Tanya Z. Berardini, Leonore Reiser, Donghui Li, Yarik Mezheritsky, Robert Muller, Emily Strait and Eva Huala (2015) The Arabidopsis Information Resource: Making and mining the "gold standard" annotated reference plant genome. genesis 53: 474-485. DOI: 10.1002/dvg.22877
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Philippe Lamesch; Tanya Z. Berardini; Donghui Li; David Swarbreck; Christopher Wilks; Rajkumar Sasidharan; Robert Muller; Kate Dreher; Debbie L. Alexander; Margarita Garcia-Hernandez; Athikkattuvalasu S. Karthikeyan; Cynthia H. Lee; William D. Nelson; Larry Ploetz; Shanker Singh; April Wensel; Eva Huala (2011) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research; doi: 10.1093/nar/gkr1090.
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Lamesch P, Dreher K, Swarbreck D, Sasidharan R, Reiser L, Huala E (2010) Using the Arabidopsis in-formation resource (TAIR) to find information about Arabidopsis genes. Curr Protoc Bioinformatics Chapter 1:Unit1.11.
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David Swarbreck*, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang and Eva Huala (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Research. 36:D1009-D1014.
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Ilic K, Kellogg E, Jaiswal P, Zapata F, Stevens P, Vincent L, Pujar A, Avraham S, Reiser L, McCouch SR, Sachs S, Schaeffer M, Rhee SY, Ware D and Stein L. (2006) Plant Structure Ontology: A Unified Vocabulary for Flowering Plants. Plant Physiology. 143(2):587-99.
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Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser R, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, and McCouch S. (2006) Whole Plant Growth Stage Ontology: History, Development and Application. Plant Physiology. 142(2):414-28.
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Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360
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Gene Ontology Consortium (2006) The Gene Ontology Project in 2006. Nucleic Acids Research. 34(Database issue):D322-6
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Yoo, D, Xu, I, Berardini, T, Rhee, S, Narayanasamy, V, Twigger, S (2006)
PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature in Current Protocols in Bioinformatics, © John Wiley & Sons, Inc.
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Margarita Garcia-Hernandez and Leonore Reiser (2006)
Using Information From Public Arabidopsis Databases to Aid Research. in Methods in Molecular Biology, vol. 323: Arabidopsis Protocols, Second Edition, J. Salinas and J. J. Sanchez-Serrano © Humana Press Inc., Totowa, NJ
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Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, Zapata F. (2005) Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Functional and Integrated Genomics. 6:388-397.
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Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology. 138(1):1-3.
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Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. 138(2):569-70
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Rhee SY, Zhang P, and Foerster H, and Tissier C (2005) AraCyc: Overview of an Arabidopsis Metabolism Database and Its Applications for Plant Research. In Biotechnology in Agriculture and Forestry: Plant Metabolomics. K. Saito, R. Dixon and L. Willmitzer ed., Springer. volume 57. pp. 141-153.
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Yan, T, Yoo, D, Berardini, T, Mueller, L, Weems, D, Weng, S, Cherry, JM, Rhee, SY(2005)
PatMatch: a program for finding patterns in peptide and nucleotide sequences
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Reiser, Leonore and Rhee, Seung Yon (2005)
Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes.
in Current Protocols in Bioinformatics, Andreas D. Baxevanis et.al. eds., John Wiley and Sons, NY.NY.
Available in hard copy, PDF, HTML Requires subscription.
Schlueter, SD, Wilkerson, MD, Huala, E, Rhee, SY, and Brendel, V (2005)
Community-based gene structure annotation. TRENDS in Plant Science 10(1):9-14
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Zhang, P, Foerster, H, Tissier, C, Mueller, L, Paley, S., Karp, P, Rhee, SY(2005)
MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research. Plant Physiology 2005 138: 27-37
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Bard, JL and Rhee, SY (2004)
Ontologies in biology: design, applicatioins and future challenges. Nature Review Genetics 5(3):213-22.
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Berardini, TZ, Mundodi, S, Reiser, R, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004)
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11.
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Dolan, EL, Soots, BE, Lemaux, PG, Rhee, SY, and Reiser, L (2004)
Strategies to Avoid Reinventing the Pre-college Education and Outreach Wheel. Genetics. 166:1601-1609.
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Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium. (2004)
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 Database issue:D258-61.
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Krieger, CJ, Zhang, P, Mueller, L, Wang, A, Paley, S, Arnaud, M, Pick, J, Rhee, SY, and Karp, P. (2004)
MetaCyc: Recent enhancements to a database of metabolic pathways and enzymes in microorganisms and plants. Nucleic Acids Research. 32 Database issue:D438-42.
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Rhee, SY (2004)
Carpe Diem. Retooling the Publish or Perish Model into the Share and Survive Model. Plant Physiol. 134(2):543-7
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Thimm, O, Bläsing, YG, Nagel, A, Meyer, S, Kruger, P, Selbig, J, Müller, L, Rhee, SY, and Stitt, M (2004)
MapMan: A User-Driven Tool to Display Genomics Data Sets onto Diagrams of Metabolic Pathways and other Biological Processes. The Plant Journal. 37(6):914-39.
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Tian, GW, Mohanty, A, Chary, SN, Li, S, Paap, B, Drakakis, G, Kopec, C, Li, J, Ehrhardt, E, Jackson, D, Rhee, SY, Raikhel, N, and Citovsky, V. (2004)
High-Throughput Fluorescent Tagging of Full-Length Arabidopsis Gene Products in Planta Plant Physiol. 135(1):25-38.
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Weems, D, Miller, N, Garcia-Hernandez, M, Huala, E, and Rhee, SY (2004)
Design, implementation, and maintenance of a model organism database for Arabidopsis thaliana. Comparative and Functional Genomics. 5(4):362-369.
Clark B, Lambrecht M, Rhee SY. (2003)
Arabidopsis genomic information for interpreting wheat EST sequences.
Functional and Integrative Genomics 2003 3(1):33
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Meinke DW, Meinke LK, Showalter TC, Schissel AM, Mueller LA, Tzafrir I. (2003)
A sequence-based map of Arabidopsis genes with mutant phenotypes. Plant Physiol. 2003 Feb;131(2):409-18
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Mueller, LA., Zhang, P., Rhee SY (2003)
AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology. 2003 132(2):453-60
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Garcia-Hernandez, M.; Berardini, T. Z.; Chen, G.; Crist, D.; Doyle, A.; Huala, E.; Knee, E.; Lambrecht, M.; Miller, N.; Mueller, L. A.; Mundodi, S.; Reiser, L.; Rhee, S. Y.; Scholl, R.; Tacklind, J.; Weems, D. C.; Wu, Y.; Xu, I.; Yoo, D.; Yoon, J.; Zhang, P. (2002)
TAIR: a resource for integrated Arabidopsis data. Functional and Integrative Genomics 2002 2(6):239
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Mitra M.; Shah N.; Mueller, L.; Pin S.; and Fedoroff N. (2002)
StressDB: A locally installable web-based relational microarray database designed for small user communities.
Comparative and Functional Genomics 2002 3(2):91-96.
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Reiser, L; Mueller, LA; and Rhee, SY (2002)
Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems.
Plant Molecular Biology 2002 Jan;48(1):59-74.
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Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P.
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 2003 31(1):224
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The Gene Ontology Consortium
Creating the Gene Ontology Resource: Design and Implementation. (2001)
Genome Research 2001 Aug;11(8):1425-1433.
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Huala, E; Dickerman, A; Garcia-Hernandez, M; Weems, D; Reiser, L; LaFond, F; Hanley, D; Kiphart, D; Zhuang, J; Huang, W; Mueller, L; Bhattacharyya, D; Bhaya, D; Sobral, B; Beavis, B, Somerville, C; and Rhee, SY (2001)
The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
Nucleic Acids Res. 2001 Jan 1;29(1):102-5.
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Rhee, SY (2001)
Extending the Frontiers of Plant Biology: Large scale biology, bioinformatics, and information management. Plant Biotechnology Institute Bulletin May:10-12
Rhee, SY
Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. (2000)
Plant Physiol. 2000 Dec;124(4):1460-4.
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Rhee SY and Flanders, DJ
Web-based bioinformatic tools for Arabidopsis researchers. In Arabidopsis: A Practical Approach. 2000 pp. 225-265
Zoe Wilson ed., Oxford University Press, UK.
