Book chapters

1. Rhee SY and Flanders, DJ. (2000) Web-based bioinformatic tools for Arabidopsis researchers. In Arabidopsis: A Practical Approach. 2000 pp. 225-265. Zoe Wilson ed., Oxford University Press, UK.

2. Berardini TA and Rhee SY (2004) Arabidopsis thaliana: Characteristics and Annotation of a Model Genome. Encyclopedia of Plant & Crop Science. Marcel Dekker, Inc. 47-50.

3. Reiser L and Rhee SY (2005) Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Current Protocols in Bioinformatics. Chapter 9. In press.

Papers

4. Ruan ZS, Anantharam V, Crawford IT, Ambudkar SV, Rhee SY, Allison MJ, Maloney, PC. (1992) Identification, purification, and reconstitution of OxlT, the oxalate: formate antiport protein of Oxalobacter formigenes. J Biol Chem. 267(15):10537-43.

5. Preuss D, Rhee SY, Davis RW. (1994) Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes. Science. 1994 Jun 3;264(5164):1458-60.

6. Rhee SY, Somerville CR. (1994) Flat-Surface Grafting in Arabidopsis thaliana Plant Molecular Biology Reporter. 13:118-123.

7. Rhee SY, Somerville CR. (1998) Tetrad pollen formation in quartet mutants of Arabidopsis thaliana is associated with persistence of pectic polysaccharides of the pollen mother cell wall. Plant J. 15(1):79-88.

8. Rhee SY, Weng S, Flanders D, Cherry JM, Dean C, Lister C, Anderson M, Koornneef M, Meinke DW, Nickle T, Smith K, Rounsley SD. (1998) Genome maps 9. Arabidopsis thaliana. Wall chart. Science. 282(5389):663-7.

9. Rhee SY, Weng S, Bongard-Pierce DK, Garcia-Hernandez M, Malekian A, Flanders, DJ, Cherry JM. (1999) Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database. Nucleic Acids Res. 27(1):79-84.

10. Rhee, SY (2000) Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. Plant Physiol. 2000 Dec;124(4):1460-4.

11. 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. 29(1):102-5.

12. The Gene Ontology Consortium (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Research. 11(8):1425-1433.

13. Rhee, SY (2001) Extending the Frontiers of Plant Biology: Large scale biology, bioinformatics, and information management. Plant Biotechnology Institute Bulletin May:10-12.

14. 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. 48(1):59-74.

15. Garcia-Hernandez, M., Berardini, TZ, Chen, C, Crist, D, Doyle, A, Huala, E, Knee, E, Miller, N, Mueller, L, Mundodi, S, Reiser, L, Rhee, SY, Scholl, S, Tacklind, J, Weems, D, Wu, Y, Xu, I, Yoo, D, Yoon, J (2002) TAIR: A Resource for Integrated Arabidopsis Data. Functional and Integrated Genomics. 2(6):239-253.

16. Clarke, BC, Lambrecht, M and Rhee, SY (2003) Assessing the utility of Arabidopsis genomic information for interpreting wheat EST sequences. Functional and Integrated Genomics. 3(1):33-38.

17. 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. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 31(1):224-228.

18. Mueller, LA., Zhang, P., Rhee SY (2003) AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology. 132(2):453-60.

19. Rhee SY, Osborne, E, Poindexter, P, Somerville, CR (2003) Microspore separation in the quartet 3 mutants of Arabidopsis is impaired by a defect in a developmentally regulated pectinase required for pollen mother cell degradation. Plant Physiology. 133(3):1170-80.

20. 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.

21. 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.

22. Rhee, SY (2004) Carpe Diem. Retooling the Publish or Perish Model into the Share and Survive Model. Plant Physiol. 134(2):543-7

23. Bard, JL and Rhee, SY (2004) Ontologies in biology: design, applicatioins and future challenges. Nature Review Genetics 5(3):213-22.

24. 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.

25. Weems, D, Miller, N, Garcia-Hernanzez, M, Huala, E, and Rhee, SY (2004) Design, implementation, and maintenance of a model organism database for Arabidopsis thaliana. Functional and Integrative Genomics. Comparative and Functional Genomics. 5(4):362-369.

26. 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.

27. 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.

28. 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.

29. Zhang, X, Fowler, S, Cheng, H, Lou, Y, Rhee, SY, Stockinger, EJ, and Thomashow, MF (2004) Freezing Sensitive Tomato has a Functional CBF Cold Response Pathway, but a CBF Regulon that Differs from that of Freezing Tolerant Arabidopsis. The Plant Journal. 39(6):905-19.

30. Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka K, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee, SY, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wurtele ES, Kell, DB. (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology. 22(12):1601-6.

31. 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.

32. Bard, J, Rhee, SY, Ashburner, M (2005) An ontology for cell types. Genome Biology. 6:R21

33. Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp P, Rhee SY. (2005) MetaCyc and AraCyc: metabolic pathway databases for plant research Plant Physiology. 2005 138: 27-37.

34. 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. Nucleic Acids Research.

35. Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. In press.