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METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters.
Banf M, Zhao K, Rhee SY. Banf M, et al. Among authors: rhee sy. Bioinformatics. 2019 Sep 1;35(17):3178-3180. doi: 10.1093/bioinformatics/btz021. Bioinformatics. 2019. PMID: 30657869 Free PMC article.
Using the Arabidopsis Information Resource (TAIR) to find information about Arabidopsis genes.
Reiser L, Rhee SY. Reiser L, et al. Among authors: rhee sy. Curr Protoc Bioinformatics. 2005 Apr;Chapter 1:Unit 1.11. doi: 10.1002/0471250953.bi0111s9. Curr Protoc Bioinformatics. 2005. PMID: 18428741
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.
Peng J, Uygun S, Kim T, Wang Y, Rhee SY, Chen J. Peng J, et al. Among authors: rhee sy. BMC Bioinformatics. 2015 Feb 14;16:44. doi: 10.1186/s12859-015-0474-7. BMC Bioinformatics. 2015. PMID: 25886899 Free PMC article.
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.
Schläpfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, Dreher K, Chavali AK, Nilo-Poyanco R, Bernard T, Kahn D, Rhee SY. Schläpfer P, et al. Among authors: rhee sy. Plant Physiol. 2017 Apr;173(4):2041-2059. doi: 10.1104/pp.16.01942. Epub 2017 Feb 22. Plant Physiol. 2017. PMID: 28228535 Free PMC article.
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites.
Chavali AK, Rhee SY. Chavali AK, et al. Among authors: rhee sy. Brief Bioinform. 2018 Sep 28;19(5):1022-1034. doi: 10.1093/bib/bbx020. Brief Bioinform. 2018. PMID: 28398567 Free PMC article. Review.
First plant cell atlas workshop report.
Rice S, Fryer E, Ghosh Jha S, Malkovskiy A, Meyer H, Thomas J, Weizbauer R, Zhao K, Birnbaum K, Ehrhardt D, Wang Z, Rhee SY; Plant Cell Atlas Consortium. Rice S, et al. Among authors: rhee sy. Plant Direct. 2020 Oct 15;4(10):e00271. doi: 10.1002/pld3.271. eCollection 2020 Oct. Plant Direct. 2020. PMID: 33083684 Free PMC article.
Genome-enabled discovery of anthraquinone biosynthesis in Senna tora.
Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Kang SH, et al. Among authors: rhee sy. Nat Commun. 2020 Nov 18;11(1):5875. doi: 10.1038/s41467-020-19681-1. Nat Commun. 2020. PMID: 33208749 Free PMC article.
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.
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. Zhang P, et al. Among authors: rhee sy. Plant Physiol. 2010 Aug;153(4):1479-91. doi: 10.1104/pp.110.157396. Epub 2010 Jun 3. Plant Physiol. 2010. PMID: 20522724 Free PMC article.
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize.
Walsh JR, Schaeffer ML, Zhang P, Rhee SY, Dickerson JA, Sen TZ. Walsh JR, et al. Among authors: rhee sy. BMC Syst Biol. 2016 Nov 29;10(1):129. doi: 10.1186/s12918-016-0369-x. BMC Syst Biol. 2016. PMID: 27899149 Free PMC article.
Enhancing gene regulatory network inference through data integration with markov random fields.
Banf M, Rhee SY. Banf M, et al. Among authors: rhee sy. Sci Rep. 2017 Feb 1;7:41174. doi: 10.1038/srep41174. Sci Rep. 2017. PMID: 28145456 Free PMC article.
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