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Books

Cronin, T. W. Johnsen, S., Marshall, N. J. and E. J. Warrant (2014). Visual Ecology. Princeton University Press: Princeton, NJ. (pre-order from Amazon) (pre-order from Princeton Press)

Johnsen, S. (2012). The Optics of Life: A Biologist's Guide to Light in Nature. Princeton University Press: Princeton, NJ. (get it from Amazon) (get it from Princeton Press)

 

Papers

Zylinski, S. and S. Johnsen (in press). Visual cognition in deep-sea cephalopods: What we don’t know and why we don’t know it. In: Cephalopod Cognition, Editors: S. Darmaillacq and J. Mather.

Nilsson, D. E., Warrant, E. J., and S. Johnsen (2014). Computational visual ecology in the pelagic realm. Philosophical Transactions of the Royal Society of London, Series B. 369: 20130038.

Johnsen, S. (2014). Hide and seek in the open sea: Pelagic camouflage and visual countermeasures. Annual Review of Marine Science 6: 369-392.

Mohamed, A., Gilliland, K. O., Metlapally, S., Johnsen, S., and M. J. Costello (2013). Simple fixation and storage protocol for preserving the internal structure of intact human donor lenses and extracted human nuclear cataract specimens. Molecular Vision 19, 2352-2359.

Nilsson, D. E., Warrant, E. J., Johnsen, S., Hanlon, R. T., and N. Shashar (2013). The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales. BMC Evolutionary Ecology 13, 187-189.

Costello, M. J., Mohamed, A., Gilliland, K. O., Fowler, W. C., and S. Johnsen (2013) Ultrastructural analysis of the human lens fiber cell remodeling zone and the initiation of cellular compaction. Experimental Eye Research 116, 411-418.

Warrant, E. J., and S. Johnsen (2013). Vision and the light environment. Current Biology 23, R990-R994.

Costello, M. J., Chauss, D., Mohamed, A., Gilliland, K. O., Johnsen, S., Bates, M., Brennan, L. A., and M. Kantorow (2013). Autophagy and mitophagy in ocular lens organelle degradation. Experimental Eye Research 116: 141-150.

Gagnon, Y. L., Sutton, T. T., and S. Johnsen (2013). Visual acuity in pelagic fishes and mollusks. Vision Research 92: 1-9.

Brandley, N. C., Speiser, D. I., and S. Johnsen (2013). Eavesdropping on visual secrets. Evolutionary Ecology. (on-line: pages not yet assigned).

Tedore, C. A., and S. Johnsen (2013). Pheromones exert top-down effects on visual recognition in the jumping spider Lyssomanes viridis. Journal of Experimental Biology 216: 1744-1756.

Moore, B. A., Kamilar, J. M., Collin, S. P., Bininda-Emonds, O. R. P., Dominy, N. J., Hall, M. I., Heesy, C. P., Iwaniuk, A. N., Johnsen, S., Lisney, T. J., Loew, E. R., Moritz, G., Nava, S. S., Warrant, E. J., Yopak, K. E., and E. Fernández-Juricic (2012). A novel method for comparative analysis of retinal specialization traits from topographic maps. Journal of Vision 12, 1-24.

Johnsen, S., Frank, T. M., Haddock, S. H. D., Widder, E. A., and C. G. Messing (2012). Light and vision in the deep-sea benthos. I. Bioluminescence at 500-1000 m depth in the Bahamian Islands. Journal of Experimental Biology 215: 3335-3343.

Frank, T. M., Johnsen, S., and T. W. Cronin (2012). Light and vision in the deep-sea benthos. II. Special visual adaptations in deep-sea benthic crustaceans. Journal of Experimental Biology 215: 3344-3353.

Costello, M. J., Burette, A., Weber, M., Metlapally, S., Gilliland, K. O., Fowler, W. C., Mohamed, A., and S. Johnsen (2012). Electron tomography of fiber cell cytoplasm and dense cores of multilamellar bodies from human age-related nuclear cataracts. Experimental Eye Research 101: 71-82

Nilsson, D. E., Warrant, E. J., Johnsen, S., Hanlon, R. T., and N. Shashar (2012). A unique advantage for giant eyes in giant squid. Current Biology 22: 683-688. (with Perspectives article)

Baldwin, J. L., and S. Johnsen (2012). The male blue crab, Callinectes sapidus, uses both chromatic and achromatic cues during mate choice. Journal of Experimental Biology 215: 1184-1191.

Johnsen, S. (2012). Q&A: Sönke Johnsen. Current Biology 22: R6-R7. (self interview)

Tedore, C. A., and S. Johnsen (2012). Weaponry, color, and contest success in the jumping spider Lyssomanes viridis. Behavioural Processes 89: 203-211.

Marshall, N. J. and S. Johnsen (2011). Camouflage in Marine fish. In Animal Camouflage: Current issues and new perspectives. Cambridge University Press: Cambridge UK.

Zylinski, S. and S. Johnsen (2011). Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep. Current Biology 21: 1937-1941. (with cover and Perspectives article)

Baldwin, J. L., and S. Johnsen (2011). The effects of molting on the visual acuity of the blue crab Callinectes sapidus. Journal of Experimental Biology. 214: 3055-3061.

Jackson, E., and S. Johnsen (2011). Orientation to objects in the sea urchin Strongylocentrotus purpuratus depends on apparent and not actual object size. Biological Bulletin 220: 86-88.

Speiser, D. I., Eernisse, D. and S. Johnsen (2011). Chitons eye have calcitic lenses and provide spatial vision. Current Biology 21: 665-670. (with Perspectives article)

Holt, A., Sweeney, A. M., Johnsen, S., and D. E. Morse (2011). A highly-distributed Bragg stack with unique geometry provides effective camouflage for Loliginid squid eyes. Proceedings of the Royal Society: Interface

Bhandiwad, A., and S. Johnsen (2011). The effects of salinity and temperature on the transparency of the grass shrimp Palaemonetes pugio. Journal of Experimental Biology 214: 709-716.

Sweeney, A. M., Boch, C. A., Johnsen, S., and D. E. Morse (2011). Twilight spectral dynamics and the coral reef invertebrate spawning response. Journal of Experimental Biology 214: 770-777.

Shashar, N., Johnsen, S., Lerner, A., Sabbah, S., Chiao, C-C., Mäthger, L. M., and R. T. Hanlon (2011). Underwater linear polarization- physical limitations to biological functions. Philosophical Transactions of the Royal Society of London, Series B 366: 649–654.

Johnsen, S., Marshall, N. J., and E. A. Widder (2011). Polarization sensitivity as a contrast enhancer in pelagic predators: Lessons from in situ polarization imaging of transparent zooplankton. Philosophical Transactions of the Royal Society of London, Series B 366: 655–670.

Speiser, D. I., Loew, E. R., and S. Johnsen (2011). Spectral sensitivity of the concave mirror eyes of scallops: The influence of habitat and longitudinal chromatic aberration. Journal of Experimental Biology 214: 422-431.

Costello, M. J., Johnsen, S., Frame, L., Gilliland, K. O., Metlapally, S., and D. Balasubramanian (2010). Multilamellar spherical particles as potential sources of excess light scattering in human age-related nuclear cataracts. Experimental Eye Research 91: 881-889.

Yerramilli, D. and S. Johnsen (2010). Spatial vision in the purple sea urchin Strongylocentrotus purpuratus (Echinoidea). Journal of Experimental Biology 213: 249-255.

Baldwin, J. L., and S. Johnsen (2009). The importance of color in mate choice in the blue crab Callinectes sapidus. Journal of Experimental Biology 212: 3762-3768.

Leech, D. M. and S. Johnsen (2009). Light, photoreceptors and UV vision. In Encyclopedia of Inland Waters, (ed. G. E. Likens) Vol 2, pp 671-681.

Speiser, D. I., and S. Johnsen (2008). Comparative morphology of the mirror-based eyes of scallops (Pectinoidea). American Malacological Bulletin 26: 27-34.

Matz. M. V., Frank, T. M., Marshall, N. J., Widder, E. A., Johnsen, S. (2008) Giant deep-sea protist produces bilaterian-like traces. Current Biology 18: 1849-1854. (with Perspectives article)

Costello, M. J., Johnsen, S., Gilliland, K. O., Metlapally, S., Ramamurthy, B., Krishna, P. V., Balasubramanian, D. (2008) Ultrastructural analysis of damage to nuclear fiber cell membranes in advanced age-related cataracts from India. Experimental Eye Research 87:147-158.

Speiser, D. I., and S. Johnsen (2008). Scallops visually respond to the presence and speed of virtual particles. Journal of Experimental Biology. 211: 2066-2070.

Johnsen, S., and K. J. Lohmann (2008). Magnetoreception in animals. Physics Today. 61(3): 29-35.

Gilliland, K. O., Johnsen, S., Metlapally, S., Costello, M. J., Ramamurthy, B., Krishna, P. V. and D. Balasubramanian (2008). Mie light scattering calculations for multilamellar bodies in indian age-related nuclear cataracts. Molecular Vision 14: 572-582.

Metlapally, S., Costello, M. J., Gilliland, K. O., Ramamurthy, B., Krishna, P. V., Balasubramanian, D., and S. Johnsen (2008). Analysis of nuclear lens fiber cell cytoplasmic texture in advanced cataractous lenses from Indian subjects using Debye-Bueche theory. Experimental Eye Research 86: 434-444.

Gagnon, Y. L., Shashar, N., Warrant, E. J., and S. Johnsen (2007). Light scattering from selected zooplankton from the Gulf of Aqaba. Journal of Experimental Biology 210: 3728-3735.

Sweeney, A., Haddock, S. H. D., and S. Johnsen (2007). Comparative visual acuity of coleoid cephalopods. Integrative and Comparative Biology 47: 808-814.

Johnsen, S., Mattern, E. and T. Ritz (2007). Light-dependent magnetoreception: quantum catches and opponency mechanisms of possible photosensitive molecules. Journal of Experimental Biology 210: 3171-3178.

Martin, C. H. and S. Johnsen (2007). A Field Test of the Hamilton-Zuk Hypothesis in the Trinidadian guppy (Poecilia reticulata). Behavioral Ecology and Sociobiology 61: 1897-1909.

Johnsen, S. (2007). Does new technology inspire new directions? Examples drawn from pelagic visual ecology. Integrative and Comparative Biology 47: 799-807.

Cummings, M. M. and S. Johnsen (2007). Light in the rocky shores. Pp. 327-331 in Encyclopedia of Tidepools and Rocky Shores, (M. Denny and S. Gaines Eds.), University of California Press.

Sweeney, A. M., Des Marais, D. L., Ban, Y. A., and S. Johnsen (2007). Evolution of graded refractive index in squid lenses. Journal of the Royal Society: Interface 4: 685-698.

Costello, M. J., Johnsen, S., Gilliland, K. O., Freel, C. D., and C. Fowler (2006). Predicted light scattering from particles observed in human age-related nuclear cataracts using Mie scattering theory. Investigative Ophthalmology and Visual Science. 48: 303-312.

Leech, D. M. and S. Johnsen (2006). Ultraviolet vision and foraging in juvenile bluegill (Lepomis macrochirus). Can. J. Fish. Aquat. Sci. 63: 2183-2190.

Tuthill, J. and S. Johnsen (2006) Polarization sensitivity in the red swamp crayfish Procambarus clarkii enhances the detection of moving transparent objects. Journal of Experimental Biology 209:1612-1616.

Johnsen, S., Kelber, A., Warrant, E. J., Sweeney, A. M., Widder, E. A., Lee Jr., R. L., and J. Hernandez-Andres (2006). Crepuscular and nocturnal illumination and its effects on the color perception of the nocturnal hawkmoth Deilephila elpenor. Journal of Experimental Biology 209: 789-800. (with commentary by Kelber and Roth)

Johnsen, S. and K. J. Lohmann (2005). The physics and neurobiology of magnetoreception. Nature Reviews Neuroscience 6: 703-712.

Johnsen, S. (2005). The red and the black: Bioluminescence and the color of animals in the deep sea. Integrative and Comparative Biology. 45: 234-246.

Johnsen S. (2005). Visual ecology on the high seas. Marine Ecology Progress Series. 287: 281-285

Blevins, E., and S. Johnsen (2004). Spatial vision in the echinoid genus Echinometra. Journal of Experimental Biology 207: 4249-4253.

Marsili, S., Salganik, R. I., Albright, C. D., Freel, C. D., Johnsen, S., Peiffer, R. L., and M. J. Costello (2004). Cataract formation in a strain of rats selected for high oxidative stress. Experimental Eye Research 79: 595-612.

Johnsen, S. and H. M. Sosik (2004). Shedding light on light in the ocean. Oceanus 43: 24-28.

Gilliland, K. O., Freel, C. D., Johnsen, S., Fowler, C., and M. J. Costello (2004). Random distribution of multilamellar bodies in human age-related nuclear cataracts. Experimental Eye Research. 79: 563-576.

Johnsen, S., Widder, E. A., Mobley, C. D., and P. J. Herring (2004). Propagation and perception of bioluminescence: factors affecting the success of counterillumination as a cryptic strategy. Biological Bulletin: 207: 1-16.

Johnsen, S., and K. J. Lohmann (2004). Neurobiology of geomagnetic orientation in animals. In Encyclopedia of Neuroscience (G. Adelman, B. H. Smith eds.), Elsevier Science, New York.

Johnsen, S. (2003). Lifting the cloak of invisibility: the effects of changing optical conditions on pelagic crypsis. Integrative and Comparative Biology 43: 580-590.

Sweeney, A. M., Jiggins, C., and S. Johnsen (2003). Polarized light as a butterfly mating signal. Nature 423: 31-32.

Johnsen, S. and H. M. Sosik (2003). Cryptic coloration and mirrored sides as camouflage strategies in near-surface pelagic habitats: implications for foraging and predator avoidance. Limnology and Oceanography 48: 1277-1288.

Avens, L., Wang, J., Johnsen, S., Dukes, P., and K. J. Lohmann (2003). Responses of hatchling sea turtles to rotational displacements. Journal of Experimental Marine Biology and Ecology 288: 111-124.

Leech, D. and S. Johnsen (2003). Avoidance and UV vision. Pp. 455-484 in UV Effects in Aquatic Organisms and Ecosystems, (W. Helbling, H. Zagarese eds.), Royal Society of Chemistry, London.

Johnsen, S. (2002). Cryptic and conspicuous coloration in the pelagic environment. Proceedings of the Royal Society of London: Biological Sciences 269: 243-256.

Johnsen, S. (2001). Hidden in plain sight: the ecology and physiology of organismal transparency. Biological Bulletin 201: 301-138.

Johnsen, S., and E. A. Widder (2001). Ultraviolet absorption in transparent zooplankton and its implications for depth distribution and visual predation. Marine Biology 138: 717-730.

Widder, E. A., and S. Johnsen (2000). 3D spatial point patterns of bioluminescent plankton: a map of the minefield. Journal of Plankton Research 22: 409-420.

Johnsen, S. (2000). Transparent animals. Scientific American 282(2): 62-71.

Lohmann, K. J., and S. Johnsen (2000). The neurobiology of magnetoreception in vertebrate animals. Trends in Neurosciences 23: 153-159.

Widder, E. A., Johnsen, S., Bernstein, S. A., Case, J. F., and D. J. Neilson (1999). Thin layers of bioluminescent copepods found at density discontinuities in the water column. Marine Biology 134: 429-437.

Johnsen, S., and E. A. Widder (1999). The physical basis of transparency in biological tissue: ultrastructure and the minimization of light scattering. Journal of Theoretical Biology 199: 181-198.

Johnsen, S., and W. M. Kier (1999). Shade-seeking behavior under polarized light by the brittlestar Ophioderma brevispinum. Journal of the Marine Biological Association of the United Kingdom 79: 761-763.

Johnsen, S., Balser, E. J., and E. A. Widder (1999). Light-emitting suckers in an octopus. Nature 398: 113-114.

Johnsen, S., Balser, E. J., Fisher, E. C., and E. A. Widder (1999). Bioluminescence in the deep-sea cirrate octopod Stauroteuthis syrtensis Verrill (Mollusca: Cephalopoda). Biological Bulletin 197: 26-39.

Johnsen, S., and E. A. Widder (1998). The transparency and visibility of gelatinous zooplankton from the north west Atlantic and Gulf of Mexico. Biological Bulletin 195: 337-348.

Johnsen, S., and E. A. Widder (1998). The transparency and visibility of gelatinous zooplankton. Proceedings of the Fourteenth Conference of the Ocean Optics Society, Kailua-Kona, HI, USA.

Johnsen, S., and W. M. Kier (1998). Damage due to solar ultraviolet radiation in the brittlestar Ophioderma brevispinum (Echinodermata: Ophiuroidea). Journal of the Marine Biological Association of the United Kingdom 78: 681-684.

Widder, E. A., and S. Johnsen (1998). Optical imaging, identification and 3D analysis of spatial distribution patterns of bioluminescent plankton. Proceedings of the Fourteenth Conference of the Ocean Optics Society, Kailua-Kona, HI, USA.

Johnsen, S. (1997). Identification and localization of a possible rhodopsin in the echinoderms Asterias forbesi (Asteroidea) and Ophioderma brevispinum (Ophiuroidea). Biological Bulletin 193: 97-105.

Johnsen, S. (1994). Extraocular sensitivity to polarized light in an echinoderm. Journal of Experimental Biology 195: 281-291.

Smith, A. M., Kier, W. M., and S. Johnsen (1993). The effect of depth on the attachment force of limpets. Biological Bulletin 184: 338-341.

Johnsen, S., and W. M. Kier (1993). Intramuscular crossed connective tissue fibers: skeletal support in the lateral fins of squid and cuttlefish. Journal of Zoology 231: 311-338.

Kauffman, S. A., and S. Johnsen (1991). Coevolution to the edge of chaos: Coupled fitness landscapes, poised states and coevolutionary avalanches. Journal of Theoretical Biology 149: 467-505.

Kauffman, S. A., and S. Johnsen (1991). Co-evolution to the edge of chaos. Pp. 325-369 in Artificial Life II, SFI Studies in the Sciences of Complexity vol. X (C. Langton, C. Taylor, J. Farmer, S. Rasmussen eds.) Addison-Wesley, New York.

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