Selected Research Articles

Papers from our group are highly cited with a current h-Index of 59 (as of August 2024) on Google Scholar (See citation page). Some of our papers are listed below.​
  1. Ginzburg D, Bossi F, and Rhee SY (2022) Uncoupling differential water usage from drought resistance in a dwarf Arabidopsis mutant. Plant Physiology 190(4):2115–2121 BioRXiv (2021) ​https://www.biorxiv.org/content/10.1101/2021.11.25.470014v1
  2. Bossi F, Jin B, Lazarus E, Cartwright H, Dorone Y, Rhee SY (2022) CHIQUITA1 maintains temporal transition between proliferation and differentiation in Arabidopsis thaliana Development 149(11):dev200565. doi: 10.1242/dev.200565 BioRXiv (2021) 2021.11.24.469926; doi: https://doi.org/10.1101/2021.11.24.469926
  3. Nam H-I, Shahzad Z, Dorone Y, Clowez S, Zhao K, Bouain N, Cho H, Rhee SY and Rouached H (2021) Interdependent nutrient availability controls photosynthesis through retrograde signaling.  Nature Communications 12:7211 https://doi.org/10.1038/s41467-021-27548-2 BioRXiv doi: https://doi.org/10.1101/2021.02.11.430802
  4. Zhao K, Kong D, Jin B, Smolke CD, Rhee SY (2021) A Novel Form of Bivalent Chromatin Associates with Rapid Induction of Camalexin Biosynthesis Genes in Response to a Pathogen Signal in Arabidopsis. eLife https://elifesciences.org/articles/69508 BioRxiv 589036; doi: https://doi.org/10.1101/589036 
  5. Dorone Y, Boeynaems S, Jin B, Bossi F, Flores E, Lazarus E, Michiels E, De Decker M, Baatsen P, Holehouse AS, Sukenik S, Gitler AD, Rhee SY (2021) Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress. Cell 184(16), 4284-4298.e27 [highlighted by Developmental Cell, PNAS, Nature Chemical Biology, F1000, Science] BioRxiv 2020.08.07.242172; doi: https://doi.org/10.1101/2020.08.07.242172

Selected Reviews

  1. Field S, Jang G-J, Dean C, Strader L, Rhee SY (2023) Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development The Plant Cell https://doi.org/10.1093/plcell/koad062
  2. Zhao K and Rhee SY (2023) Enzyme and pathway enrichment analyses using omics data. Trends in Genetics https://doi.org/10.1016/j.tig.2023.01.003
  3. Dwyer W, Ibe C, and Rhee SY (2022) Renaming Indigenous crops and addressing colonial bias in scientific language. Trends in Plant Science 27(12): 1189-1192 https://doi.org/10.1016/j.tplants.2022.08.022
  4. BERAC (2022) U.S. Scientific Leadership Addressing Energy, Ecosystems, Climate, and Sustainable Prosperity: Report from the BERAC Subcommittee on International Benchmarking, DOE/SC-0208. M. McCann and P. Reed, eds. Biological and Environmental Research Advisory Committee. doi: 10.2172/1895129.
  5. Zhao K, Rhee SY (2022) Omics-guided functional discovery of plant metabolic pathways. Current Opinion in Plant Biology 67:102222. doi: https://doi.org/10.1016/j.pbi.2022.102222 

All Peer-reviewed Publications (*corresponding author)

  1. Fryer E, Guha S, Rogel-Hernandez LE, Logan-Garbisch T, Farah H, Rezaei E, Mollhoff IN, Nekimken AL, Xu A, Seyahi LS, Fechner S, Druckmann S, Clandinin TR, Rhee SY, Goodman MB (2024) A high-throughput behavioral screening platform for measuring chemotaxis by C. elegans PLOS Biology doi: https://doi.org/10.1371/journal.pbio.3002672
  2. Ginzburg D, Cox J, Rhee SY (2024) Non‐destructive, whole‐plant phenotyping reveals dynamic changes in water use efficiency, photosynthesis, and rhizosphere acidification of sorghum accessions under osmotic stress Plant Direct doi: https://doi.org/10.1002/pld3.571
  3. Xue B, Prado K, Rhee SY, Stata M (2024) UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome biorRXiv doi: https://doi.org/10.1101/2024.08.19.60864
  4. Meyer E, Saldivar E, Kokot M, Xue B, Deorowicz S, Rhee SY, Salzman J (2024) A reference-free algorithm discovers regulation in the plant transcriptome bioRXiv doi: https://doi.org/10.1101/2024.05.23.595613
  5. Field S, Drone Y, Dwyer WP, Cox JA, Raba D, Froehlich J, Blea M, Carmo OMS, Wallace IS, Hastings R, Boeynaems S, Rhee SY (2024) bioRXiv doi: https://doi.org/10.1101/2024.02.15.580454
  6. VanBuren R, Nguyen A, Marks RA, Mercado C, Pardo A, Pargo J, Schuster J, St. Augin B, Lipham Wilson M, Rhee SY (2024) Variability in drought gene expression datasets highlight the need for community standardization bioRXiv doi: https://doi.org/10.1101/2024.02.04.578814
  7. Ginzburg D, Cox J, Rhee SY (2023) Closed-chamber hydroponics for whole-plant phenotyping protocols.io doi: dx.doi.org/10.17504/protocols.io.q26g7p6m1gwz/v1
  8. Ruffley MR, Lutz U, Levanthal L, Hateley S, Yuan W, Keck J, Rhee SY, Weigel D, Exposito-Alonso M (2023) Selection constraints of plant adaptation can be relaxed by gene editing bioRXiv doi: doi.org/10.1101/2023.10.16.562583
  9. Cho H, Banf M, Shahzad Z, Bossi F, Ruffel S, Van Leene J, Krouk G, Brandizzi F, De Jaeger G, Lacombe B, Rhee SY, and Rouached H (2023) ARSK1 activates TOR signaling to adjust growth to phosphate availability in Arabidopsis Current Biology In press
  10. Field S, Jang G-J, Dean C, Strader L, Rhee SY (2023) Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development The Plant Cell doi: https://doi.org/10.1093/plcell/koad062 
  11. Zhao K and Rhee SY (2023) Enzyme and pathway enrichment analyses using omics data. Trends in Genetics doi: https://doi.org/10.1016/j.tig.2023.01.003 
  12. Ginzburg D and Rhee SY (2023) Evaluating drought resistance with a Raspberry Pi and time-lapse photography. Bio-protocol 13(2): e4593. doi:10.21769/BioProtoc.4593
  13. Dwyer W, Ibe C, and Rhee SY (2022) Renaming Indigenous crops and addressing colonial bias in scientific language. Trends in Plant Science doi: https://doi.org/10.1016/j.tplants.2022.08.022  
  14. Xue B and Rhee SY (2022) Status of Genome Function Annotation in Model Organisms and Crops BioRXiv doi:   https://biorxiv.org/cgi/content/short/2022.07.03.498619v1                  
  15. Rice S, Lazarus E, Anderton C, Birnbaum K, Brophy J, Cole B, Dickel D, Ehrhardt D, Fahlgren N, Frank M, Haswell E, Huang S-S, Leiboff S, Libault M, Otegui M, Provart N, Uhrig GR, and Rhee SY (2022) First Plant Cell Atlas Symposium Report Plant Direct 6(6):e406 doi: https://doi.org/10.1002/pld3.406                        
  16. Zhao K, Rhee SY (2022) Leveraging omics data to mine plant metabolism: resources, approaches, and challenges. Current Opinion in Plant Biology 67:102222. doi: https://doi.org/10.1016/j.pbi.2022.102222                 
  17. Bossi F, Jin B, Lazarus E, Cartwright H, Dorone Y, Rhee SY (2022) CHIQUITA1 maintains temporal transition between proliferation and differentiation in Arabidopsis thaliana Development 149(11):dev200565. doi: 10.1242/dev.200565 BioRXiv 2021.11.24.469926; doi: https://doi.org/10.1101/2021.11.24.469926                        
  18. Ginzburg D, Bossi F, and Rhee SY (2022) Uncoupling differential water usage from drought resistance in a dwarf Arabidopsis mutant. Plant Physiology 190(4):2115–2121 BioRXiv https://www.biorxiv.org/content/10.1101/2021.11.25.470014v1
  19. Birnbaum KD, Otegui MS, Bailey-Serres J, Rhee SY (2021) The Plant Cell Atlas: Focusing New Technologies on the Kingdom that Nourishes the Planet. Plant Physiology doi: 10.1093/plphys/kiab584. Epub ahead of print. PMID: 34935969.                        
  20. Dorone Y, Boeynaems S, Rhee SY (2021) Live imaging Arabidopsis thaliana embryos under different hydration conditions. STAR Protocols 2(4): 101025. https://doi.org/10.1016/j.xpro.2021.101025                        
  21. Nam H-I, Shahzad Z, Dorone Y, Clowez S, Zhao K, Bouain N, Cho H, Rhee SY and Rouached H (2021) Interdependent nutrient availability controls photosynthesis through retrograde signalling. Nature Communications 12:7211 https://doi.org/10.1038/s41467-021-27548-2                        
  22. Therby-Vale R, Lacombe B, Rhee SY, Nussaume L, Rouached H (2021) Mineral Nutrient Signaling Controls Photosynthesis: A focus on iron-deficiency induced chlorosis. Trends in Plant Science https://doi.org/10.1016/j.tplants.2021.11.005                        
  23. Silva TN, Thomas JB, Dahlberg J, Rhee SY, Mortimer JC (2021) Progress and Challenges in Sorghum Biotechnology, a Multi-Purpose Feedstock for the Bioeconomy. Journal of Experimental Botany 73(3): 646–664. https://doi.org/10.1093/jxb/erab450         
  24. Zhao K, Kong D, Jin B, Smolke CD, Rhee SY (2021) A Novel Form of Bivalent Chromatin Associates with Rapid Induction of Camalexin Biosynthesis Genes in Response to a Pathogen Signal in Arabidopsis. eLife https://elifesciences.org/articles/69508            
  25. Plant Cell Atlas Consortium, Ghosh Jha S, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY (2021) Vision, challenges and opportunities for a Plant Cell Atlas. eLife DOI: 10.7554/eLife.66877                
  26. Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, and Rhee SY (2021) Plant Metabolic Network: A comprehensive resource of plant metabolic information. Journal of Integrated Plant Biology. https://doi.org/10.1111/jipb.13163       
  27. Eckelbarger M, Rice S, Osano A, Peng J, Ullah H, Rhee SY (2021) Recognizing Pioneering Black Plant Biologists in Our Schools and Society. Trends in Plant Science http://doi.org/10.1016/j.tplants.2021.07.021                        
  28. Cole B, Bergmann D, Blaby-Haas C, Blaby I, Bouchard K, Brady S, Ciobanu D, Coleman-Derr D, Leiboff S, Mortimer J, Nobori T, Rhee SY, Schmutz J, Simmons BA Singh A, Sinha N, Vogel J, O’Malley R, Visel A (2021) Plant Single-Cell Solutions for Energy and the Environment. Communications Biology 4:962.                        
  29. Dorone Y, Boeynaems S, Jin B, Bossi F, Flores E, Lazarus E, Michiels E, De Decker M, Baatsen P, Holehouse AS, Sukenik S, Gitler AD, Rhee SY (2021) Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress. Cell 184(16), 4284-4298.e27 [highlighted by Developmental Cell, PNAS, Nature Chemical Biology, F1000, Science] 
  30. Demirer GS, Silva TN, Thomas JB, Jackson CT, Ehrhardt DW, Rhee SY, Mortimer JC, and Landry MP (2021) Nanotechnology to advance CRISPR/Cas genetic engineering of plants. Nature Nanotechnology 16, 243–250.                        
  31. Kang S-H, Pandey RP, Lee C-M, Jeong J-T, Choi B-S, Sim JS, Jung M, Won SY, Oh T-J, Yu Y, Lee OK, Kim HH, Lee T-H, Kim N-H, Bashyal P, Kim T-S, Kim C-K, Kim J-S, Ahn B-O, Rhee SY, Sohng JK (2020) Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nature Communications 11, 5875. https://doi.org/10.1038/s41467-020-19681-1                        
  32. Rice S, Fryer E, Jha SG, Malkovskiy A, Meyer H, Thomas J, Weizbauer R, Zhao K, Birnbaum KD, Ehrhardt DW, Wang Z, Rhee SY, and The Plant Cell Atlas Consortium (2020) First Plant Cell Atlas Workshop Report. Plant Direct 00: 1– 10. https://doi.org/10.1002/pld3.271                        
  33. Parry G, Provart NJ, Brady SM, Uzilday B, The Multinational Arabidopsis Steering Committee (2020) Current status of the multinational Arabidopsis community. Plant Direct 00:1-9.                        
  34. Lin F, Lazarus E, Rhee SY (2020) QTG-Finder2: a generalized machine learning algorithm for prioritizing QTL causal genes in plants. bioRxiv doi: https://doi.org/10.1101/2020.02.03.931444 Genes|Genomes|Genetics 10(7): 2411–2421.                        
  35. Bouain N, Korte A, Satbhai SB, Rhee SY, Busch W, Rouached H (2019) Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation. PLOS Genetics 6;15(11):e1008392.                        
  36. Rhee SY, Birnbaum KD, Ehrhardt DW (2019) Towards Building a Plant Cell Atlas. Trends in Plant Science 24(4):303-310                        
  37. Banf M, Zhao K, Rhee SY (2019) METACLUSTER - an R package for context-specific functionality analysis of metabolic gene clusters. Bioinformatics btz021, https://doi.org/10.1093/bioinformatics/btz021                        
  38. Lin F, Fan J, Rhee SY (2018) QTG-Finder: a machine-learning algorithm to prioritize causal genes of quantitative trait loci in plants. bioRxiv 484204; doi: https://doi.org/10.1101/484204 Genes|Genomes|Genetics 9(10):3129-3138.                        
  39. Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee SY, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiology 175(4):1499-1509. doi: 10.1104/pp.17.01490. PubMed PMID: 29208732; PubMed Central PMCID: PMC5717721.                        
  40. Bossi F, Fan J, Xiao J, Chandra L, Shen M, Dorone Y, Wagner D, Rhee SY (2017) Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC Genomics 18(1):480                        
  41. Rouchard H and Rhee SY (2017) System-level understanding of plant mineral nutrition in the big data era. Current Opinion in Systems Biology 4:71-77                        
  42. Schalpfer P, Zhang P, Chuan W, Kim T, Banf M, Chae L, Dreher K, Arvind C, Nilo-Poyanco R, Bernard T, Kahn D, and Rhee SY (2017) Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiology 173(4):2041-2059        
  43. Chavali A and Rhee SY (2017) Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites. Briefings in Bioinformatics. doi: 10.1093/bib/bbx020                        
  44. Banf M and Rhee SY (2017) Enhancing gene regulatory network inference through data integration with markov random fields. Nature Scientific Reports 7:41174.                        
  45. Banf M and Rhee SY (2016) Computational inference of gene regulatory networks: approaches, limitations and opportunities. BBA Gene Regulatory Mechanisms S1874-9399(16)30188-2.                        
  46. Walsh JR, Schaeffer ML, Zhang, Rhee SY, Dickerson JA, Sen TZ (2016) The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. BMC Systems Biology 10:129.                        
  47. Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin GB, Giovannoni JJ, Zhao PX, Rhee SY, Fei Z (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant S1674-2052(16)30223-4.                        
  48. Rhee SY, Parker J, and Mockler T (2016) A glimpse into the future of genome-enabled plant biology from the shores of Cold Spring Harbor. Genome Biology 17(1):3.                        
  49. Fiume E, de Klein N, Rhee SY, and Magnani E (2015) A framework for discovering, designing, and testing microProteins to regulate synthetic transcriptional modules. Methods in Molecular Biology 1482:175-88.
  50. Guo J, Fan J, Hauser B, and Rhee SY (2015) Target enrichment improves mapping of complex traits by deep sequencing. Genes | Genomes | Genetics 6(1):67-77.
  51. Ladics G, Bartholomaeus A, Bregitzer P, Doerrer N, Gray A, Holzhauser T, Jordan M, Keese P, Kok E, Macdonald P, Parrott W, Privalle L, Raybould A, Rhee SY, Rice E, Romeis J, Vaughn J, Wal J-M, and Glenn K (2015) Genetic basis and detection of unintended effects in genetically modified crop plants. Transgenic Research 24(4):587-603.                        
  52. Kim T, He K, Dreher K, Lee I, Moon S, Bais P, Dickerson J, Dixon P, Fiehn O, Lange BM, Sumner LW, Welti R, Wurtele ES, Nikolau BJ, and Rhee SY (2015) Patterns of metabolite changes from large-scale gene perturbations in Arabidopsis thaliana using genome-scale metabolic networks. Plant Physiology 167(4):1685-98.
  53. de Klein N, Magnani E, and Rhee SY microProtein Prediction Program (miP3): a software for predicting microProteins and their target transcription factors. (2015) International Journal of Genomics Article ID 734147. 1-4.
  54. Peng J, Uygun S, Kim T, Wang Y, Rhee SY, and Chen J (2015) Measuring genome-specific semantic similarities using Gene Ontology and Gene Co-Function networks. BMC Bioinformatics 16(1):44.
  55. Xu M and Rhee SY (2014) Becoming data-savvy in a big-data world. Trends in Plant Science 19(10):619–622.
  56. 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, and Frommer WB (2014) Border control – a membrane-linked interactome of Arabidopsis. Science 344:711-716. [highlighted in F1000]                        
  57. Chae L, Kim T, Nilo-Poyanco R, and Rhee SY Genomic signatures of specialized metabolism in plants. (2014) Science 344:510-513. [highlighted in F1000]                        
  58. 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):149-159.
  59. Rhee SY and Mutwil M (2014) Towards revealing the functions of all genes in plants. Trends in Plant Science 19(4):212-221.
  60. 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. Plant Cell 24(10):3859-75.
  61. 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.                        
  62. Moon S, He Kun, Bais P, Dickerson J, Dixon P, Rhee SY, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange B, Cortes D, Shuman J, Shulaev V, Huhman D, Sumner L, Roth M, Welti R, Ilarslan H, Wurtele E, Brachova L, Campbell A, Perera A, and Nikolau B (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.                        
  63. Chae L, Lee I, Shin J, and Rhee SY (2012) Towards an understanding of how molecular networks evolve in plants. Current Opinion in Plant Biology 15(2):177-184.                        
  64. Hwang S, Rhee SY, 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.                        
  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. 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 Science 1(24):1-14.   
  67. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, and 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.
  68. 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, and Dickerson JA (2010) PlantMetabolomics.org: A web portal for Plant Metabolomics Experiments. Plant Physiology 152(4):1807-16.
  69. 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. [highlighted in F1000]
  70. Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLOS Computational Biology 5(7): e1000431.
  71. 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.
  72. 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.
  73. 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, and Rhee SY (2008) The future of biocuration. Nature 455:47-50.
  74. 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.
  75. 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.                        
  76. 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. Plant Journal 53(4):610-35.
  77. 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.
  78. Fiehn O, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, and Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics 3(3):195-201.
  79. 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 (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research 38(Database issue):D473-9.                        
  80. The Gene Ontology Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Research 36(Database issue):D440-4.  
  81. Ilic K, Kellogg E, Jaiswal P, Zapata F, Stevens P, Vincent L, Pujar A, Avraham S, Reiser L, McCouch SR, Sachs S, Schaeffer M, Ware D, Stein L, and Rhee SY (2006) Plant Structure Ontology: A Unified Vocabulary for Flowering Plants. Plant Physiology 143(2):587-99.                        
  82. Stein LD, Beavis WD, Gessler DD, Huala E, Lawrence CJ, Main D, Mueller LA, Rhee SY, and Rokhsar DS (2006) Save our data! Scientist 20(4):24-25.   
  83. ​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.
  84. 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.                        
  85. Rhee SY, Dickerson J, and Xu D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology 57:335-360. 
  86. Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee SY, Wagner U, and Hennig L. (2006) MIAME/Plant – adding value to plant microarrray experiments. Plant Methods 2:1-3.                    
  87. Gene Ontology Consortium (2006) The Gene Ontology Project in 2006. Nucleic Acids Research 34(Database issue):D322-6.   
  88. Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, and Karp P (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 34(Database issue):D511-6.                        
  89. 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 141(2):527-39. [highlighted in F1000]
  90. 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, and Zapata F. (2005) Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Functional and Integrated Genomics 6:388-397.                        
  91. Rhee SY (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology 138(2):569-70.                        
  92. 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.                        
  93. 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. Bard J, Rhee SY, and Ashburner M (2005) An ontology for cell types. Genome Biology 6:R21.                        
  94. 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.                    
  95. 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, and Kell DB (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology 22(12):1601-6.                        
  96. 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. Plant Journal 39(6):905-19.                        
  97. 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.                        
  98. 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. [highlighted in F1000]
  99. 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. 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.
  100. 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. Plant Journal 37(6):914-39. [highlighted in F1000]  
  101. Bard JL and Rhee SY (2004) Ontologies in biology: design, applications and future challenges. Nature Review Genetics 5(3):213-22.                        
  102. Rhee SY (2004) Carpe Diem. Retooling the Publish or Perish Model into the Share and Survive Model. Plant Physiology 134(2):543-7.                        
  103. 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.                        
  104. 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, and White R; Gene Ontology Consortium. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research 32 Database issue:D258-61.                        
  105. Rhee SY, Osborne E, Poindexter P, and 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.                        
  106. Mueller LA, Zhang P, and Rhee SY (2003) AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology 132(2):453-60.                        
  107. 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, and 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.​
  108. Clarke BC, Lambrecht M, and Rhee SY (2003) Arabidopsis genomic information for interpreting wheat EST sequences. Functional and Integrated Genomics 3(1):33-38.                        
  109. 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 R, Tacklind J, Weems D, Wu Y, Xu I, Yoo D, Yoon J, and Zhang P (2002) Functional and Integrated Genomics 2(6):239-253.
  110. 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.                        
  111. The Gene Ontology Consortium (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11(8):1425-1433.      
  112. ​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.
  113. Rhee SY (2000) Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. Plant Physiology 2000 124(4):1460-4. 
  114. Rhee SY, Weng S, Bongard-Pierce DK, Garcia-Hernandez M, Malekian A, Flanders, DJ, and Cherry JM (1999) Unified display of Arabidopsis thaliana physical maps from AtDB, the A. thaliana database. Nucleic Acids Research 27(1):79-84.
  115. Rhee SY, Weng S, Flanders D, Cherry JM, Dean C, Lister C, Anderson M, Koornneef M, Meinke DW, Nickle T, Smith K, and Rounsley SD (1998) Genome maps 9. Arabidopsis thaliana. Wall chart. Science 282(5389):663-7.
  116. Rhee SY and 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 15:79-88.
  117. Rhee SY and Somerville CR (1994) Flat-Surface Grafting in Arabidopsis thaliana. Plant Molecular Biology Reporter 13:118-123. [PDF Link]
  118. Preuss D, Rhee SY, Davis RW (1994) Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes. Science 264:1458-60.
  119. Ruan ZS, Anantharam V, Crawford IT, Ambudkar SV, Rhee SY, Allison MJ, and Maloney PC (1992) Identification, purification, and reconstitution of OxlT, the oxalate: formate antiport protein of Oxalobacter formigenes. Journal of Biological Chemistry 267:10537-43. 

Book Chapters and Other Publications

  1. Rhee SY (2014) An interview with Seung Yon (Sue) Rhee. Trends in Plant Science 19(4):198-199.
    Ilic K, Stevens PF, Kellogg EA, and 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
  2. Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology 138(1):1-3
  3. 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
  4. 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
  5. Berardini TA and Rhee SY (2004) Arabidopsis thaliana: Characteristics and Annotation of a Model Genome. In Encyclopedia of Plant & Crop Science. Marcel Dekker, Inc. 47-50
  6. 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
  7. Rhee SY (2001) Extending the Frontiers of Plant Biology: Large scale biology, bioinformatics, and information management. Plant Biotechnology Institute Bulletin May Issue:10-12
  8. Rhee SY and Flanders DJ (2000) Web-based bioinformatic tools for Arabidopsis researchers. In Arabidopsis: A Practical Approach. pp. 225-265. Zoe Wilson ed., Oxford University Press, UK.
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