Journals
2024
Genome Biology and Evolution, Volume 16, Issue 8, August 2024, evae163,
Haomin Lyu, Won Cheol Yim, Qingyi Yu
C4 photosynthesis has independently evolved over 62 times within 19 angiosperm families. The recurrent evolution of C4 photosynthesis appears to contradict the complex anatomical and biochemical...
2024
Plant Methods 20, 140 (2024)
Haibao Tang, Wenqian Kong, Pheonah Nabukalu, Johnathan S Lomas, Michel Moser, Jisen Zhang, Mengwei Jiang, Xingtan Zhang, Andrew H Paterson, Won Cheol Yim
GRABSEEDS streamlines the plant phenotyping process and is effective in a variety of seed, floral and leaf trait studies for association with agronomic traits and stress conditions. Source code and...
2024
iMeta Volume3, Issue4 August 2024 e211
Haibao Tang, Vivek Krishnakumar, Xiaofei Zeng, Zhougeng Xu, Adam Taranto, Johnathan S Lomas, Yixing Zhang, Yumin Huang, Yibin Wang, Won Cheol Yim, Jisen Zhang, Xingtan Zhang
The JCVI library is a versatile Python-based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high-level utilities for tasks...
2024
New Phytologist, 241(1), 471-489
Pucker, B., Walker-Hale, N., Dzurlic, J., Yim, W. C., Cushman, J. C., Crum, A., Yang, Y., & Brockington, S. F.
2024
General and Comparative Endocrinology
Meet Zandawala, Muhammad Bilal Amir, Joel Shin, Won Cheol Yim and Luis Alfonso Yáñez-Guerra
2024
Genome Biology and Evolution, Volume 16, Issue 8, August 2024, evae163
Valentina J Alaasam, Cassandra Hui, Johnathan Lomas, Stephen M Ferguson, Yong Zhang, Won Cheol Yim, Jenny Q Ouyang
We present evidence of tolerance to chronic exposure, persistent behavioral responses lasting 8 weeks post-exposure, and attenuation of responses to re-exposure. Oxidative stress decreased under...
2023
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
2022
Journal of Experimental Botany, Vol. 73, No. 9 pp. 2889–2904
Santos, P., Busta, L., Yim, W. C., Cahoon, E., Kosma, D.
2022
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.
2021
Heliyon. 7 (8): e07854. DOI: 10.1016/j.heliyon.2021.e07854
Blair BB, Yim WC, Cushman JC.
2021
Systematic Biology. DOI: 10.1093/sysbio/syaa066. PubMed PMID: 32785686.
Moreles-Briones, D.F., Kadereit, G., Tefarikis, D., Moore, M.J., Smith, S.A., Brockington, S.F., Timoneda, A., Yim, W.C., Cushman, J.C., and Yang, Y.
Membrane profiling by free flow Electrophoresis and SWATH-MS to characterize subcellular compartment proteomes in Mesembryanthemum crystallinum.
2021
International Journal of Molecular Sciences. 22:5020. DOI: 10.3390/ijms22095020.
Guo Q, Liu L, Yim WC, Cushman JC, Barkla BJ.
2021
The Plant Journal, 107(1), 77–99
Z. Wahrenburg, E. Benesch, C. Lowe, J. Jimenez, V. K. R. V., S. Lü, R. Hammerschmidt, D. Douches, W. C. Yim, P. Santos, D. K. Kosma
2020
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.
2020
Systematic biology
Morales-Briones, D. F., Kadereit, G., Tefarikis, D. T., Moore, M. J., Smith, S. A., Brockington, S. F., Timoneda, A., Yim, W. C., Cushman, J. C., Yang, Y.
2020
The New phytologist, 227(3), 914-929
Sheehan, H., Feng, T., Walker-Hale, N., Lopez-Nieves, S., Pucker, B., Guo, R., Yim, W. C., et.al.
2020
Algal Research Vol 50, September, 101990
Polle, J. E. W., Calhoun, S., McKie-Krisberg, Z., Prochnik, S., Neofotis, P., Yim, W. C., et.al.
2020
Plant Journal, 103(3), 1049-1072
Lim, S. D., Mayer, J. A., Yim, W. C., Cushman, J. C.
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
2019
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
2019
Front Plant Sci. 2019; 10: 129.
Amin AB, Rathnayake KN, Yim WC, Garcia TM, Wone B, Cushman JC, Wone BWM
2019
New Phytologist. 227: 914–929. DOI: 10.1111/nph.16089.
Sheehan H, Feng T, Walker-Hale N, Lopez-Nieves S, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson MJ, Cushman JC, Moore MJ, Smith SA, Brockington SF
2019
Mitochondrion Volume 46, May 2019, Pages 134-139
Wone BWM, Yim WC, Schutz H, Meek TH, Garland T
Mitochondrial haplotypes have been associated with human and rodent phenotypes, including nonshivering thermogenesis capacity, learning capability, and disease risk. Although the mammalian...
The bracteatus pineapple genome and domestication of clonally propagated crops.
2019
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.
2018
Plant Biotechnology Journal 09 March 2018
Lim SD, Yim WC, Liu D, Hu R, Yang X, Cushman JC
2018
Plant Physiology December 2018
Busta L, Yim WC, LaBrant EW, Wang P, Grimes L, Malyszka K, Cushman JC, Santos P, Kosma DK, Cahoon EB
Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running.
2018
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.
2017
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.
2017
PeerJ. 5: e3486.
Yim WC, Cushman JC
2017
Genome Announcements doi:10.1128/genomeA.01105-17
Polle JEW, Barry K, Cushman JC, Schmutz J, Tran D, Hathwaik LT, Yim WC, Jenkins J, McKie-Krisberg Z, Prochnik S, Lindquist S, Dockter R, Adam C, Molina H, Bunkenborg J, Jin ES, Buchheim M, Magnuson J.
Expression of Heat Shock Proteins by Heat Stress in Soybean.
2017
Plant Breed. Biotech. 5(4):344~353 doi:10.9787/PBB.2017.5.4.344
Song K, Yim WC, Lee B-M.
2017
BMC Plant Biol doi: 10.1186/s12870-017-1013-7.
Yobi A, Schlauch KA, Tillett RL, Yim WC, Espinoza C, Wone BWM, Cushman JC, Oliver MJ
Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.
2017
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.
2017
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.
2016
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.
2016
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
