The first paper to apply advanced machine learning techniques to better understand sperm whale bioacoustics.
Gruber, D.F., Phillips, B.T., O’Brien, R., Boominathan, V., Veeraraghavan, A., Vasan, G., O’Brien, P., Pieribone, V.A., Sparks, J.S. 2019. Bioluminescent Flashes Drive Nighttime Schooling Behavior and Synchronized Swimming Dynamics in Flashlight Fish. PLOS ONE. 10.1371/journal.pone.0219852.
Park, H.B., Lam, Y.C., Gaffney, J.P., Weaver, J.C., Krivoshik, S.R., Hamchand, R., Pieribone, V., Gruber, D.F.†, Crawford, J.M.† 2019. Bright-green biofluorescence in sharks derives from bromo-kynurenine metabolism. iScience. doi.org/10.1016/j.isci.2019.07.019.
Phillips, B.T., Becker, K.P., Kurumaya, S., Galloway, K.C., Whittredge, G., Vogt, D., Teeple, C., Rosen, M.H., Pieribone, V.A., Gruber, D.F., and R.J. Wood. 2018. A Dexterous, Glove-Based Teleoperable Low-Power Soft Robotic Arm for Delicate Deep-Sea Biological Exploration, Scientific Reports 8:14779.
Tessler, M., Gaffney, J.P., Crawford, J.M., Trautman, E., Gujarati, N.A., Alatalo, P., Pieribone, V.A. and D.F. Gruber. 2018. Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens. PeerJ 6:e5506 https://doi.org/10.7717/peerj.5506
Vogt, D.M., Becker, K.P., Phillips, B.T., Graule, M.A., Rotjan, R.D., Shank, T.M., Cordes, E.E., Wood, R.J. and D.F. Gruber. 2018. Shipboard design and fabrication of custom 3D-printed soft robotic manipulators for the investigation of delicate deep-sea organisms. PLoS ONE 13(8): e0200386. https://doi.org/10.1371/journal. pone.0200386
Teoh, Z.E., Phillips, B.T., Becker, K., Whittredge, G., Weaver, J.C., Hoberman, C., Gruber, D.F. and R.J. Wood. 2018. Rotary-actuated folding polyhedrons for midwater investigation of delicate marine organisms. Science Robotics, 3, eaat5276.
A new device to safely enclose delicate sea creatures, such as jellyfish, inside a folding polyhedral enclosure and lets them go without harm. This uses a novel, folding rotary design that only requires one motor to operate.
Kurumaya, S., Phillips, B.T., Becker, K.P., Rosen, M.H., Gruber, D.F., Galloway, K.C., Suzumori, K., and R.J. Wood. 2018. A Modular Soft Robotic Wrist for Underwater Manipulation. Soft Robotics, 5:399-409. 10.1089/soro.2017.0097.
D.F. Gruber, Phillips, B.T., Marsh, L., and J.S. Sparks. 2018. In situ Observations of the Meso-Bathypelagic Scyphozoan, Deepstaria enigmatica (Semaeostomeae: Ulmaridae). American Museum Novitates, 3900, 1-14.
Gruber DF, Loew ER, Deheyn DD, Akkaynak D, Gaffney JP, Smith WL, Davis MP, Stern JH, Pieribone VA, Sparks JS. 2016. Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology. Scientific Reports. doi: 10.1038/srep24751.
The development of a “shark-eye” camera to study what biofluorescence may mean to sharks.
Phillips B, Gruber DF, Vasan G, Roman CN, Pieribone V, Sparks JS. 2016. Observations of in situ deep-sea marine bioluminescence with a high-speed, high-resolution sCMOS camera. Deep Sea Research Part I: Oceanographic Research Papers. 111:102-109.
The use of a extremly sensitive low-light camera to study deep sea bioluminescence.
Phillips, B.T., D.F. Gruber, G. Vasan, V.A. Pieribone, J.S. Sparks, and C.N. Roman. 2016. First evidence of bioluminescence on a “black smoker” hydrothermal chimney. Oceanography 29(2):10–11, http://dx.doi.org/10.5670/oceanog.2016.27.
Einbinder, S., Gruber, D.F., Solomon, E., Keren, N., Tchernov, D. 2016. “Novel adaptive photosynthetic characteristics of mesophotic symbiotic microalgae within the reef-building coral, Stylophora pistillata.” Frontiers in Marine Science. doi: 10.3389/fmars.2016.00195.
A new type of photosynthesis invented by algae on the deep coral reef.
Bhattacharya, D., S. Agrawal, M. Aranda, S. Baumgarten, M. Belcaid, J.L. Drake, D. Erwin, S. Foret, R.D. Gates, D.F. Gruber, B. Kamel, M.P. Lesser, O. Levy, Y.J. Liew, M. MacManes, T. Mass, M. Medina, S. Mehr, E. Meyer, D.C. Price, H.M. Putnam, H. Qiu, C. Shinzato, E. Shoguchi, A.J. Stokes, S. Tambutte, D. Tchernov, C.R. Voolstra, N. Wagner, C.W. Walker, A.P. Weber, V. Weis, E. Zelzion, D. Zoccola, and P.G. Falkowski. 2016. “Comparative Genomics Explains the Evolutionary Success of Reef-Forming Corals.” eLife 5. doi:10.7554/eLife.13288.
A comprehensive analysis of coral genomics.
Dishon, G., Fisch, J., Horn, I., Kaczmarek, K., Bijma, J., Gruber, D.F., Nir, O., Popovich, Y. and D. Tchernov. 2015. A novel paleo-bleaching proxy using boron isotopes and high-resolution laser ablation to reconstruct coral bleaching events, Biogeosciences, 12, 5677-5687.
2015_Novel paleo-bleaching proxy using boron isotopes
D. F. Gruber, J.P. Gaffney, S. Mehr, J.S. Sparks, J. Platisa, V.A. Pieribone. 2015. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment, PLoS ONE. 10(11): e0140972. doi:10.1371/journal.pone.0140972.
The discovery of a new family of fluorescent proteins from marine eels
Mehr, S.F.M., Verdes, A., DeSalle, R., Sparks, J., Pieribone, V. and D. F. Gruber. 2015. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)”, BMC Genomics, 16:445.
The most comprehensive genomic analysis of the Bearded Fireworm. This is also the first report of biofluorescence in this stinging species.
Sparks, J. S., Schelly, R. C., Smith, W. L., Davis, M. P., Tchernov, D., Pieribone, V. A., and D. F. Gruber. 2014. The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon. PLoS ONE 9(1): e83259.
The discovery of over 180 new species of biofluorescent fish and sharks.
Gruber, D.F., Kao, H-T and V.A. Pieribone. 2014. Isolated australian coral reef fluorescent proteins and cell-based kinase or phosphatase platforms for cancer drug development, US Patent # US 8,709,981.
Rubin-Blum, M., Tsadok, R., Shemesh, E., Goodman-Tchernov, B. N., Austin, J. A., Coleman, D. F. Gruber. (2014). Distribution of the Lamellibrachia spp. (Siboglinidae, Annelida) and their trophosome endosymbiont phylotypes in the Mediterranean Sea. Mar. Biol. 161, 1229–1239. doi:10.1007/s00227-014-2413-y.
This study used the Hercules Remotely Operated Vehicle to show how a deep sea tube worm is distributed along the bottom of the Mediterranean Sea.
Mehr, S.F.M., DeSalle, R., Kao, H-T, Narechania, A., Han, Z., Tchernov, D., Pieribone, V. and D. F. Gruber. 2013. De novo RNA-seq assembly and clustering of expressed proteins from uncharacterized corals, BMC Genomics 14:546.
The use of transcriptomics to discover several new fluorescent proteins from a mesophotic coral.
Gruber, D.F, Mass, T., Tchernov, D. 2012. Symbiotic Transition of Algae-Coral Triggered by Paleo-Climatic Events? Trends in Ecology and Evolution, 27(4), 194-195.
A hypothesis that low oxygen concentrations following a major mass extinction event helped forge the symbiotic relationship between coral and algae.
Nir, O., Gruber, D.F., Einbinder, S. Kark, S., and D. Tchernov. 2011. Changes in scleractinian coral Seriatopora hystrix morphology and its endocellular Symbiodinium characteristics along a bathymetric gradient from shallow to mesophotic reef, Coral Reefs. 30:1089-1100.
How the composition of algal inside a coral shifts as they descend into the deep reef.
Kuguru, B., Achituv, Y., Gruber, D.F. and D. Tchernov. 2010. Photoacclimation mechanisms of corallimorpharians on coral reefs: Photosynthetic parameters of zooxanthellae and host cellular responses to variation in irradiance, J. Exp. Mar. Biol. Ecol. 394:53-62.
How algae and corals coral respond changes in sunlight.
Gruber, D.F., DeSalle, R., Lienau, E.K., Tchernov, D., Pieribone, V.A. and H-T Kao. 2009. Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns, Molecular Biology and Evolution. 26(12):2841-2848. (Highlighted in: Oct 1, 2009 Nature 461:572)
The discovery of 18 new fluorescent proteins – and the finding that an internal region of the fluorescent protein molecule has undergone divergent evolution.
Gruber, D.F., Simjouw, J-P. Seitzinger, S.P. and G. L. Taghon. 2006. Dynamics and Characterization of Refractory Dissolved Organic Matter Produced by a Pure Bacterial Culture in an Experimental Predator-Prey System. Applied and Environmental Microbiology 72(6): 4184-4191.
How the predator-prey relationship of bacteria and protozoa impacts the production of refractory carbon in the ocean.
Pieribone, V., and D. F. Gruber. 2006. Aglow in the Dark: The Revolutionary Science of Biofluorescence. Harvard University Press, Cambridge, MA. 288 pp.
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A journalistic narrative of the discovery of fluorescent proteins. Three scientists profiled in the study were later awarded the 2008 Nobel Prize for Chemistry “for the discovery and development of the green fluorescent protein.”
Nasar, S. and Gruber, D. 2006. Manifold Destiny. The New Yorker, Aug. 28 issue, p. 44-57. (Also included in The Best American Science Writing 2007, Harper Perennial).
An investigative journalism article on the solution to the Poincare Conjecture by Gregori Perelman. This article led to the retraction a competing scientific publication that claimed to provide the “complete proof.”