Publications

Aguero, F; Al-Lazikani, B; Aslett, M; Berriman, M; Buckner, FS; Campbell, RK; Carmona, S; Carruthers, IM; Chan, AWE; Chen, F; Crowther, GJ; Doyle, MA; Hertz-Fowler, C; Hopkins, AL; McAllister, G; Nwaka, S; Overington, JP; Pain, A; Paolini, GV; Pieper, U; Ralph, SA; Riechers, A; Roos, DS; Sali, A; Shanmugam, D; Suzuki, T; Van Voorhis, WC; Verlinde, CLMJ. 2008. INNOVATION Genomic-scale prioritization of drug targets: the TDR Targets database. Nature Reviews Drug Discovery. 7 (11): 900-907.

Alliegro, MC. 2008. The implications of centrosomal RNA. RNA Biology. 5 (4): 198-200.

Amaral-Zettler L; Peplies J; Ramette A; Fuchs B; Ludwig W; Glockner FO. 2008. Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany. Systematic and Applied Microbiology. 31 (4): 258-68.

Amaral-Zettler, LA; Rocca, JD; Lamontagne, MG; Dennett, MR; Gast, RJ. 2008. Changes in microbial community structure in the wake of Hurricanes Katrina and Rita. Environmental Science & Technology. 42 (24): 9072-9078.

Armstrong, P; Conrad, M. 2008. Blood collection from the American Horseshoe Crab, Limulus polyphemus. Journal of Visualized Experiments. 19. 10.3791/958

Aurrecoechea, C; Brestelli, J; Brunk, BP; Carlton, JM; Dommer, J; Fischer, S; Gajria, B; Gao, X; Gingle, A; Grant, G; Harb, OS; Heiges, M; Innamorato, F; Iodice, J; Kissinger, JC; Kraemer, E; Li, W; Miller, JA; Morrison, HG; Nayak, V; Pennington, C; Pinney, DF; Roos, DS; Ross, C; Stoeckert, CJ; Sullivan, S; Treatman, C; Wang, H. 2009. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Research. 37 (suppl 1): D526-D530. 10.1093/nar/gkn631

Bernier, JC; Birkeland, SR; Cipriano, MJ; McArthur, AG; Banks, MA. 2008. Differential Gene Expression between Fall- and Spring-Run Chinook Salmon Assessed by Long Serial Analysis of Gene Expression. Transactions of the American Fisheries Society. 137 (5): 1378-1388.

Bordenstein, SR; Paraskevopoulos, C; Dunning Hotopp, JC; Sapountzis, P; Lo, N; Bandi, C; Tettelin, H; Werren, JH; Bourtzis, K. 2009. Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and can not say. Molecular Biology and Evolution. 26 (1): 231-241.

Bradford, MA; Davies, CA; Frey, SD; Maddox, TR; Melillo, JM; Mohan, JE; Reynolds, JF; Treseder, KK; Wallenstein, MD. 2008. Thermal adaptation of soil microbial respiration to elevated temperature. Ecology Letters. 11 (12): 1316-1327.

Breneman, KD; Highstein, SM; Boyle, RD; Rabbitt, RD. 2008. The passive cable properties of hair cell stereocilia and their contribution to somatic capacitance measurements. Biophysical Journal. E-first. 10.1529/biophysj.108.137356

Brito, DA; Yang, Z; Rieder, CL. 2008. Microtubules do not promote mitotic slippage when the spindle assembly checkpoint cannot be satisfied. Journal of Cell Biology. 182 (4): 623-629.

Burton, AJ; Melillo, JM; Frey, SD. 2008. Adjustment of Forest Ecosystem Root Respiration as Temperature Warms. Journal of Integrative Plant Biology. 50 (11) 1467-1483.

Carmichael, RH; Hattenrath, T; Valiela, I; Michener, RH. 2008. Nitrogen stable isotopes in the shell of Mercenaria mercenaria trace wastewater inputs from watersheds to estuarine ecosystems. Aquatic Biology. 4 (2): 99-111.

Chappell RL; Anastassov I; Lugo P; Ripps H. 2008. Zinc-mediated feedback at the synaptic terminals of vertebrate photoreceptors. Experimental Eye Research. 87 (4): 394-397.

Clay JR; Paydarfar D; Forger DB. 2008. A simple modification of the Hodgkin and Huxley equations explains type 3 excitability in squid giant axons. Journal of the Royal Society Interface. 5 (29): 1421-1428.

Cooper, LW; McClelland, JW; Holmes, RM; Raymond, PA; Gibson, JJ; Guay, CK; Peterson, BJ. 2008. Flow-weighted values of runoff tracers (delta 18O, DOC, Ba, alkalinity) from the six largest Arctic rivers. Geophysical Research Letters. 35 (18): Art. No. L18606.

Crook, DJ; Kerr, LM; Mastro, VC. 2008. Distribution and Fine Structure of Antennal Sensilla in Emerald Ash Borer (Coleoptera: Buprestidae). Annals of the Entomological Society of America. 101 (6): 1103-1111.

Crook, DJ; Kerr, LM; Mastro, VC. 2008. Sensilla on the Antennal Flagellum of Sirex noctilio (Hymenoptera: Siricidae). Annals of the Entomological Society of America. 101 (6): 1094-1102.

DeGiorgis, JA; Petukhova, TA; Evans, TA; Reese, TS. 2008. Kinesin-3 is an Organelle Motor in the Squid Giant Axon. Traffic. 9 (11): 1867-1877.

Dethlefsen, L; Huse, S; Sogin, ML; Relman, DA. 2008. The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing. PLoS Biology. 6 (11): 2383-2400.

Ducklow, H. 2008. Microbial services: Challenges for microbial ecologists in a changing world. Aquatic Microbial Ecology. 53 (1): 13-19.

Ducklow, HW. 2008. Long-term studies of the marine ecosystem along the west Antarctic Peninsula. Deep Sea Research Part II. 55 (18-19): 1945-1948.

Ducklow, HW; Doney, SC; Steinberg, DK. 2008. Contributions of long-term research and time-series observations to marine ecology and biogeochemistry. Annual Review of Marine Science. E-first. 10.1146/annurev.marine.010908.163801

Ducklow, HW; Erickson, M; Kelly, J; Montes-Hugo, M; Ribic, CA; Smith, RC; Stammerjohn, SE; Karl, DM. 2008. Particle export from the upper ocean over the continental shelf of the west Antarctic Peninsula: A long-term record, 1992-2007. Deep Sea Research Part II. 55 (18-19): 2118-2131.

Edds-Walton, PL; Fay, RR. 2008. Directional and frequency response characteristics in the descending octaval nucleus of the toadfish (Opsanus tau). Journal of Comparative Physiology A: Sensory, Neural, and Behavioral Physiology. 194 (12): 1013-1029.

Frey, SD; Drijber, R; Smith, H; Melillo, J. 2008. Microbial biomass, functional capacity, and community structure after 12 years of soil warming. Soil Biology & Biochemistry. 40 (11): 2904-2907.

Fry, B; Cieri, M; Hughes, J; Tobias, C; Deegan, LA; Peterson, B. 2008. Stable isotope monitoring of benthic-planktonic coupling using salt marsh fish. Marine Ecology Progress Series. 369: 193-204.

Gage, DJ; Herron, PM; Arango Pinedo, C; Cardon, ZG. 2008. Live reports from the soil grain – the promise and challenge of microbiosensors. Functional Ecology. 22 (6): 983-989.

Gasol, JM; Pinhassi, J; Alonso-Saez, L; Ducklow, H; Herndl, GJ; Koblízek, M; Labrenz, M; Luo, Y; Moran, XAG; Reinthaler, T; Simon, M. 2008. Towards a better understanding of microbial carbon flux in the sea. Aquatic Microbial Ecology. 53 (1): 21-38.

Gast, RJ; Moran, DM; Audemard, C; Lyons, MM; DeFavari, J; Reece, KS; Leavitt, D; Smolowitz, R. 2008. Environmental distribution and persistence of Quahog Parasite Unknown (QPX). Diseases of Aquatic Organisms. 81 (3) 219-229.

Guo, YX; Liu, YF; Oldenbourg, R; Tang, JX; Valles, JM. 2008. Effects of osmotic force and torque on microtubule bundling and pattern formation. Physical Review E. 78 (4): Art. No. 041910.

Halvorson HO; Duff J. 2008. Offshore aquaculture legislation designed to balance production and protection. Marine Pollution Bulletin. 56 (10): 1673-1675.

Hanlon, RT; Chiao, CC; Mathger, LM; Barbosa, A; Buresch, KC; Chubb C. 2009. Cephalopod dynamic camouflage: bridging the continuum between background matching and disruptive coloration. Philosophical Transactions of the Royal Society B: Biological Sciences. 364 (1516): 429-437.

Hobbie, EA; Hobbie, JE. 2008. Natural abundance of N-15 in nitrogen-limited forests and trundra can estimate nitrogen cycling through mycoorrhizal fungi: A review. Ecosystems. 11 (5): 815-830.

Huang, S; Conte, MH. 2009. Source/process apportionment of major and trace elements in sinking particles in the Sargasso sea. Geochimica et Cosmochimica Acta. 73 (1): 65-90.

Huse, SM; Dethlefsen, L; Huber, JA; Welch, DM; Relman, DA; Sogin, ML. 2008. Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing. PLoS Genetics. 4 (11): Art. No. e1000255.

Inoue S. 2008. Microtubule Dynamics in Cell Division: Exploring Living Cells with Polarized Light Microscopy. Annual Review of Cell and Developmental Biology. 24: 1-28.

Lasek-Nesselquist, E; Bogomolni, AL; Gast, RJ; Welch, DM; Ellis, JC; Sogin, ML; Moore, MJ. 2008. Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential. Diseases of Aquatic Organisms. 81 (1): 39-51.

Madsen, PT; Wilson, M; Johnson, M; Hanlon, RT; Bocconcelli, A; de Soto, NA; Tyack, PL. 2007. Clicking for calamari: toothed whales can echolocate squid Loligo pealeii. Aquatic Biology. 1 (2): 141-150.

Maresca, TJ; Salmon, ED. 2009. Intrakinetochore stretch is associated with changes in kinetochore phosphorylation and spindle assembly checkpoint activity. Journal of Cell Biology. 184 (3): 373-381.

Maruska KP; Korzan WJ; Mensinger AF. 2009. Individual, temporal, and population-level variations in circulating 11-ketotestosterone and 17beta-estradiol concentrations in the oyster toadfish Opsanus tau. Comparative Biochemistry & Physiology A. E-first. 10.1016/j.cbpa.2009.01.002

Mathger LM; Denton EJ; Marshall NJ; Hanlon RT. 2008. Mechanisms and behavioural functions of structural coloration in cephalopods. Journal of the Royal Society Interface. E-first. 10.1098/rsif.2008.0366.focus

McNamara, JP; Kane, DL; Hobbie, JE; Kling, GW. 2008. Hydrologic and biogeochemical controls on the spatial and temporal patterns of nitrogen and phosphorus in the Kuparuk River, arctic Alaska. Hydrological Processes. 22 (17): 3294-3309.

Miller-Sims, VC; Gerlach, G; Kingsford, MJ; Atema, J. 2008. Dispersal in the spiny damselfish, Acanthochromis polyacanthus, a coral reef fish species without a larval pelagic stage. Molecular Ecology. 17 (23): 5036-5048.

Moran, XAG; Calvo-Díaz, A. 2008. Single-cell vs. bulk activity properties of coastal bacterioplankton over an annual cycle in a temperate ecosystem. FEMS Microbiology Ecology. E-first. 10.1111/j.1574-6941.2008.00601.x

Nahum, LA; Pereira, SL. 2008. Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence. Applications of Computational Intelligence in Biology. 122: 259-279.

Norton, CN. 2008. The Encyclopedia of Life, Biodiversity Heritage Library, Biodiversity Informatics and Beyond Web 2.0. First Monday. 13 (8).

Oldenbourg R. 2008. Polarized light field microscopy: an analytical method using a microlens array to simultaneously capture both conoscopic and orthoscopic views of birefringent objects. Journal of Microscopy. 231 (3): 419-32.

Patterson, DJ; Faulwetter, S; Shipunov, A. 2008. Principles for a names-based cyberinfrastructure to serve all of biology. Zootaxa. (1950): 153-163.

Pomeroy, LR; Williams, PJI; Azam, F; Hobbie, JE. 2007. The Microbial Loop. Oceanography. 20 (2): 28-33.

Reznikoff WS. 2008. Transposon Tn5. Annual Review of Genetics. 42: 269-286.

Ripps, H. 2008. The color purple: milestones in photochemistry. FASEB Journal. 22 (12): 4038-4043.

Robertson, GP; Dale, VH; Doering, OC; Hamburg, SP; Melillo, JM; Wander, MM; Parton, WJ; Adler, PR; Barney, JN; Cruse, RM; Duke, CS; Fearnside, PM; Follett, RF; Gibbs, HK; Goldemberg, J; Mladenoff, DJ; Ojima, D; Palmer, MW; Sharpley, A; Wallace, L; Weathers, KC; Wiens, JA; Wilhelm, WW. 2008. Sustainable Biofuels Redux. Science. 322 (5898): 49-50.

Sarkar, IN; Planet, PJ; Desalle, R. 2008. CAOS software for use in character-based DNA barcoding. Molecular Ecology Resources. 8 (6): 1256-1259.

Schneider, MJ; Ulland, M; Sloboda, RD. 2008. A Protein Methylation Pathway in Chlamydomonas Flagella Is Active During Flagellar Resorption. Molecular Biology of the Cell. 19 (10): 4319-4327.

Shribak, M; LaFountain, J; Biggs, D; Inoue, S. 2007. Quantitative orientation-independent differential interference contrast (DIC) microscopy coupled with orientation-independent polarization microscopy. Microscopy and Microanalysis. 13: 10-11.

Shtutman, M; Chausovsky, A; Prager-Khoutorsky, M; Schiefermeier, N; Boguslavsky, S; Kam, Z; Fuchs, E; Geiger, B; Borisy, GG; Bershadsky, AD. 2008. Signaling function of alpha-catenin in microtubule regulation. Cell Cycle. 7 (15): 2377-2383.

Shum, WWC; Da Silva, N; Mckee, M; Smith, PJS; Brown, D; Breton, S. 2008. Transepithelial Projections from Basal Cells Are Luminal Sensors in Pseudostratified Epithelia. Cell. 135 (6): 1108-1117.

Stewart, JR; Gast, RJ; Fujioka, RS; Solo-Gabriele, HM; Meschke, JS; Amaral-Zettler, LA; del Castillo, E; Polz, MF; Collier, TK; Strom, MS; Sinigalliano, CD; Moeller, PDR; Holland, AF. 2008. The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs. Environmental Health. 7: Art. No. S3.

Sussman, R. 2008. Serendipity. Journal of Biological Chemistry. E-first. 10.1074/jbc.X800013200

Sutherland, RL; Mathger, LM; Hanlon, RT; Urbas, AM; Stone, MO. 2008. Cephalopod coloration model. II. Multiple layer skin effects. Journal of the Optical Society of America A. Optics, Image Science and Vision. 25 (8): 2044-2054.

Szabo, TM; Brookings, T; Preuss, T; Faber, DS. 2008. Effects of temperature acclimation on a central neural circuit and its behavioral output. Journal of Neurophysiology. E-first. 10.1152/jn.91033.2008

Tang, JW; Bolstad, PV; Martin, JG. 2009. Soil carbon fluxes and stocks in a Great Lakes forest chronosequence. Global Change Biology. 15 (1): 145-155.

Teichberg, M; Fox, SE; Aguila, C; Olsen, YS; Valiela, I. 2008. Macroalgal responses to experimental nutrient enrichment in shallow coastal waters: growth, internal nutrient pools, and isotopic signatures. Marine Ecology Progress Series. 368: 117-126.

Turanov, AA; Lobanov, AV; Fomenko, DE; Morrison, HG; Sogin, ML; Klobutcher, LA; Hatfield, DL; Gladyshev, VN. 2009. Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Science. 323 (5911): 259-261.

Turnbaugh, PJ; Hamady, M; Yatsunenko, T; Cantarel, BL; Duncan, A; Ley, RE; Sogin, ML; Jones, WJ; Roe, BA; Affourtit, JP; Egholm, M; Henrissat, B; Heath, AC; Knight, R; Gordon, JI. 2009. A core gut microbiome in obese and lean twins. Nature. 457 (7228): 480-U7.

Wollheim, WM; Peterson, BJ; Thomas, SM; Hopkinson, CH; Vorosmarty, CJ. 2008. Dynamics of N removal over annual time periods in a suburban river network. Journal of Geophysical Research G: Biogeosciences. 113 (G3): Art. No. G03038.

Yu, E; Kanno, E; Choi, S; Sugimori, M; Moreira, JE; Llinas, RR; Fukuda, M. 2008. Role of Rab27 in synaptic transmission at the squid giant synapse. Proceedings of the National Academy of Sciences. 105 (41): 16003-16008.

Zhang, Z; Bodznick, D. 2008. Plasticity in a cerebellar-like structure: suppressing reafference during episodic behaviors. Journal of Experimental Biology. 211 (23): 3720-3728.

Zimmermann, A; Germer, S; Neill, C; Krusche, AV; Elsenbeer, H. 2008. Spatio-temporal patterns of throughfall and solute deposition in an open tropical rain forest. Journal of Hydrology. 360 (1-4): 87-102.