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- Creator:
- Arighi, Cecilia N., Carterette, Ben, Cohen, K. Bretonnel, Krallinger, Martin, Wilbur, W. John, Fey, Petra, Dodson, Robert, Cooper, Laurel, Van Slyke, Ceri E., Dahdul, Wasila, Mabee, Paula, Li, Donghui, Harris, Bethany, Gillespie, Marc, Jimenez, Silvia, Roberts, Phoebe, Matthews, Lisa, Becker, Kevin, Drabkin, Harold, Bello, Susan, Licata, Luana, Chatr-aryamontri, Andrew, Schaeffer, Mary L., Park, Julie, Haendel, Melissa, Van Auken, Kimberly, Li, Yuling, Chan, Juancarlos, Muller, Hans-Michael, Cui, Hong, Balhoff, James P., Wu, Johnny Chi-Yang, Lu, Zhiyong, Wei, Chih-Hsuan, Tudor, Catalina O., Raja, Kalpana, Subramani, Suresh, Natarajan, Jeyakumar, Cejuela, Juan Miguel, Dubey, Pratibha, and Wu, Cathy
- Abstract:
- In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have...
- Resource Type:
- Article
- Full Text:
- . Bretonnel Cohen3, Martin Krallinger4, W. John Wilbur5, Petra Fey6, Robert Dodson6, Laurel Cooper7, Ceri E
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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...
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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:
- , Antonio Fabregat3, Sheldon McKay4, Joel Weiser4, Peter D’Eustachio5, Lincoln Stein4, Robert Petryszak3
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- Creator:
- Abberton, Michael, Batley, Jacqueline, Bentley, Alison, Bryant, John, Cai, Hongwei, Cockram, James, Costa de Oliveira, Antonio, Cseke, Leland J., Dempewolf, Hannes, De Pace, Ciro, Edwards, David, Gepts, Paul, Greenland, Andy, Hall, Anthony E., Henry, Robert, Hori, Kiyosumi, Howe, Glenn Thomas, Hughes, Stephen, Humphreys, Mike, Lightfoot, David, Marshall, Athole, Mayes, Sean, Nguyen, Henry T., Ogbonnaya, Francis C., Ortiz, Rodomiro, Paterson, Andrew H., Tuberosa, Roberto, Valliyodan, Babu, Varshney, Rajeev K., and Yano, Masahiro
- Abstract:
- Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on...
- Resource Type:
- Article
- Full Text:
- Edwards2*, Paul Gepts12, Andy Greenland4, Anthony E. Hall13, Robert Henry14, Kiyosumi Hori15, Glenn Thomas
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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:
- Miadlikowska, Jolanta, Kauff, Frank, Högnabba, Filip, Oliver, Jeffrey C., Molnár, Katalin, Fraker, Emily, Gaya, Ester, Hafellner, Josef, Hofstetter, Valérie, Gueidan, Cécile, Otálora, Mónica A. G., Hodkinson, Brendan, Kukwa, Martin, Lücking, Robert, Björk, Curtis, Sipman, Harrie J. M., Burgaz, Ana R., Thell, Arne, Passo, Alfredo, Myllys, Leena, Goward, Trevor, Fernández-Brime, Samantha, Hestmark, Geir, Lendemer, James, Lumbsch, H. Thorsten, Schmull, Michaela, Schoch, Conrad L., Sérusiaux, Emmanuël, Arnold, A. Elizabeth, Maddison, David R., Lutzoni, François, and Stenroos, Soili
- Abstract:
- The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa,...
- 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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- Creator:
- Condon, Bradford J., Leng, Yueqiang, Wu, Dongliang, Bushley, Kathryn E., Ohm, Robin A., Otillar, Robert, Martin, Joel, Schackwitz, Wendy, Grimwood, Jane, MohdZainudin, NurAinIzzati, Xue, Chunsheng, Wang, Rui, Manning, Viola A., Dhillon, Braham, Tu, Zheng Jin, Steffenson, Brian J., Salamov, Asaf, Sun, Hui, Lowry, Steve, LaButti, Kurt, Han, James, Copeland, Alex, Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Baker, Scott E., Ciuffetti, Lynda M., Grigoriev, Igor V., Zhong, Shaobin, and Turgeon, B. Gillian
- Abstract:
- The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary...
- Resource Type:
- Article
- Full Text:
- ., Dongliang Wu1., Kathryn E. Bushley3, Robin A. Ohm4, Robert Otillar4, Joel Martin4, Wendy Schackwitz4, Jane
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- Creator:
- Jones, Julia A., Creed, Irena F., Hatcher, Kendra L., Warren, Robert J., Adams, Mary Beth, Benson, Melinda H., Boose, Emery, Brown, Warren A., Campbell, John L., Covich, Alan, Clow, David W., Dahm, Clifford N., Elder, Kelly, Ford, Chelcy R., Grimm, Nancy B., Henshaw, Donald L., Larson, Kelli L., Miles, Evan S., Miles, Kathleen M., Sebestyen, Stephen D., Spargo, Adam T., Stone, Asa B., Vose, James M., and Williams, Mark W.
- Abstract:
- Analyses of long-term records at 35 headwater basins in the United States and Canada indicate that climate change effects on streamflow are not as clear as might be expected, perhaps because of ecosystem processes and human influences. Evapotranspiration was higher than was predicted by temperature in water-surplus ecosystems and lower...
- Resource Type:
- Article
- Full Text:
- Ecological Research Sites JULIA A. JONES, IRENA F. CREED, KENDRA L. HATCHER, ROBERT J. WARREN, MARY BETH
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- Creator:
- McPhillie, Martin, Zhou, Ying, El Bissati, Kamal, Dubey, Jitender, Lorenzi, Hernan, Capper, Michael, Lukens, Amanda K, Hickman, Mark, Muench, Stephen, Verma, Shiv Kumar, Weber, Christopher R., Wheeler, Kelsey, Gordon, James, Sanders, Justin, Moulton, Hong, Wang, Kai, Kim, Taek-Kyun, He, Yuqing, Santos, Tatiana, Woods, Stuart, Lee, Patty, Donkin, David, Kim, Eric, Fraczek, Laura, Lykins, Joseph, Esaa, Farida, Alibana-Clouser, Fatima, Dovgin, Sarah, Weiss, Louis, Brasseur, Gael, Wirth, Dyann, Kent, Michael, Hood, Leroy, Meunieur, Brigitte, Roberts, Craig W., Hasnain, S. Samar, Antonyuk, Svetlana V., Fishwick, Colin, and McLeod, Rima
- Abstract:
- Toxoplasma gondii, the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to facilitate drug development: EGS strain T. gondii forms cysts in vitro that induce oocysts in...