster, P.J., J. Lindholm, S. Schaub, G. Funnell, L.S. Kaufman, and P.C. Valentine. 2003. Use of sand wave habitats by silver hake Merluccius bilinearis (Mitchill). Journal of Fish Biology 62: 143-152.

Lindholm, J. and P.J. Auster. 2002. Marine protected area design: toward a generalized life history approach. Pages 1126-1136 in: Bondrup-Nielsen, S., N.W.P. Munro, G. Nelson, J.H.M. Willison, T.B. Herman and P. Eagles (eds). Managing Protected Areas in a Changing World. SAMPAA, Wolfville, Nova Scotia.

Auster, P. and J. Lindholm. 2002. Patterns in the local diversity of coral reef fishes versus rates of social foraging. Caribbean Journal of Science 38: 263-266.

Ruth, M and J. Lindholm (Eds). 2002. Dynamic Modeling for Marine Conservation. Springer-Verlag, New York. 449 pp.

Lindholm, J. and B. Barr. 2001. Comparison of marine and terrestrial protected areas under Federal jurisdiction in the United States. Conservation Biology 15: 1441-1444.

Lindholm, J., P.J. Auster, M. Ruth, and L. Kaufman. 2001. Modeling the effects of fishing and implications for the design of marine protected areas: juvenile fish responses to variations in seafloor habitat. Conservation Biology 15: 424-437.

Lindholm, J., Auster, PJ. and L. Kaufman. 1999. Habitat-mediated survivorship of juvenile (0-year) Atlantic cod (Gadus morhua). Marine Ecology Progress Series 180: 247-255.

Lindholm, J., M. Ruth, L. Kaufman, and P. Auster. 1998. The Marine Refuge as a Fishery Management Tool: A Modeling Approach to the Design of Marine Refugia. In: Munro, N.W.P. and Willison, J.H.M. (eds). Linking Protected Areas with Working Landscapes. SAMPAA, Wolfville, Nova Scotia.

Ruth, M. and J. Lindholm. 1997. Dynamic Modeling of Multispecies Fisheries for Consensus Building and Management. Environmental Conservation 23: 332-342.