BOOKS

ESSAYS and OPINION

SCIENTIFIC PAPERS

Dot • indicates papers of interest.
  1. Beckmann, L.M., B.A. Vincent, A. De León, J. Masterman, E.S. Lau, S.H.D. Haddock (submitted) Fluorescence patterns and diversity of hydrozoans from Bocas del Toro, Panama. Ciencias Marinas [PDF]
  2. • Haddock, S.H.D, and C.A. Choy. (2024, in press) Life in the midwater: The ecology of deep pelagic animals. Annu. Rev. Mar. Sci. 16: 383–416
  3. Bessho-Uehara, M., J. Mallefet, and S.H.D. Haddock. (2024) “Glowing sea cucumbers: Bioluminescence in Holothuroidea.” Chapter 22 in The World of Sea Cucumbers: Challenges, Advances, and Innovations, ed. A Mercier, J-F Hamel, A Suhrbier, C Pearce. San Diego, CA. 361-375.
  4. • Schultz, D.T., S.H.D. Haddock, J.V. Bredeson, R.E. Green, O. Simakov, D.S. Rokhsar. (2023) Ancient gene linkages support ctenophores as the sister to other animals. Nature. 618: 110-117
  5. Haddock, S.H.D. (2023) “Two Enigmatic phyla: Placozoa and Ctenophora; The Comb Jellies” Chapter 6 in the textbook Invertebrates, edited by Brusca, Giribet, and Moore. Oxford University Press.
  6. Hoving, Henk-Jan; Haddock, S. H.D.; Robison, B.R.; Seibel, B. A. (in press) Giant eggs in a deep-sea squid. Ecology
  7. Mills, C.E., S.H.D. Haddock, N, Bezio (in press) “Kingdom Animalia, phylum Ctenophora (comb jellies)” Chapter 5 in Taxonomic keys for the fauna of New Zealand.
  8. Ahuja, N., ... C.W. Dunn. (in review) Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores. Genome Biology and Evolution
  9. • Winnikoff, J.R., D. Milshteyn, M. Angel P. Joya, A.M. Armando, O. Quehenberger, A. Sodt, E.A. Dennis, E. Lyman, S.H.D. Haddock, and I. Budin. (in review) Phase behavior of plasmalogens defines pressure specialization in deep-sea invertebrates. Science
  10. Robison, B.H. and S.H.D. Haddock (in review) Discovery and description of a remarkable bathypelagic nudibranch, Bathydevius caudactylus, gen. nov., sp. nov. Proc. Roy. Soc. B.
  11. Hetherington, E.D.,H.G. Close, S.H.D. Haddock, A.D. Serrano, C.W. Dunn, N.J. Wallsgrove, S.C. Doherty, C.A. Choy (in review) Vertical trophic structure and niche partitioning of gelatinous predators in a pelagic food web: insights from stable isotopes of siphonophores. Limnol. Oceanogr.
  12. • Johnson, S.B., J.R. Winnikoff, D.T. Schultz, L.M. Christianson, W.L. Patry, C.E. Mills and S.H.D. Haddock (2022) Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores. Frontiers in Genetics. 13:970314. doi.org/10.3389/fgene.2022.97
  13. Damian-Serrano, A., E.D. Hetherington, C.A. Choy, A. Lapides, S.H.D. Haddock, C.W. Dunn (2022). Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding. PLOS One. 17(5): e0267761
  14. Matsumoto, G.I., L.M. Christianson, B.H. Robison, S.H.D. Haddock (2022) Atolla reynoldsi (Cnidaria, Scyphozoa, Coronatae, Atollidae): A new species of coronate scyphozoan found in the Eastern North Pacific Ocean. MDPI Animals 12(6), 742; doi.org/10.3390/ani12060742
  15. • Hetherington, E.D., C.A. Choy, E.V. Thuesen, S.H.D. Haddock (2022) Three distinct views of deep pelagic community composition based on complementary sampling approaches. Front. Mar. Sci. 9: 864004 http://doi.org/10.3389/fmars.2022.864004
  16. Hetherington, E.D., A. Damian-Serrano, S.H.D. Haddock, C.W. Dunn, C.A. Choy (2022) Integrating siphonophores into marine food-web ecology. Limnol. Oceanogr. Letters. 7: 81-95. doi.org/10.1002/lol2.10235
  17. • Winnikoff, J.R., S.H.D. Haddock, I. Budin (2021) Depth- and temperature-specific fatty acid adaptations in ctenophores from extreme habitats. J. Exp. Biol. 224: jeb242800 doi.org/10.1242/jeb.242800
  18. Elor, A., Thang, T., Hughes, B.P., Crosby, A., Phung, A., Gonzalez, E., Katija, K., Haddock, S.H.D., Martin, E.J., Erwin, B.E., and Takayama, L. (2021). Catching jellies in immersive virtual reality: a comparative teleoperation study of ROVs in underwater capture tasks. Proc. 27th ACM Symposium on Virtual Reality Software and Technology. Article17:1-10. doi.org/10.1145/3489849.3489861 (best paper award)
  19. • Miller, S.D., S.H.D. Haddock, W.C. Straka III, et al. (2021) Honing in on bioluminescent milky seas from space. Nature Sci. Rep. 11: 15443
  20. • Christianson, L.M., S.B. Johnson, D.T. Schultz, S.H.D. Haddock (2021) Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences. Molec. Ecol. Resources. doi.org/10.1111/1755-0998.13459
  21. • Schultz, D.T., W.R. Francis, J. McBroome, L.M. Christianson, S.H.D. Haddock, R.E. Green (2021) A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 Genes,Genomes,Genetics. jkab302. doi.org/10.1093/g3journal/jkab302 (cover)
  22. Damian-Serrano, A., S.H.D. Haddock, C.W. Dunn (2021) The evolutionary history of siphonophore tentilla: novelties, convergence, and integration. Integrative Organismal Biol. vol 3. pbab019 doi.org/10.1093/iob/obab019
  23. Meech, M.E., C.E. Mills, S.H.D. Haddock, R.W. Meech. (2021). Two swimming modes in Trachymedusae: bell kinematics and the role of giant axons. J. Exp. Biol. doi.org/10.1242/jeb.239830 (cover)
  24. Stefanoudis, P. V., L.M. Biancani, S. Cambronero-Solano, M.R. Clark, J.T. Copley, E. Easton, F. Elmer, S.H.D. Haddock, S. Herrera, I.S. Iglesias, A.M. Quattrini, J. Sigwart, C. Yesson, A.G. Glover. (2021) Moving conferences online: lessons learned from an international virtual meeting. Proc. R. Soc. B. 20211769. http://doi.org/10.1098/rspb.2021.1769
  25. Damian-Serrano, A., S.H.D. Haddock, C.W. Dunn (2021). The evolution of siphonophore tentilla for specialized prey capture in the open ocean. Proc. Nat. Acad. Sci. 118 (8) e2005063118 (cover)
  26. Puente-Tapia, F. A., R. Gasca, A. Schiariti, S.H.D. Haddock (2021) An updated checklist of ctenophores (Ctenophora: Nuda and Tentaculata) of Mexican seas. Regional Studies in Marine Science. 41:101555
  27. Gibbons, M.J., S.H.D. Haddock, G.I. Matsumoto, C. Foster. (2021) Records of ctenophores from South Africa. PeerJ. 9:e10697 doi.org/10.7717/peerj.10697
  28. • Bessho-Uehara, M., W. Huang, W.L. Patry, W.E. Browne, J.-K. Weng, S.H.D. Haddock (2020) Evidence for de novo biosynthesis of the luminous substrate coelenterazine in ctenophores. iScience. 23, 101859
  29. • Leonardi, N.D., E.V. Thuesen, S.H.D. Haddock (2020). A sticky thicket of glue cells: A comparative morphometric analysis of colloblasts in 20 species of comb jelly (phylum Ctenophora). Ciencias Marinas. 6:211–225 doi.org/10.7773/cm.v46i4.3118
  30. Martini, S.M., D.T. Schultz, L. Lundsten, S.H.D. Haddock (2020) Bioluminescence in an undescribed species of carnivorous sponge (Cladorhizidae) from the deep sea. Frontiers in Marine Science. 7:576476
  31. • Drazen, J.C., C.R. Smith, K.M. Gjerde, S.H.D. Haddock, et al. (2020). Midwater ecosystems must be considered when evaluating environmental risks of deep-sea mining. Proc. Nat. Acad. Sci.
  32. • Bessho-Uehara, M., W.R. Francis, S.H.D. Haddock (2020). Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems. Marine Biology167: 114. http://j.mp/coral-biolum
  33. Schultz, D.T., J.M Eizenga, R.B. Corbett-Detig, W.R. Francis, L.M. Christianson, S.H.D. Haddock. (2020). Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ. 8:e8356
  34. Martini, S.M., L. Kuhnz, J. Mallefet, S.H.D. Haddock. (2019) Distribution and quantification of bioluminescence as an ecological trait in the deep sea benthos. Nature Scientific Reports.
  35. • Winnikoff, J.R., W.R. Francis, E.V. Thuesen, and S.H.D. Haddock. (2019) Combing transcriptomes for secrets of deep-sea survival: Environmental diversity drives patterns of protein evolution. Integrative and Comparative Biology. 63:1-13
  36. Messié, M., I. Shulman, S. Martini, S.H.D. Haddock (2019) Using fluorescence and bioluminescence sensors to characterize auto- and heterotrophic plankton communities. Progress in Oceanography. 171:76-92.
  37. Schultz, D.T., A.A. Kotlobay, R. Ziganshin, A. Bannikov, N.M. Markina, T.V. Chepurnyh, E.S. Shakhova, K. Palkina, S.H.D. Haddock, I.V. Yampolsky, Y. Oba (2018). Luciferase of the Japanese syllid polychaete Odontosyllis undecimdonta. Biochem. Biophys. Res. Comm. 502: 318–23.
  38. Babonis, L., M.B. Debiasse, W.R. Francis, L.M. Christianson, S.H.D. Haddock, M.Q. Martindale, J.F. Ryan. (2018) Integrating embryonic development and evolutionary history to characterize tentacle-specific cell types in a ctenophore. Molecular Biol. Evol. 35:2940–2956 doi.org/10.1093/molbev/msy171
  39. Munro, C., S. Siebert, F. Zapata, M. Howison, A. Damian-Serrano, S. Church, F.E. Goetz, P.R. Pugh, S.H.D. Haddock, C.W. Dunn (2018) Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution. Mol. Phylo. Evol. 127:823-833 doi.org/10.1016/j.ympev.2018.06.030
  40. Pugh, P.R., C.W. Dunn, and S.H.D. Haddock (2018) A description of Tottonophyes enigmatica gen. nov., sp. nov. in a new family of calycophoran siphonophores (Hydrozoa), with notes on calycophoran canals. Zootaxa 4415: 452-472
  41. Haddock, SHD, LM Christianson, WR Francis, S Martini, ML Powers, CW Dunn, PR Pugh, CE Mills, KJ Osborn, BA Seibel, CA Choy, CE Schnitzler, GI Matsumoto, M Messié, DT Schultz, JR Winnikoff, R Gasca, WE Browne, S Johnsen, KL Schlining, S von Thun, BE Erwin, JF Ryan, EV Thuesen (2017). Insights into the biodiversity, behavior, and bioluminescence of deep-sea organisms using molecular and maritime technology. Oceanography. 30(4):38–47, https://doi.org/10.5670/oceanog.2017.422
  42. • Choy, C.A., S.H.D. Haddock, B.H. Robison (2017) Deep pelagic food web structure as revealed by in situ feeding observations. Proc. Roy. Soc. B. 284: 20172116 dx.doi.org/10.1098/rspb.2017.2116
  43. Hoving, H.J.T., S.L. Bush, S.H.D. Haddock, B.H. Robison (2017) Bathyal feasting: post-spawning squid as a source of carbon for deep-sea communities. Proc. Roy. Soc. B. 284: 20172096
  44. Francis, W.R., L.M. Christianson, S.H.D. Haddock (2017) Symplectin evolved from multiple duplications in bioluminescent squid. PeerJ. 5:e3633 dx.doi.org/10.7717/peerj.3633
  45. • Martini, S.M and S.H.D. Haddock (2017) Quantification of bioluminescence from the surface to the deep sea demonstrates its predominance as an ecological trait. Nature Scientific Reports. 7:45750. nature.com/articles/srep45750
  46. • Hoving, H.J.T. and S.H.D. Haddock (2017) The giant deep-sea octopus Haliphron atlanticus forages on gelatinous fauna. Nature Scientific Reports. 7: 44952, nature.com/articles/srep44952
  47. Francis,W.R., L.M. Christianson, C.E. Schnitzler, M.L. Powers, and S.H.D. Haddock (2016) Non-excitable fluorescent protein orthologs found in ctenophores. BMC Evolutionary Biology. 16:167
  48. Fossette, S., K. Katija, J. A. Goldbogen, S. Bograd, W. Patry, M. J. Howard, T. Knowles, S.H.D. Haddock, L. Bedell, E.L. Hazen, B.H. Robison, T. A. Mooney, K. A. Shorter, T. Bastian, and A.C. Gleiss (2016) How to tag a jellyfish? A methodological review and guidelines to successful jellyfish tagging. J. Plankton Res. 38:1347-1363
  49. Gasca, R. and S.H.D. Haddock (2016). The rare deep-living hyperiid amphipod Megalanceoloides remipes (Barnard, 1932): complementary description and symbiosis. Zootaxa.4178: 138
  50. • Pugh, P.R. and S.H.D. Haddock (2016). A description of two new species of the genus Erenna (Siphonophora, Physonectae, Erennidae), with notes on recently collected specimens of other Erenna species. Zootaxa. 4189: 401-446.
  51. Francis, W.R., M.L. Powers, S.H.D. Haddock (2016) Bioluminescence spectra from three deep-sea polychaete worms. Marine Biology. 163:255 http://rdcu.be/mJvC
  52. • Haddock, S.H.D. and C.W. Dunn (2015) Fluorescent proteins function as a prey attractant: Experimental evidence from the hydromedusa Olindias formosus and other marine organisms. Biology Open. 4: 1094-1104. http://dx.doi.org/10.1242/bio.012138 (cover)
  53. Siebert, S., F.E. Goetz, S.H. Church, P. Bhattacharyya, F. Zapata, S.H.D. Haddock and C. W. Dunn (2015) Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones. EvoDevo. 6:22
  54. Zapata F, FE Goetz, SA Smith, M Howison, S Siebert, S Church, SM Sanders, C Lewis Ames, CS McFadden, SC France, M Daly, AG Collins, SHD Haddock, CW Dunn, P Cartwright (2015) Phylogenomic analyses support traditional relationships within Cnidaria. PLOS One. 10:e 013068.
  55. • Francis, W.R., N.C. Shaner, L.M. Christianson, M.L. Powers, S.H.D. Haddock (2015) Occurrence of isopenicillin-N-synthase homologs in bioluminescent ctenophores and implications for coelenterazine biosynthesis. PLoS One. 10(6): e0128742
  56. Gasca, R, E. Suárez-Morales & S.H.D. Haddock (2015) Sapphirina iris Dana and S. sinuicauda Brady (Copepoda, Cyclopoida), Predators of salps in Monterey Bay and the Gulf of California. Crustaceana 88:689-699
  57. • Dunn, C.W., S. Leys, S.H.D., Haddock. (2015) The hidden biology of sponges and ctenophores. Trends in Ecology and Evolution. 30: 282-291 (cover)
  58. Cazenave, F., C. Kecy, M. Risi, S.H.D. Haddock (2014) SeeStar: a low-cost, modular and open-source camera system for subsea observations. IEEE Oceans. 2014:1-7
  59. Gasca, R., R. Hoover, S.H.D. Haddock. (2014). New symbiotic associations of hyperiid amphipods (Peracarida) with gelatinous zooplankton in deep waters off California. JMBAUK. 95:503-511
  60. • Wilson, G. D.A. Aruliah, C.T. Brown, N.P. Chue Hong, M. Davis, R.T. Guy, S.H.D. Haddock, K.D. Huff, I.M. Mitchell, M.D. Plumbley, B. Waugh, E.P. White, and P. Wilson. (2014) Best practices for scientific computing. PLoS Biology. 12: e1001745. [*most-accessed PLoS Biology paper of 2014]
  61. Global Invertebrate Genomics Alliance Community of Scientists [primary member of consortium author group]. (2014) The Global Invertebrate Genomics Alliance (GIGA): Developing community resources to study diverse invertebrates. Journal of Heredity. 105:1-18
  62. • Francis, W.R., M.L. Powers, S.H.D. Haddock (2014). Characterization of an anthraquinone fluor from the bioluminescent, pelagic polychaete Tomopteris. Luminescence 29:1135-1140
  63. • Ryan, J.F. K. Pang, C.E. Schnitzler, [...] W.R. Francis, [...] S.H.D. Haddock, [...] A.D. Baxevanis. (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications on cell type evolution. Science. 342:1336-1344
  64. Siebert, S., P.R. Pugh, S.H.D. Haddock, C.W. Dunn. (2013) Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California. Zootaxa 3702: 201-232
  65. Thuesen, E. V. and S.H.D. Haddock (2013) Archeterokrohnia docrickettsae (Chaetognatha: Phragmophora: Heterokrohniidae), a new species of deep-sea arrow worm from the Gulf of California. Zootaxa. 3717:320-328
  66. Powers, M.L., 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
  67. • Francis, W.R., L.M. Christianson. 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 (highly accessed)
  68. Hurt, C; S.H.D. Haddock, Browne, W.E., (2013) Molecular phylogenetic evidence for the reorganization of the Hyperiid amphipods, a diverse group of pelagic crustaceans. Mol. Phy. Evol. 67:28-37
  69. • Condon, R.H., 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
  70. Madin, L.P., W.M. Hamner, S.H.D. Haddock, G.I. Matsumoto (2013) 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. Pages 71-82.
  71. • Schnitzler, C.E., 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
  72. Johnsen, S., T.M. Frank, S.H.D. Haddock, E.A. Widder, C.G. Messing (2012) Light and vision in the deep-sea benthos: 1. Bioluminescence at 500-1000 m depth in the Bahamian Islands. J. Exp. Biol. 215:3335-3343
  73. Condon, R.H., 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
  74. Shulman, I. B.F. Penta, M.A. Moline, S.H.D. Haddock, S. Anderson, M.J. Oliver, P. Sakalaukus (2012) Can vertical migrations of dinoflagellates explain observed bioluminescence patterns during an upwelling event? JGR Oceans.117, C01016, doi:10.1029/2011JC007480
  75. Osborn, K.J., S.H.D. Haddock, G.W. Rouse. (2011) Swima (Annelida, Acrocirridae), holopelagic worms from the deep Pacific. Zool. Jour. Linnean Soc. 163: 663-678
  76. 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, 12pp.
  77. 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.
  78. • Haddock, S.H.D., N. Mastroianni, L.M. Christianson (2010) A photoactivatable green-fluorescent protein from the phylum Ctenophora. Proc. Roy. Soc. B. 277:1155–1160.
  79. • Haddock, S.H.D., M.A. Moline, J.F. Case (2010) Bioluminescence in the sea. Ann. Rev. Mar. Sci. 2: 293-343. (highly accessed)
  80. 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.
  81. • 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.
  82. 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.
  83. • Osborn, K.J., S.H.D. Haddock, F. Pleijel, L.P. Madin, G.W. Rouse (2009) Deep-sea, swimming worms with luminescent “bombs”. Science. 325: 964
  84. 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. Oceanogr.54:2025-2033
  85. 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
  86. • Haddock, S.H.D. (2008). Reconsidering evidence for potential climate-related increases in jellyfish. Limnol. Oceanogr. 53: 2759-2762
  87. • 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, & G. Giribet. (2008) Broad phylogenomic sampling improves resolution of the Animal Tree of Life. Nature. 452:745-749 (cover)
  88. Collins, A.G., Bentlage, B., Lindner, A., Lindsay, D., Haddock, S.H.D., Jarms, G., Norenburg, J.L., Jankowski, T. & Cartwright, P. (2008) Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa. J. Mar. Biol. A. U.K.88:1673-1685
  89. • Schnitzler, C.E., R.J. Keenan, R. McCord, A. Matysik, L.M. Christianson, S.H.D. Haddock (2008). Spectral diversity of fluorescent proteins from the anthozoan Corynactis californica. Marine Biotech. 10: 328-342 (cover)
  90. 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.
  91. 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
  92. Sweeney, A.M., Haddock, S.H.D., Johnsen, S. (2007). Comparative visual acuity of coleoid cephalopods. Integr. Comp. Biol. 47: 808-814
  93. • Haddock, S.H.D. (2007). Comparative feeding behavior of planktonic ctenophores. Integr. Comp. Biol. 47: 847-853
  94. • Mills, C.E. and S.H.D. Haddock. (2007) Key to the Ctenophora. Light and Smith’s Manual: Intertidal invertebrates of the central California coast. J.T. Carlton, ed. U.C. Press. p 189-199
  95. Mills, C.E. and S.H.D. Haddock, C.W. Dunn, P.R. Pugh. (2007) Key to the Siphonophora. Light and Smith’s Manual: Intertidal invertebrates of the central California coast. J.T. Carlton, ed. Univ of California Press. p. 150-166.
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  97. Miller, S.D., S.H.D. Haddock, C.D. Elvidge, T.F. Lee. (2006) Twenty-thousand leagues over the seas: the first satellite perspective on bioluminescent ‘milky seas’. Intl. J. Remote Sens. 27: 5131-5143 (cover)
  98. • Haddock, S.H.D. (2006) “Luminous marine organisms” in Photoproteins in Bioanalysis, S. Daunert & S.K. Deo, eds. Wiley-VCH. New York, p. 25-47.
  99. • Collins, A.G., B. Bentlage, G.I. Matsumoto, S.H.D. Haddock, K. Osborn, B. Schierwater. (2006) Solution to the phylogenetic enigma of Tetraplatia, a worm-shaped cnidarian. Biology Letters (Royal Society). 2: 120-124
  100. Seibel, B.A., B.H. Robison, S.H.D. Haddock. (2005) First observations of brooding in a squid. Nature. 438: 929
  101. 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.
  102. • 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. (cover)
  103. • 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
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  105. 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.
  106. • Miller, S.D., S.H.D. Haddock, C.D. Elvidge, T.F. Lee. (2005) Detection of a bioluminescent milky sea from space. Proc. Nat. Acad. Sci. 102:14181-14184.
  107. 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
  108. 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 Res. 52: 2077-2085.
  109. • Haddock, S.H.D. (2004) A golden age of gelata: past and future research on planktonic cnidarians and ctenophores. Hydrobiologia 530/531:549-556.
  110. • 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.
  111. 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
  112. 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.
  113. • Haddock, S.H.D., T.J. Rivers, and B.H. Robison. (2001) Can coelenterates make coelenterazine? Dietary requirement for luciferin in cnidarian bioluminescence. Proc. Nat. Acad. Sci. 98: 11148-11151.
  114. • Podar, M., S.H.D. Haddock, M.L. Sogin, G.R. Harbison. (2001) A molecular phylogenetic framework for the phylum Ctenophora based on 18s rRNA genes. Mol. Phyl. Evol. 21: 218-230.
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  116. 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.
  117. 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 Work. Rep. no. 142. Amsterdam. pp. 137-142.
  118. 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 Res. 20:393-406.
  119. 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.
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  124. 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). Mar. Biol. 112 (2): 293-298.
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