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. In Current Protocols in Bioinformatics. John Wiley & Sons. Chapter 1.11.

4. 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.

5. Yoo D, Xu I, Berardini, T, Rhee, SY, Narayanasami, V, and Twigger S (2005) PubSearch and PubFetch, a simple management system for semi-automated retrieval and annotation of biological information from the literature. In Current Protocols in Bioinformatics. John Wiley & Sons. Chapter 9. Unit 9.7

6. Ilic K, Stevens PF, Kellogg EA, Rhee SY (2008) Plant Structure Ontology –anatomical ontology of flowering plants. In: Anatomy Ontologies for Bioinformatics: Principles and Practice. A. Burger, D. Davidson and R. Baldock (Eds). Springer. 27-42. ISBN: 184628884.

Papers

7. 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. Journal of Biological Chemistry 267(15):10537-43.

8. 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.

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

10. 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 Journal. 15(1):79-88.

11. 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.

12. 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 Research. 27(1):79-84.

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

14. 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 Research. 29(1):102-5.

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

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

17. 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.

18. 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.

19. 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.

20. 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.

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

22. 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.

23. 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 Research. 32 Database issue:D258-61.

24. 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.

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

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

27. 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.

28. 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. Comparative and Functional Genomics. 5(4):362-369.

29. 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.

30. 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 Physiology. 135(1):25-38.

31. 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 Physiology. 135(2):1-11.

32. 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.

33. 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.

34. 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.

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

36. Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp P, and Rhee SY. (2005) MetaCyc and AraCyc: metabolic pathway databases for plant research. Plant Physiology. 138(1):27-37.

37. Yan, T, Yoo D, Berardini, T, Mueller, L, Weems, D, Weng, S, Cherry, JM, and Rhee SY. (2005) PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Research. 33(Web Server issue):W262-6.

38. Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. 138(2):569-70

39. Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology. 138(1):1-3.

40. 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.

41. Li, S, Ehrhardt, D, and Rhee SY (2006) Systematic Analysis of Arabidopsis Protein Localization and Software Tools for Fluorescent Tagging of Full-Length Arabidopsis Proteins. Plant Physiology. 10.1104/pp.106.078881

42. Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp P (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research. 34(Database issue):D511-6.

43. Gene Ontology Consortium (2006) The Gene Ontology Project in 2006. Nucleic Acids Research. 34(Database issue):D322-6

44. Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee SY, Wagner U, Hennig L. (2006) MIAME/Plant – adding value to plant microarrray experiments. Plant Methods. 2:1

45. Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360

46. Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Kellogg EA, Koonin EV, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevens P, Stevenson DW, Warnow T, and Zmasek C. (2006) Taking the First Steps Towards a Standard for Reporting on Phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMICS. 10(2):231-237.

47. 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.

48. Stein LD, Beavis WD, Gessler DD, Huala E, Lawrence CJ, Main D, Mueller LA, Rhee SY, Rokhsar DS (2006) Save our data! Scientist. 20(4):24-25.

49. 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

50. The Gene Ontology Consortium (2007) The Gene Ontology project in 2008. Nucleic Acids Research. doi: 10.1093/nar/gkm883

51. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P and Karp PD. (2007) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research. doi:10.1093/nar/gkm900

52. Fiehn O, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics. 3(3):195-201.

53. Avraham S, Tung C-W, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F and Ware D. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research. 36:D449-D454

54. Lalonde S, Ehrhardt D, Loqué D, Chen J, Rhee SY, and Frommer WB (2008) Molecular and cellular approaches for the detection of protein-protein interactions and generation of protein interaction maps. The Plant Journal. 53(4):610-35

55. Pennycooke JC, Cheng H, Roberts SM, Yang Q, Rhee SY and Stockinger E. (2008) The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions, and rearrangements. Plant Molecular Biology. 67(5):483-97.

56. Rhee SY, Wood V, Dolinski K and Draghici S. (2008) Use and Misuse of the Gene Ontology (GO) Annotations. Nature Review Genetics. 9(7):509-15.

57. Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St. Pierre S, Twigger S, White O, Rhee SY (2008) The future of biocuration. Nature. 455:47-50.

58. Aceituno FF, Moseyko N, Rhee SY and Gutierrez RA (2008) The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics. 9:438.

59. Chen J, Ji L, Hsu W, Tan K-L, and Rhee SY (2009) Exploiting Domain Knowledge to Improve Biological Significance of Biclusters with Key Missing Genes. IEEE Technical Committee on Data Engineering Conference. ICED.2009.205: 1219 - 1222

60. Reference Genome Group of the Gene Onology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLOS Computational Biology. 5(7): e1000431.

61. Lee I, Ambaru B, Thakkar P, Marcotte E, and Rhee SY (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nature Biotechnology. 2(28):149-156.

62. Bais P, Moon S, He K, Leitao R, Dreher K, Walk T, Sucaet Y, Barkan L, Wohlgemuth G, Wurtele ES, Dixon P, Fiehn O, Lange BM, Shulaev V, Sumner LW, Welti R, Nikolau B, Rhee SY, Dickerson JA (2010) PlantMetabolomics.org: A web portal for Plant Metabolomics Experiments. Plant Physiology. 152(4): 1807-16.

63. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY (2010) Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants.  Plant Physiology. 153(4):1479-91.

64. Lalonde S, Sero A, Pratelli R, Pilot G, Chen J, Sardi MA, Parsa SA, Kim D-Y, Acharya BR, Stein EV, Hu H-C, Villiers F, Takeda K, Yang Y, Han YS, Schwacke R, Chiang W, Kato N, Loqué D, Assmann SM, Kwak JM, Schroeder J, Rhee SY and Frommer WB (2010) A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2. Frontiers in Plant Physiology. 1(24):1-14.

65. Sun Y, Fan X-Y, Cao D-M, He K, Tang W, Zhu J-Y, He J-X, Bai M-Y, Zhu S, Oh E, Patil S, Kim TW, Ji H, Wong WH, Rhee SY, and Wang J-Y (2010) Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis. Developmental Cell. 19(5):765-77.

66. Hwang S, RheeSY, Marcotte EM and Lee I. (2011) Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana. Nature Protocols. 6(9):1429-1442.

67. Chae L, Lee I, Shin J, Rhee SY (2012) Towards understanding how molecular networks evolve in plants. Current Opinion in Plant Biology. 15:177-184. [pdf]

68. Quanbeck, SM, Brachova L, Campbell AA, Guan X, Perera  A, He K, Rhee SY, Preeti Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, Lee I, Cortes D, Salazar C, Shuman J, Shulaev V, HuhmanDV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES and Nikolau BJ (2012) Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. Frontiers in Plant Science. 3(15):1-12.

69. Chen J, Lalonde S, Obrdlik P, Noorani Vatani A, Parsa SA, Vilariño C, Revuelta JL, Frommer WB and Rhee SY (2012) Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Frontiers in Plant Science. 3(124): 1-14.

70. Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, and Smet ID (2012) Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. The Plant Cell. 24(10):3859-75. [pdf]

71. Rhee SY and Mutwil M (2014) Towards revealing the functions of all genes in plants. Trends in Plant Science. 19(4):198-199. [pdf]

72. Magnani E, De Klein N, Nam H-I, Kim J-G, Pham KL, Fiume E, Mudgett MB, and Rhee SY (2014) A comprehensive analysis of microProteins reveals their potentially widespread mechanism of transcriptional regulation. Plant Physiology. 165(1):149-15. [pdf]

73. Rhee SY (2014) Interview with Seung Yon (Sue) Rhee. Trends in Plant Science. 19(4):212-221. [pdf]

74. Chae L, Kim T, Dreher K, and Rhee SY. Genomic signatures of specialized metabolism in plants. (2014) Science. 344:510-513. [pdf] [supplemental info]

75. Jones AM, Xuan Y, Xu M, Wang R-S, Ho C-H, Lalonde S, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder JI, Albert R, Rhee SY, Frommer WB (2014) Border control – a membrane-linked interactome of Arabidopsis. (2014) Science. 344:711-716. [pdf] [supplemental info]