Zoller, U., Ashash, E., Ayali, G., Shafir, S., Azmon, B. (1990) Nonionic detergents as tracers of ground water pollution caused by municipal sewage. Environment Internatonal 16: 301-306.
Shafir, S., Tom, M., Ovadia, M., Lubzens, E. (1992) Protein, vitellogenin, and vitellin levels in the hemolymph and ovaries during ovarian development in Penaeus semisulcatus (de Haan). Biological Bulletin 183: 394-400.
Fainzilber, M., Tom, M., Shafir, S., Applebaum, S.W., Lubzens, E. (1992) Is there extraovarian synthesis of vitellogenin in penaeid shrimp? Biological Bulletin 183: 233-241.
Shafir, S., Ovadia, M., Tom, M. (1992) In vivo incorporation of labeled methionine into proteins, vitellogenin, and vitellin in females of the penaeid shrimp Penaeus semisulcatus de Haan. Biological Bulletin 183: 242-247.
Rinkevich, B., Shafir, S. (2000) Ex-situ culture of colonial marine ornamental invertebrates: Concepts for domestication. Aquarium Sciences and Conservation 2: 237-250.
Shafir, S., Van Rijn, J., Rinkevich, B. (2001) Nubbins of coral colonies: A novel approach for the development of inland broodstocks. Aquarium Sciences and Conservation 3: 183-190.
Bongiorni, L., Shafir, S., Angel, D., Rinkevich, B. (2003) Survival, growth and reproduction of hermatypic corals subjected to in situ fish farm nutrient enrichment. Marine Ecology Progress Series 253: 137-144.
Bongiorni, L., Shafir, S., Rinkevich, B. (2003) Effects of particulate matter released by a fish farm (Eilat, Red Sea) on survival and growth of Stylophora pistillata coral nubbins. Marine Pollution Bulletin 46: 1120-1124.
Shafir, S., Van-Rijn, J., Rinkevich, B., (2003) The use of coral nubbins in coral reef ecotoxicology testing. Biomolecular Engineering 20: 401-406
Rinkevich, B., Angel, D., Shafir, S., Bongiorni, L. (2003) ‘Fair is foul and foul is fair’: response to a critique. Marine Ecology Progress Series 261: 305-309
Shafir, S., Van Rijn, J., Rinkevich, B. (2006) Steps in the construction of underwater coral nursery, an essential component in reef restoration acts. Marine Biology 149: 679-687.
Shafir, S., Van Rijn, J., Rinkevich, B. (2006) Coral nubbins as source material for coral biological research: a prospectus. Aquaculture 259: 444-448
Shafir, S., Van Rijn, J., Rinkevich, B. (2007) Short and long term toxicity of crude oil and oil dispersants to two representative coral species. Environmental Science and Technology 41: 5571-5574.
Shafir, S., Gur, O., Rinkevich, B. (2008) A Drupella cornus outbreak in the northern Gulf of Eilat and changes in coral prey. Coral Reefs 27: 379
Shafir, S., Abady, S. Rinkevich, B. (in press) Improved sustainable maintenance for mid-water coral nursery by the application of an anti-fouling agent. Journal of Experimental Marine Biology and Ecology.
Shafir, S., Rinkevich, B. (2008) The underwater silviculture approach for reef restoration: an emergent aquaculture theme. In: Aquaculture Research Trends. F. Columbus (editor). Nova Science Publishers, New York.
Shafir, S., Edwards, A., Rinkevich, B. Bongiorni, L., Levy, G., Shaish, L. (2010). Constructing and managing nurseries for asexual rearing of corals. Chapter 4, In: Edwards, A.J. (ed.) Reef Restoration Manual. Coral Reef Targeted Research & Capacity Building for Management Program: St Lucia, Australia. ii: 49-72.
Shafir S. and Rinkevich B. (2010) Integrated Long-Term Mid-Water Coral Nurseries: A Management Instrument Evolving into a Floating Ecosystem. University of Mauritius Research Journal 16:365-386.
Osinga, R., M. Schutter, B. Griffioen, R. Wijffels, J. Verreth, S. Shafir, S. Henard, M. Taruffi, C. Gili, and S. Lavorano. (2011). The Biology and Economics of Coral Growth. Marine Biotechnology:1-14.
Osinga, R., M. Schutter, T. Wijgerde, B. Rinkevich, S. Shafir, M. Shpigel, G. M. Luna, R. Danovaro, L. Bongiorni, A. Deutsch, M. Kuecken, B. Hiddinga, M. Janse, A. McLeod, C. Gili, S. Lavorano, S. Henard, D. Barthelemy, G. Westhoff, N. Baylina, E. Santos, A. Weissenbacher, M. Kuba, R. Jones, R. Leewis, D. Petersen, and M. Laterveer. (2012). The CORALZOO project: a synopsis of four years of public aquarium science. Journal of the Marine Biological Association of the United Kingdom 92:753-768.
Shafir, S., Halperin, I., and Rinkevich, B. (2014). Toxicology of Household Detergents to Reef Corals. Water, Air, & Soil Pollution, 225(3), 1-10.