Steve Haddock's publications

(* indicates papers which may be of special interest)

• M.L. Powers, A.G. McDermott, N.C. Shaner, S.H.D. Haddock (2013) Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: insights into light-sensitive photoproteins. Biochem. Biophys. Res. Comm. 431:360-366 [PDF]

• * C.E. Schnitzler, K. Pang, M.L. Powers, A.M. Reitzel, J.F. Ryan, D. Simmons, T. Tada, M. Park, J. Gupta, S.Y. Brooks, R.W. Blakesley, S. Yokoyama, S.H.D. Haddock, M.Q. Martindale and A.D. Baxevanis. (2012) Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biology 10:107 [PDF]

• W.E. Browne,C. Hurt, S.H.D. Haddock (2013) Molecular phylogenetic evidence for the reorganization of the Hyperiid amphipods, a diverse group of pelagic crustaceans. Mol. Phyl. Evol. 67:28-37 [PDF]

• Francis, W.R., L.M. Christianson, R. Kiko, M.L. Powers, N.C. Shaner, and S.H.D. Haddock (2013) A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genomics 14:167 [PDF]

• R.H. Condon, C.M. Duarte, K.A. Pitt, K.L. Robinson, C.H. Lucas, K.R. Sutherland, H.W. Mianzan, M. Bogeberg, J.E. Purcell, M.B. Decker, S.-I. Uye, L.P. Madin, R.D. Brodeur, S.H.D. Haddock, A. Malej, G.D. Parry, E. Eriksen, J. Quiñones, M. Acha, M Harvey, J.M. Arthur, W.M. Graham. (2013) Recurrent jellyfish blooms are a consequence of global oscillations. Proc. Nat. Acad. Sci. 110:1000-1005 [PDF]

• Madin, L.P., W.M. Hamner, S.H.D. Haddock, G.I. Matsumoto (in press) Scuba diving in blue-water. In Research and Discovery: The Revolution of Science through Scuba. M.A. Lang, R.L. Marinelli, S.J. Roberts, and P.R. Taylor, eds.

• S. Johnsen, T.M. Frank, S.H.D. Haddock, E.A. Widder, C.G. Messing (2012) Light and vision in the deep-sea benthos: I. Bioluminescence at 500-1000m depth in the Bahamian Islands. J. Exp. Biol 215: 3335-3343 [PDF]

• R.H. Condon, W.M. Graham, C.M. Duarte, K.A. Pitt, C.H. Lucas, S.H.D. Haddock, K.R. Sutherland, K.L. Robinson, M.N. Dawson, M. Decker, C.E. Mills, J.E. Purcell, A. Malej, H. Mianzan, S. Uye, S. Gelcich, L.P. Madin. (2012) Questioning the rise of gelatinous zooplankton in the world's oceans. BioScience 62: 160-169 [PDF]

• Shulman, I., B.F. Penta, M. A. Moline, S. H. D. Haddock, S. Anderson, M. J. Oliver, and P. Sakalaukus (2012), Can vertical migrations of dinoflagellates explain observed bioluminescence patterns during an upwelling event in Monterey Bay, California?, J. Geophys. Res., 117, C01016, doi:10.1029/2011JC007480 [PDF]

• Osborn, K.J., Haddock, S.H.D., Rouse, G.W. (2011) Swima (Annelida, Acrocirridae), holopelagic worms from the deep Pacific. Zool. Jour. Linnean Soc. 163: 663-678 [PDF]

• Siebert, S., M.D. Robinson, S.C. Tintori, F.E. Goetz, R.R. Helm, S.A. Smith, N.C. Shaner, S.H.D. Haddock, C.W. Dunn. (2011) Differential gene expression in the Siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next generation sequencing workflows. PLoS ONE 6(7):e22953 [PDF]

• Shulman, I., M.A. Moline, B. Penta, S. Anderson, M. Oliver and S.H.D. Haddock. (2011) Observed and modeled bio-optical, bioluminescent and physical properties during an upwelling event. JGR Oceans 116:C01018. 13 pp. [PDF]

• Haddock, S.H.D. (2011) Photographing your jellyfish. Make Magazine 27:91[PDF] (how-to guide, not peer-reviewed)

• * Haddock, S.H.D. and C.W. Dunn (2010) Practical Computing for Biologists. Sinauer Associates. 538 color pages.
  

• * Haddock, S.H.D., M.A. Moline, and J.F. Case (2010) Bioluminescence in the Sea. Ann. Rev. Mar. Sci. 2:443-493. [PDF]

• * Thuesen, E.V., F.E. Goetz, and S.H.D. Haddock (2010) Bioluminescent organs of two deep-sea arrow worms, Eukrohnia fowleri and Caecosagitta macrocephala, with further observations on bioluminescence in chaetognaths. Biol. Bull. 219:100-111[PDF]

• * Haddock, S.H.D., N. Mastroianni, and L.M. Christianson (2010) A photoactivatable green-fluorescent protein from the phylum Ctenophora. Proc. Roy. Soc. B 277:1155-1160 [PDF]

• Bayha, K.M., M.N. Dawson, A.G. Collins, M.S. Barbeitos, and S.H.D. Haddock (2010) Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA. Integr. Comp. Biol. 50:436-455 [PDF]

• Pugh, P.R., and S.H.D. Haddock (2010) Three new species of resomiid siphonophores (Siphonophora, Physonectae). J. Mar. Biol. Assoc. U.K. 90:1119-1143. [PDF]

• Haddock, S.H.D. (2010) A plea for meaningful colors in ODV. Limnol. Oceanogr. Bulletin 19:44-45 [PDF] (Opinion, not peer-reviewed)

• * Osborn, K.J., S.H.D. Haddock, F. Pleijel, L.P. Madin, and G.W. Rouse (2009) Deep-sea, swimming worms with luminescent "bombs". Science. 325:964. [PDF]

• Gorokhova, E., M. Lehtiniemi, S. Viitasalo-Frösen, and S.H.D. Haddock (2009) Molecular evidence for the occurrence of ctenophore Mertensia ovum in the northern Baltic Sea and implications for current distribution of the invasive species Mnemiopsis leidyi. Limnol. Oceangr. 54: 2025-2033 [PDF]

• Moline, M.A., S.M. Blackwell, J.F. Case, S.H.D. Haddock, C.M. Herren, C.M. Orrico, E. Terrill (2009) Bioluminescence to reveal structure and interaction of coastal planktonic communities. Deep-Sea Res. II 56: 232-245. [PDF]

• * Dunn, C.W., A. Hejnol, D.Q. Matus, K. Pang, W.E. Browne, S.A. Smith, E. Seaver, G.W. Rouse, M. Obst, G.D. Edgecombe, M.V. Sørensen, S.H.D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R.M. Kristensen, W.C. Wheeler, M.Q. Martindale and G. Giribet. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749 [PDF]

• Haddock, S.H.D. (2008). Reconsidering evidence for potential climate-related increases in jellyfish. Limnol. Oceanogr. 53: 2759-2762 [PDF]

• * Schnitzler, C.E., R.J. Keenan, R. McCord, A. Matysik, L.M. Christianson, and S.H.D. Haddock. (2008) Spectral diversity of fluorescent proteins from the anthozoan Corynactis californica. Marine Biotech. 10: 328-342 [PDF]

• Collins, A.G., B. Bentlage, A. Lindner, D. Lindsay, S.H.D. Haddock, G. Jarms, J.L. Norenburg, T. Jankowski, and P. Cartwright. (2008) Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa. J. Mar. Biol. Assoc. U.K. 88:1673-1685 [PDF]

• Staaf, D. J. S. Camarillo-Coop, S.H.D. Haddock, A.C. Nyack, J. Payne, R. Ramirez-Rojo, C.A. Salinas-Zavala, B.A. Seibel, L. Trueblood, C. Widmer, W.F. Gilly. (2008) Natural egg deposition by the Humboldt squid (Dosidicus gigas) in the Gulf of California and characteristics of paralarvae. J. Mar. Biol. Assoc. U.K. 88:759-770 [PDF]

• Haddock, S.H.D. (2007) Comparative feeding behavior of planktonic ctenophores. Integr. Comp. Biol. 47: 847-853 [PDF]

• Sweeney, A.M., S.H.D. Haddock, and S. Johnsen. (2007) Comparative visual acuity of coleoid cephalopods. Integr. Comp. Biol. 47: 808-814 [PDF]

• Browne, W.E., S.H.D. Haddock, M.Q. Martindale (2007). Phylogenetic analysis of lineage relationships among hyperiid amphipods as revealed by examination of the mitochondrial gene, cytochrome oxidase I (COI). Integr. Comp. Biol. 47: 815-830 [PDF]

• * Mills, C.E. and S.H.D. Haddock. (2007) Key to the Ctenophora. p. 189-199 in Light and Smith's Manual: Intertidal invertebrates of the central California coast. J.T. Carlton, ed. U.C. Press. [PDF]

• Mills, C.E. and S.H.D. Haddock, C.W. Dunn, and P.R. Pugh. (2007) Key to the Siphonophora. p. 150-166 in Light and Smith's Manual: Intertidal invertebrates of the central California coast. J.T. Carlton, ed. Univ of California Press. [PDF excerpt]

• Gasca, R., E. Suárez-Morales, and S.H.D. Haddock. (2007) Symbiotic associations between crustaceans and gelatinous zooplankton in deep and surface waters off California. Marine Biology 151:233-242 [PDF]

• Miller, S.D., S.H.D. Haddock, C.D. Elvidge, and T.F. Lee. (2006) Twenty thousand leagues over the seas: the first satellite perspective on bioluminescent milky seas. Intl. J. Remote Sensing. 27: 5131-5143 [See Miller below for related papers].

• Haddock, S.H.D. (2006) "Luminous marine organisms" in Photoproteins in Bioanalysis, S.Daunert & S.Deo, eds. Wiley-VCH. New York, p. 25-47. [Marked Proofs Only]

• Collins, A.G., B. Bentlage, G.I. Matsumoto, S.H.D. Haddock, K.J. Osborn, and B. Schierwater. (2006) Solution to the phylogenetic enigma of Tetraplatia, a worm-shaped cnidarian. Biology Letters. [PDF]

• * Haddock, S.H.D., C.W. Dunn, P.R. Pugh. and C.E. Schnitzler. (2005) Bioluminescent and red-fluorescent lures in a deep-sea siphonophore. Science. 309:263. [PDF] [NY Times article] [NPR Story] [Web Site]

• * Dunn, C.W., P.R. Pugh, and S.H.D. Haddock. (2005). Molecular phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specialization. Systematic Biology. 54: 916-935. [PDF]

• * Haddock, S.H.D., C.W. Dunn, and P.R. Pugh. (2005) A reexamination of siphonophore terminology and morphology, applied to the description of two new prayine species with remarkable bio-optical properties. J. Mar. Biol. Assoc. U.K. 85:695-707. [PDF]

• * Miller, S.D., S.H.D. Haddock, C.D. Elvidge, and T.F. Lee. (2005) Detection of a bioluminescent milky sea from space. Proc. Nat. Acad. Sci. 102:14181-14184. [PDF] [NPR Story] [Web Site] [Perspective article]

• * Haddock, S.H.D. and J.N. Heine. (2005) Scientific blue-water diving. Calif. Sea Grant, La Jolla, California. [PDF] Note: do NOT buy the printed copy from Amazon but get it directly from California SeaGrant instead.

• Dunn, C.W., P.R. Pugh, and S.H.D. Haddock. (2005) Marrus claudanielis, a new species of deep-sea physonect siphonophore, (Siphonophora, Physonectae). Bull. Mar. Sci. 76: 699-714. [PDF]

• Seibel, B.A., B.H. Robison, and S.H.D. Haddock. (2005) Post-spawning egg care by a squid. Nature 438: 929 [PDF] [NY Times article]

• Haddock, S.H.D. and C.W. Dunn. (2005). The complex world of siphonophores. JMBA Global Marine Environment 2:24-25. [PDF] (popular press - not peer-reviewed)

• Herren, C.M., S.H.D. Haddock, C. Johnson, M.A. Moline, C.M. Orrico, J.F. Case. (2005) A multi-platform bathyphotometer for fine-scale, coastal bioluminescence research. Limnology and Oceanogr. Methods. 3:247-262. [PDF]

• Shulman, I., D.J. McGillicuddy, Jr., M.A. Moline, S.H.D. Haddock, J.C. Kindle, D. Nechaev, and M.W. Phelps (2005) Bioluminescence intensity modeling and sampling strategy optimization. J. Atmospheric and Oceanic Technol. 22:1267-1281 [PDF]

• Widder, E.A., B.H. Robison, K.R. Reisenbichler, and S.H.D. Haddock. (2005) Using red light for in situ observations of deep-sea fishes. Deep Sea Research I 52:2077-2085. [PDF]

• * Haddock, S.H.D. (2004) A golden age of gelata: past and future research on planktonic cnidarians and ctenophores. Hydrobiologia 530/531:549-556. [PDF]

• Gasca, R. and S.H.D. Haddock. (2004) Associations between gelatinous zooplankton and hyperiid amphipods (Crustacea: Peracarida) in the Gulf of California. Hydrobiologia 530/531:529-535. [PDF]

• Robison, B.R., K.R. Reisenbichler, J.C. Hunt, and S.H.D. Haddock. (2003) Light production by the arm tips of the deep-sea cephalopod Vampyroteuthis infernalis. Biol. Bull. 205:102-109 [PDF]

• Shulman, I., S.H.D. Haddock, D.J. McGillicuddy, Jr., J.D. Paduan, and P.W. Bissett. (2003) Numerical modeling of bioluminescence distributions in the coastal ocean. J. Atmospheric and Oceanic Technol. 20:1060-1068. [PDF]

• Cairns, S.D., D.R. Calder, A. Brinckmann-Voss, C.B. Castro, D.G. Fautin, P.R. Pugh, C.E. Mills, W.C. Jaap, M.N. Arai, S.H.D. Haddock and D.M. Opresko, (2002). Common and Scientific Names of Aquatic Invertebrates from the United States and Canada: Cnidaria and Ctenophora. Second Edition. Amer. Fish. Soc. Special Pub. #28, Bethesda, Maryland, 115 pp.

• * Haddock, S.H.D., Rivers, T.J. and B.H. Robison. (2001) Can coelenterates make coelenterazine? Dietary requirement for luciferin in cnidarian bioluminescence. Proc. Nat. Acad. Sci. 98: 11148-11151. [PDF]

• * Podar, M., Haddock, S.H.D., Sogin, M., and G.R. Harbison (2001) Molecular phylogenetic framework for the phylum Ctenophora based on 18s rRNA sequences. Molec. Phyl. Evol.21: 218-230. [PDF]

• Bioluminescence and Chemiluminescence: Proceedings of the 11th International Symposium. (2001) edited by JF Case, PJ Herring, BH Robison, SHD Haddock, LJ Kricka, PE Stanley, World Scientific Publishing Company. 540 pp.

• * Haddock, S.H.D. and J.F. Case. (1999) Bioluminescence spectra of shallow and deep-sea gelatinous zooplankton: ctenophores, medusae, and siphonophores.Marine Biology. 133: 571-582. [PDF]

• White, G.B., A. Pfahnl, S. Haddock, S. Lamers, R.M. Greenberg, and P.A.V. Anderson. (1998) Structure of a putative sodium channel from the sea anemone Aiptasia pallida. Invert. Neurosci. 3: 317-326.

• Alldredge, A.L., U. Passow, and S.H.D. Haddock. (1998) The characteristics and transparent exopolymer particle (TEP) content of marine snow formed from thecate dinoflagellates. J. Plankton Research. 20: 393-406. [PDF]

• Haddock, S.H.D., D.J. Neilson, E.A. Widder, and J.F. Case. (1998) Feasibility of using in situ measurements of bioluminescence spectra to determine the vertical distribution of plankton. Proc. Int. Conf. Pelagic Biogeogr. II. Eds. A. C. Pierrot-Bults and S. van der Spoel. IOC Workshop Report no. 142. Amsterdam. pp. 137-142.

• Ling, H-Y, and S.H.D. Haddock. (1997) The enclosing latticed sphere of Tuscaridium cygneum (Murray), a eurybathyal phaeodarian Radiolaria, from the North Pacific. Paleontological Res. 1: 144-149. [PDF]

• Mills, C.E., P.R. Pugh, G.R. Harbison and S.H.D. Haddock. (1996) Medusae, siphonophores and ctenophores of the Alborán Sea, south western Mediterranean. Scientia Marina, 60: 145-163. [PDF]

• Haddock, S.H.D. and J.F. Case. (1995) Not all ctenophores are bioluminescent: Pleurobrachia. Biol. Bull. 189: 356-362. [PDF]

• Case, J.F., S.H.D. Haddock, and R.D. Harper. (1994) "The ecology of bioluminescence" in Bioluminescence and chemiluminescence: fundamentals and applied aspects. Campbell, Kricka and Stanley, eds. New York: John Wiley and Sons. pp. 115-122.

• * Haddock, S.H.D. and J.F. Case. (1994) A bioluminescent chaetognath. Nature 367: 225-226. [PDF]

• Herring, P.J., E.A. Widder and S.H.D. Haddock. (1992) Correlation of bioluminescence emissions with ventral photophores in the mesopelagic squid Abralia veranyi (Cephalopoda: Enoploteuthidae). Marine Biology 112: 293-298. [PDF]

• Haddock, S.H.D. (1989) Air pockets: A subtidal habitat for the intertidal pulmonate limpet Trimusculus reticulatus. Veliger 32: 403-405. [PDF]

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