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- Creator:
- Deans, Andrew R., Lewis, Suzanna E., Huala, Eva, Anzaldo, Salvatore S., Ashburner, Michael, Balhoff, James P., Blackburn, David C., Blake, Judith A., Burleigh, J. Gordon, Chanet, Bruno, Cooper, Lauren D., Courtot, Mélanie, Csösz, Sándor, Cul, Hong, Dahdul, Wasila, Das, Sandip, Dececchi, T. Alexander, Dettal, Agnes, Diogo, Rui, Druzinsky, Robert E., Dumontier, Michel, Franz, Nico M., Friedrich, Frank, Gkoutos, George V., Haendel, Melissa, Harmon, Luke J., Hayamizu, Terry F., He, Yongqun, Hines, Heather M., Ibrahim, Nizar, Jackson, Laura M., Jaiswal, Pankaj, James-Zorn, Christina, Köhler, Sebastian, Lecointre, Guillaume, Lapp, Hilmar, Lawrence, Carolyn J., Le Novère, Nicolas, Lundberg, John G., Macklin, James, Mast, Austin R., Midford, Peter E., Mikó, István, Mungall, Christopher J., Oellrich, Anika, Osumi-Sutherland, David, Parkinson, Helen, Ramírez, Martín J., Richter, Stefan, Robinson, Peter N., Ruttenberg, Alan, Schulz, Katja S., Segerdell, Erik, Seltmann, Katja C., Sharkey, Michael J., Smith, Aaron D., Smith, Barry, Specht, Chelsea D., Squires, R. Burke, Thacker, Robert W., Thessen, Anne, Fernandez-Triana, Jose, Vihinen, Mauno, Vize, Peter D., Vogt, Lars, Wall, Christine E., Walls, Ramona L., Westerfeld, Monte, Wharton, Robert A., Wirkner, Christian S., Woolley, James B., Yoder, Matthew J., Zorn, Aaron M., and Mabee, Paula
- Abstract:
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
- Resource Type:
- Article
- Full Text:
- through Phenotypes Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., et al. (2015
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- Creator:
- Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
- Abstract:
- Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
- Full Text:
- aestivum (bread wheat) IWGSP1/IWGSP1 (MIPS) SNPs Triticum urartu (einkorn wheat, A-genome progenitor
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- Creator:
- Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
- Abstract:
- Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
- Full Text:
- Kerhornou3, Brandon Walts3, Nuno A. Fonseca3, Laura Huerta3, Maria Keays3, Y. Amy Tang3, Helen Parkinson3
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- Creator:
- Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
- Abstract:
- Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
- Resource Type:
- Article
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- Creator:
- Scavia, Donald, Allan, J. David, Arend, Kristin K., Brandt, Stephen B., Bartell, Steven, Bosch, Nate S., Briland, Ruth D., Daloğlu, Irem, DePinto, Joseph V., Dolan, David M., Evans, Mary Anne, Farmer, Troy M., Goto, Daisuke, Han, Haejin, Höök, Tomas O., Knight, Roger, Ludsin, Stuart A., Mason, Doran, Michalak, Anna M., Richards, R. Peter, Roberts, James J., Rucinski, Daniel K., Rutherford, Edward, Schwab, David J., Sesterhenn, Timothy M., Zhang, Hongyan, and Zhou, Yuntao
- Abstract:
- Relieving phosphorus loading is a key management tool for controlling Lake Erie eutrophication. During the 1960s and 1970s, increased phosphorus inputs degraded water quality and reduced central basin hypolimnetic oxygen levels which, in turn, eliminated thermal habitat vital to cold-water organisms and contributed to the extirpation of important benthic macroinvertebrate...
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- Article
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- addressing the re-eutrophication of Lake Erie: Central basin hypoxia Donald Scavia a,⁎, J. David Allan b
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- Creator:
- Bollmann, Annette, Sedlacek, Christopher J., Norton, Jeanette, Laanbroek, Hendrikus J., Suwa, Yuichi, Stein, Lisa Y., Klotz, Martin G., Arp, Daniel J., Sayavedra-Soto, Luis, Lu, Megan, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, James, Woyke, Tanja, Pitluck, Sam, Pennacchio, Len, Nolan, Matt, Land, Miriam L., Huntemann, Marcel, Deshpande, Shweta, Han, Cliff, Chen, Amy, Kyrpides, Nikos, Movromatis, Konstantinos, Markowitz, Victor, Szeto, Ernest, Ivonova, Natalia, Mikhailova, Natalia, Pagani, Ioanna, Pati, Amrita, Peters, Lin, Ovchinnikova, Galina, Goodwin, Lynne A., and Lucas, Susan M.
- Abstract:
- Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high...
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- Article
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- Pagani9, Amrita Pati9, Lin Peters9, Galina Ovchinnikova9, and Lynne A. Goodwin8 1 Miami University
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- Creator:
- Stoltzfus, Arlin, Lapp, Hilmar, Matasci, Naim, Deus, Helena, Sidlauskas, Brian, Zmasek, Christian M., Vaidya, Gaurav, Pontelli, Enrico, Cranston, Karen, Vos, Rutger, Webb, Campbell O, Harmon, Luke J., Pirrung, Megan, O'Meara, Brian, Pennell, Matthew W., Mirarab, Siavash, Rosenberg, Michael S., Balhoff, James P., Bik, Holly M., Heath, Tracy A., Midford, Peter E., Brown, Joseph W., McTavish, Emily Jane, Sukumaran, Jeet, Westneat, Mark, Alfaro, Michael E., Steele, Aaron, and Jordan, Greg
- Abstract:
- Background: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential...
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- Article
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- , James P Balhoff2, Holly M Bik16, Tracy A Heath17, Peter E Midford2, Joseph W Brown11, Emily Jane
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- Creator:
- Manning, Viola A., Pandelova, Iovanna, Dhillon, Braham, Wilhelm, Larry J., Goodwin, Stephen B., Berlin, Aaron M., Figueroa, Melania, Freitag, Michael, Hane, James K., Henrissat, Bernard, Holman, Wade H., Kodira, Chinnappa D., Martin, Joel, Oliver, Richard P., Robbertse, Barbara, Schackwitz, Wendy, Schwartz, David C., Spatafora, Joseph W., Turgeon, B. Gillian, Yandava, Chandri, Young, Sarah, Zhou, Shiguo, Zeng, Qiandong, Grigoriev, Igor V., Ma, Li-Jun, and Ciuffetti, Lynda M.
- Abstract:
- Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins ( HST), which are recognized by their host in a genotype-specific...
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- Article
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- GGG004044 41..63 INVESTIGATION Comparative Genomics of a Plant
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- Creator:
- Grace, James B., Adler, Peter B., Seabloom, Eric W., Borer, Elizabeth T., Hillebrand, Helmut, Hautier, Yann, Hector, Andy, Harpole, W. Stanley, O'Halloran, Lydia R., Anderson, T. Michael, Bakker, Jonathan D., Brown, Cynthia S., Buckley, Yvonne M., Collins, Scott L., Cottingham, Kathryn L., Crawley, Michael J., Damschen, Ellen I., Davies, Kendi F., DeCrappeo, Nicole M., Fay, Philip A., Firn, Jennifer, Gruner, Daniel S., Hagenah, Nicole, Jin, Virginia L., Kirkman, Kevin P., Knops, Johannes M. H., La Pierre, Kimberly J., Lambrinos, John G., Melbourne, Brett A., Mitchell, Charles E., Moore, Joslin L., Morgan, John W., Orrock, John L., Prober, Suzanne M., Stevens, Carly J., Wragg, Peter D., and Yang, Louie H.
- Abstract:
- Pan et al. claim that our results actually support a strong linear positive relationship between productivity and richness, whereas Fridley et al. contend that the data support a strong humped relationship. These responses illustrate how preoccupation with bivariate patterns distracts from a deeper understanding of the multivariate mechanisms that control...
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- Article
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- al.James B. Grace Species Richness'' Response to Comments on ''Productivity Is a Poor Predictor of Plant
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- Creator:
- Buizert, Christo, Adrian, Betty, Ahn, Jinho, Albert, Mary, Alley, Richard B., Baggenstos, Daniel, Bauska, Thomas K., Bay, Ryan C., Bencivengo, Brian B., Bentley, Charles R., Brook, Edward J., Chellman, Nathan J., Clow, Gary D., Cole-Dai, Jihong, Conway, Howard, Cravens, Eric, Cuffey, Kurt M., Dunbar, Nelia W., Edwards, Jon S., Fegyveresi, John M., Ferris, Dave G., Fitzpatrick, Joan J., Fudge, T. J., Gibson, Chris J., Gkinis, Vasileios, Goetz, Joshua J., Gregory, Stephanie, Hargreaves, Geoffrey M., Iverson, Nels, Johnson, Jay A., Jones, Tyler R., Kalk, Michael L., Kippenhan, Matthew J., Koffman, Bess G., Kreutz, Karl, Kuhl, Tanner W., Lebar, Donald A., Lee, James E., Marcott, Shaun A., Markle, Bradley R., Maselli, Olivia J., McConnell, Joseph R., McGwire, Kenneth C., Mitchell, Logan E., Mortensen, Nicolai B., Neff, Peter D., Nishiizumi, Kunihiko, Nunn, Richard M., Orsi, Anais J., Pasteris, Daniel R., Pedro, Joel B., Pettit, Erin C., Price, P. Buford, Priscu, John C., Rhodes, Rachael H., Rosen, Julia L., Schauer, Andrew J., Schoenemann, Spruce W., Sendelbach, Paul J., Severinghaus, Jeffrey P., Shturmakov, Alexander J., Sigl, Michael, Slawny, Kristina R., Souney, Joseph M., Sowers, Todd A., Spencer, Matthew K., Steig, Eric J., Taylor, Kendrick C., Twickler, Mark S., Vaughn, Bruce H., Voigt, Donald E., Waddington, Edwin D., Welten, Kees C., Wendricks, Anthony W., White, James W. C., Winstrup, Mai, Wong, Gifford J., and Woodruff, Thomas E.
- Abstract:
- The last glacial period exhibited abrupt Dansgaard–Oeschger climatic oscillations, evidence of which is preserved in a variety of Northern Hemisphere palaeoclimate archives¹. Ice cores show that Antarctica cooled during the warm phases of the Greenland Dansgaard–Oeschger cycle and vice versa[superscript 2,3], suggesting an interhemispheric redistribution of heat through a mechanism...
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- oscillations, evidence of which is preserved in a variety of Northern Hemisphere palaeoclimate archives1. Ice