2020
Ding, B., R. Xia, V. J. M. , L. E. , M. , Q. , P. K. , , . 2020. Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway and a conceptual model. Plant Cell. doi: 10.1105/tpc.18.00471
Stanley, L. E., B. Ding, W. Sun, F. Mou, C. Hill, S. Chen, Y. W. Yuan. 2020. A tetratricopeptide repeat protein regulates carotenoid biosynthesis and chromoplast development in monkeyflowers (Mimulus). Plant Cell. 32: 1536–1555. doi: 10.1105/tpc.19.00755
Baoqing Ding*, Erin L. Patterson*, Srinidhi Holalu*, Jingjian Li, Grace A. Johnson, Lauren E. Stanley, Anna B. Greenlee, Foen Peng, H. D. Bradshaw Jr., Michael L. Blinov, Benjamin K. Blackman#, Yao‐Wu Yuan#. 2020. Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30: 802–814. (*equal contribution;#Co-senior authors) [PDF]
A companion commentary by Murat Unalan and Patrick Muller. A commentary by Paula Elomaa. Highlighted in Science “Editors’ Choice”: Self-organizing floral pigmentation patterns National Geographic: Old math reveals new secrets about these alluring flowers UConn Today: How Did the Monkeyflower Get Its Spots? Berkeley News: How the monkeyflower gets its spots? Preview of this study and other Mimulus research: Meet the monkeyflower 2019
Lowry, D., Sobel, J., Angert, A., Ashman, T.‐L., Baker, R., Blackman, B., Brandvain, Y., Byers, K., Cooley, A., Coughlan, J., Dudash, M., Fenster, C., Ferris, K., Fishman, L., Friedman, J., Grossenbacher, D., Holeski, L., Ivey, C., Kay, K., Koelling, V., Kooyers, N., Murren, C., Muir, C., Nelson, T., Peterson, M., Puzey, J., Rotter, M., Seemann, J., Sexton, J., Sheth, S., Streisfeld, M., Sweigart, A., Twyford, A., Vallejo‐Marín, M., Willis, J., Wright, K., Wu, C. and Yuan, Y.‐W. 2019. The case for the continued use of the genus name Mimulus for all monkeyflowers. Taxon. 68: 617-623.
Stanley, L. E., Y. W. Yuan. 2019. Transcriptional regulation of carotenoid biosynthesis in plants: So many potential regulators, so little consensus. Frontiers in Plant Science. 10: 1017. doi:10.3389/fpls.2019.01017.
Y. W. Yuan. 2019. Monkeyflowers (Mimulus): new model for plant developmental genetics and evo-devo. New Phytologist. 222: 694-700. [PDF]
Gu Z., J. Zhu, Q. Hao, Y. W. Yuan, Y. Duan, S. Men, Q. Wang, Q. Hou, Z. Liu, Q. Shu, L. Wang. 2019. A novel R2R3-MYB transcription factor contributes to petal blotch formation by regulating organ-specific expression of PsCHS in tree peony (Paeonia suffruticosa). Plant and Cell Physiology. 60: 599-611. [PDF]
2017
LaFountain A. M.*, W. Chen*, W. Sun, S. Chen, H. A. Frank, B. Ding, Y. W. Yuan. 2017. Molecular basis of overdominance at a flower color locus. G3: GENES, GENOMES, GENETICS. 7: 3947-3954 (*equal contribution) [PDF] 
Edger P. P., R. D. Smith, M. R. McKain, A. M. Cooley, M. Vallejo-Marin, Y. W. Yuan, A. J. Bewick, L. Ji, A. E. Platts, M. J. Bowman, K. Childs, J. D. Washburn, R. Schmitz, G. D. Smith, J. C. Pires, J. R. Puzey. 2017. Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. Plant Cell. 29: 2150-2167.
Ding, B., F. Mou, W. Sun, S. Chen, F. Peng, H. D. Bradshaw Jr., Y. W. Yuan. 2017. A dominant-negative actin mutation alters corolla tube width and pollinator visitation in Mimulus lewisii. New Phytologist.
2016
Yuan Y. W., A. B. Rebocho, J. M. Sagawa, L. E. Stanley, H. D. Bradshaw, Jr. 2016. Competition between anthocyanin and flavonol biosynthesis produces spatial pattern variation of floral pigments between Mimulus species. Proceedings of the National Academy of Sciences, U.S.A. 113: 2448–2453. [PDF] [Supporting Information]
UConn Today: How Monkeyflowers Attract Both Birds and Bees?
Ding B., Y. W. Yuan. 2016. Testing the utility of fluorescent proteins in Mimulus lewisii by an Agrobacterium-mediated transient assay. Plant Cell Reports. 35: 771-777. [PDF]
Sagawa J. M.*, L. E. Stanley*, A. M. LaFountain, H. A. Frank, C. Liu, Y. W. Yuan. 2016. An R2R3-MYB transcription factor regulates carotenoid pigmentation in Mimulus lewisii flowers. New Phytologist. 209: 1049-1057. (*equal contribution) [PDF]
2015
LaFountain, A. M., H. A. Frank, Y. W. Yuan. 2015. Carotenoid composition of the flowers of Mimulus lewisii and related species: Implications regarding the prevalence and origin of two unique, allenic pigments. Archives of Biochemistry and Biophysics. 573: 32-39. [PDF]
2014
Yuan, Y. W., J. M. Sagawa, L. Frost, J. Vela, H. D. Bradshaw, Jr. 2014. The transcriptional control of anthocyanin pigmentation in monkeyflowers (Mimulus). New Phytologist. 204: 1013–1027. [PDF]
Liu, D., W. Sun, Y. W. Yuan, N. Zhang, A. Hayward, L. Liu, Y. Wang. 2014. Phylogenetic analyses give the first insights into the evolution of OVATE family proteins in land plants. Annals of Botany. 113: 1219-1233. [PDF]
2013
Hellsten, U., K. M. Wright, J. Jenkins, S. Shu, Y. W. Yuan, S. R. Wessler, J. Schmutz, J. H. Willis, D. S. Rokhsar. 2013. Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. Proceedings of the National Academy of Sciences, U.S.A. 110: 19478–19482. [PDF]
Yuan, Y. W., K. J.R.P. Byers, H. D. Bradshaw, Jr. 2013. The genetic control of flower-pollinator specificity. Current Opinion in Plant Biology. 16: 422-428. [PDF]
Yuan, Y. W., J. M. Sagawa, V. S. Di Stilio, H. D. Bradshaw, Jr. 2013. Bulk segregant analysis of an induced floral mutant identifies a MIXTA-like R2R3 MYB controlling nectar guide formation in Mimulus lewisii. Genetics. 194: 523-528. [PDF]
Featured on the Cover. A companion commentary by Daniel Ortiz-Barrientos.
Before 2013
Yuan, Y. W., S. R. Wessler. 2011. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proceedings of the National Academy of Sciences, U.S.A. 108: 7884-7889. [PDF] [Supporting Information]
Yuan, Y. W., D. J. Mabberley, D. A. Steane, R. G. Olmstead. 2010. Further disintegration and redefinition of Clerodendrum (Lamiaceae): Implications for the understanding of the evolution of an intriguing breeding strategy. Taxon. 59: 125-133. [PDF]
Yuan, Y. W., C. Liu, H. E. Marx, R. G. Olmstead. 2010. An empirical demonstration of using pentatricopeptide repeat (PPR) genes as plant phylogenetics tools: Phylogeny of Verbenaceae and the Verbena complex. Molecular Phylogenetics and Evolution. 54: 23-35. [PDF]
Marx, H. E., N. O’Leary, Y. W. Yuan, P. Lu-Irving, D. C. Tank, M. E. Mulgura, R. G. Olmstead. 2010. A molecular phylogeny and classification of Verbenaceae. American Journal of Botany. 97: 1647-1663. [PDF]
O’Leary, N., Y. W., Yuan, A. Chemisquy, R. G. Olmstead. 2009. Reassignment of species of paraphyletic Junellia s.l. to the new genus Mulguraea (Verbenaceae) and new circumscription of genus Junellia: Molecular and morphological congruence. Systematic Botany. 34: 777-786. [PDF]
Yuan, Y. W., C. Liu, H. E. Marx, R. G. Olmstead. 2009. The pentatricopeptide repeat (PPR) gene family, a tremendous resource for plant phylogenetic studies. New Phytologist. 182: 272-283. [PDF]
Yuan, Y. W., R. G. Olmstead. 2008. Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination. American Journal of Botany. 95: 1166-1176. [PDF]
Yuan, Y. W., R. G. Olmstead. 2008. A species-level phylogenetic study of the Verbena complex (Verbenaceae) indicates two independent Intergeneric chloroplast transfers. Molecular Phylogenetics and Evolution. 48: 23-33. [PDF]
Yuan, Y. W., Z. Y. Zhang, Z. D. Chen, R. G. Olmstead. 2006. Tracking ancient polyploids: A retroposon insertion reveals an extinct diploid ancestor in the polyploid origin of Belladonna. Molecular Biology and Evolution. 23: 2263-2267. [PDF]