Won Yim

Won Yim

Assistant Professor


Recent advance in genomics are generating tremendous amounts of data. As a result, the field of bioinformatics confronts an unprecedented need to move towards greater interdisciplinary to better interpret and understand these data. The goal of our research is to understand the molecular underpinnings of various plant adaptations to semi-arid and arid environments through genomics-enabled bioinformatics approaches. Our research focuses broadly on comparative genomics and gene expression from the perspectives of genomics, systems biology, and bioinformatics. We propose to undertake integrative approaches that span multiple levels of biological organization from the genome to the metabolome.

The Yim’s lab is worked on plant genomics, studying how genomes are organized and how genome structure affects gene expression, phenotypes, and genomic plasticity. We use of bioinformatics to address questions in plant diversity, with an emphasis on enabling crop improvement efforts though through diversification mechanisms associated with large scale genome duplications, while at the same time maintaining core functions. The major objectives of our lab include developing strategies for increased plant tolerance to harsh environments and increased biomass productivity through understanding the basis of polyploidy and genome conformation in plants.

Our on-going research projects include de novo assembly and analysis of multiple genomes and transcriptomes. We participate in a variety of open source software development projects and in other efforts to facilitate data sharing and improving adherence to standards among groups involved in information resource management in plant biology.

Lastly, our lab seeks to illuminate the processes regulating development, metabolomics, protein structure, evolution analysis and photosynthesis and will enable future attempts to characterize gene function in plants, insects and vertebrates.


B.S. Dongguk University, Seoul, Korea, 2006
M.S. Dongguk University, Seoul, Korea, 2008
Ph.D. Dongguk University, Seoul, Korea, 2012



The highly improved genome of with X and Y pseudochromosomes


Life science alliance 6

Andrew B Nuss, Johnathan S Lomas, Jeremiah B Reyes, Omar Garcia-Cruz, Wenlong Lei, Arvind Sharma, Michael N Pham, Saransh Beniwal, Mia L Swain, Molly McVicar, Isaac Amankona Hinne, Xingtan Zhang, Won C Yim, Monika Gulia-Nuss

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome


The Plant Cell, Volume 34, Issue 11, November 2022, Pages 4143–4172

Won Cheol Yim, Mia L Swain, Dongna Ma, Hong An, Kevin A Bird, David D Curdie, Samuel Wang, Hyun Don Ham, Agusto Luzuriaga-Neira, Jay S Kirkwood, Manhoi Hur, Juan K Q Solomon, Jeffrey F Harper, Dylan K Kosma, David Alvarez-Ponce, John C Cushman, Patrick P Edger, Annaliese S Mason, J Chris Pires, Haibao Tang, Xingtan Zhang

Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical...

Characterization of a microbial consortium for improved biological degradation of Opuntia ficus-indica biomass for biofuel production.


Heliyon. 7 (8): e07854. DOI: 10.1016/j.heliyon.2021.e07854

Blair BB, Yim WC, Cushman JC.

Membrane profiling by free flow Electrophoresis and SWATH-MS to characterize subcellular compartment proteomes in Mesembryanthemum crystallinum.


International Journal of Molecular Sciences. 22:5020. DOI: 10.3390/ijms22095020.

Guo Q, Liu L, Yim WC, Cushman JC, Barkla BJ.

Biosystems Design to Accelerate C3-to-CAM Progression.


BioDesign Research, 2020, 1-16.

Yuan, G., Hassan, M. M., Liu, D., Lim, S. D., Yim, W. C., Cushman, J. C., Markel, K., Shih, P. M., Lu, H., Weston, D. J., Chen, J.-G., Tschaplinski, T. J., Tuskan, G. A., Yang, X.

Biology and chemistry of an Umbravirus-like 2989 bp single-stranded RNA as a possible causal agent for Opuntia stunting disease (engrosamiente de cladidios) – A review


Journal of the Professional Association for Cactus Development. 21: 1–31.

Felker P, Bunch R, Russo G, Preston K, Tine JA, Suter B, Mo X, Cushman JC, Yim WC

The bracteatus pineapple genome and domestication of clonally propagated crops.


Nature Genetics. 51: 1549–1558 DOI: 10.1038/s41588-019-0506-8.

Chen L-Y, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Along M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Juang L, Wang H, Hwa T-Y, Kao S-M, Choi JY, Sharma A, Song J, Wang H, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung C-W, Wang M-L, d’Eckenbrugge GC, Sanewski GM, Purrugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R.

Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running.


Mitochondrion. doi:10.1016/j.mito.2018.04.002

Wone BWM, Yim WC, Schutz H, Meek TH, Garland Jr T.

An rbcL mRNA binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria.


Journal of Experimental Botany DOI:10.1093/jxb/erx264

Yerramsetty PK, Agar EM, Yim WC, Cushman JC, Berry JO

Divide and Conquer (DC) BLAST: Fast and easy BLAST execution within HPC environments.


PeerJ. 5: e3486.

Yim WC, Cushman JC

Expression of Heat Shock Proteins by Heat Stress in Soybean.


Plant Breed. Biotech. 5(4):344~353 doi:10.9787/PBB.2017.5.4.344

Song K, Yim WC, Lee B-M.

Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.


The Plant Journal DOI:10.1111/tpj.13630

Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger P, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.


Nature Communications doi:10.1038/s41467-017-01491-7

Yang X, Hu R. Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Yim WC, Ha J, Heyduk K, Goodstein D, Gou HB, Moseley R, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham P, Mewalal R, Beltrán J, Boxall S, Denver L, Palla K, Albion R, Garcia T, Mayer J, Lim SD, Wai CM, Peluso P, VanBuren R, De Paoli H, Borland A, Guo H, Chen JG, Muchero W, Yin Y, Jacobson D, Tschaplinski T, Hettich R, Ming R, Winter K, Leebens-Mack K, Smith JAC, Cushman JC, Schmutz J, Tuskan G.

Identification of ice plant (Mesembryanthemum crystallinum L.) microRNAs using RNA-Seq and their putative roles in high salinity responses in seedlings.


Frontiers in Plant ScienceFront Plant Sci. doi: 10.3389/fpls.2016.01143

Chiang C, Yim WC, Sun Y, Ohnishi M, Mimura T, Cushman JC, Yen HE.

The pineapple genome and the evolution of CAM photosynthesis.


Nature Genetics. 47: 1435–1442

Ming R, Van Buren R, Wai CM, Tang H, Schatz MC, Bowers, JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck F, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Yuan Q, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA