Won w88

Won w88

Assistant Professor

Summary

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 w88, and bioinformatics. We propose to undertake integrative approaches that span multiple levels of biological organization from the genome to the metabolome.

The w88’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 w88 projects include de novo assembly and analysis of multiple genomes and transcriptomes. We participate in a varietyof open sourcesoftware developmentprojects and in other efforts to facilitate data sharing and improving adherence to standards among groups involved in information resource management in plant w88.

Lastly, our lab seeks to illuminate the processes regulating development, metabolomics, protein structure, w88 analysis and photosynthesis and will enable future attempts to characterize gene function in plants, insects and vertebrates.

Education

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

Publications

Journals

GRABSEEDS: extraction of w88 organ traits through image analysis

2024

w88 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 w88

GRABSEEDS streamlines the w88 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...

JCVI: A versatile toolkit for comparative w88 analysis

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 w88, 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...

The highly improved w88 of with X and Y pseudochromosomes

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 w88, Monika Gulia-Nuss

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata w88

2022

The w88 Cell, Volume 34, Issue 11, November 2022, Pages 4143–4172

Won Cheol w88, 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 w88 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, w88, Cushman JC.

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

2021

International Journal of w88 Sciences. 22:5020. DOI: 10.3390/ijms22095020.

Guo Q, Liu L, w88, Cushman JC, Barkla BJ.

w88 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, w88

The bracteatus pineapple w88 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, w88, 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 w88 with mice selectively bred for high voluntary wheel running.

2018

Mitochondrion. doi:10.1016/j.mito.2018.04.002

Wone BWM, w88, Schutz H, Meek TH, Garland Jr T.

An rbcL mRNA binding protein is associated with C3 to C4 w88 and light-induced production of Rubisco in Flaveria.

2017

Journal of Experimental Botany DOI:10.1093/jxb/erx264

Yerramsetty PK, Agar EM, w88, Cushman JC, Berry JO

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

2017

PeerJ. 5: e3486.

w88, Cushman JC

Expression of Heat Shock Proteins by Heat Stress in Soybean.

2017

w88 Breed. Biotech. 5(4):344~353 doi:10.9787/PBB.2017.5.4.344

Song K, w88, Lee B-M.

Temporal and spatial transcriptomic and microRNA dynamics of CAM w88 in pineapple.

2017

The w88 Journal DOI:10.1111/tpj.13630

Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger P, w88, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R

The Kalanchoë w88 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, w88, 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 w88 (Mesembryanthemum crystallinum L.) microRNAs using RNA-Seq and their putative roles in high salinity responses in seedlings.

2016

Frontiers in w88 ScienceFront w88 Sci. doi: 10.3389/fpls.2016.01143

Chiang C, w88, Sun Y, Ohnishi M, Mimura T, Cushman JC, Yen HE.

The pineapple w88 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, w88, 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