Curriculum Vitae of Yim,Won Cheol

Crop Science - Genomics - Bioinformatics - Evolutions

Won Cheol Yim

Research scientist

Department of Biochemistry & Molecular Biology, University of Nevada-Reno, 
Reno, NV 89557-0330 USA.

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PROFESSIONAL PREPARATION

02/2018 – 06/2018 Research scientist, Department of Biochemistry & Molecular Biology, University of Nevada, Reno (Supervisor: John C. Cushman & Melinda K. Yerka)

01/2013 – 01/2018 Postdoctoral research associate, Department of Biochemistry & Molecular Biology, University of Nevada, Reno (Supervisor: John C. Cushman)

09/2012 – 01/2013 Postdoctoral research associate, Plant Biotechnology, Dongguk University, Seoul, Korea Rep. (Supervisor: BM Lee)

03/2008 – 08/2012 Doctor of Philosophy, Plant Biotechnology, Dongguk University, Seoul, Korea Rep. (Advisor: BM Lee)

03/2006 – 02/2008 Master of Science, Plant Biotechnology, Dongguk University, Seoul, Korea Rep.(Advisor: BM Lee)

03/1999 – 02/2006 Bachelor of Science, Plant Biotechnology, Dongguk University, Seoul, Korea Rep.

 

TRAINING & AWARDS

2012 Distinguished Ph.D. Student Award, Dongguk University, Seoul, Korea Rep.

2010 Plant bioinformatics course - Hands-on training at the EMBL-EBI, Hinxton, Cambridge, U.K.

2010 Transcriptomics and related tools from the EBI - School of Biological Science, University of Cambridge, U.K.

2009 Distinguished Paper Award & Scholarship, Dongguk University, Seoul, Korea Rep.

2008 Distinguished Paper Award & Scholarship, Dongguk University, Seoul, Korea Rep.

2008 University Scholarship, Dongguk University, Seoul, Korea Rep.

2007 Best Oral Presentation Award, The Korean Society of Breeding Science, Korea Rep.

2007 University Chancellor’s Scholarship, Dongguk University, Seoul, Korea Rep.

2006 University Scholarship, Dongguk University, Seoul, Korea Rep.


TEACHINGS AND OTHER EXPERIENCES

Spring/2017 Part-time Instructor in Functional Genomics BCH706, UNR

Spring/2016 Part-time Instructor in Plant Molecular Biology & Biotechnology BCH718, UNR

09/2013 – 01/2013 Instructor (Molecular Biology lecture), Dongguk University, Seoul, Korea Rep.

09/2012 – 12/2012 Instructor (Lab course), Dongguk University, Seoul, Korea Rep.

09/2009 – 02/2010 Instructor (Lab course), Dongguk University, Seoul, Korea Rep.

03/2008 – 01/2013 Undergraduate and graduate research mentor, Plant Biotechnology, Dongguk University, Seoul, Korea Rep.

03/2006 – 09/2009 Research Assistant, Dongguk University, Seoul, Korea Rep.


PROFESSIONAL EDUCATION AND EXPERIENCE

1) Excellent knowledge of molecular biology and characterization of molecular analysis

2) Deep knowledge of next-generation sequencing platforms, and the state-of-the-art tools for the analysis of next-generation sequencing data

3) Intensive hands-on experience with next-generation sequencing data analysis

4) Develops custom bioinformatics tools, software, databases and web interfaces

5) Solid experience of grid and supercomputing environments.


PRODUCTS

2018

Wone BWM,  Yim WC, Schutz H, Meek TH, Garland Jr T. (2018) Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running.  Mitochondrion. doi:10.1016/j.mito.2018.04.002

Lim SD, Yim WCLiu D, Hu R, Yang X, Cushman JC. (2018) A Vitis vinifera basic helix–loop–helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield. Plant Biotechnology Journal. doi:10.1111/pbi.12898


2017

Song K, Yim WC, Lee B-M. (2017) Expression of Heat Shock Proteins by Heat Stress in Soybean. Plant Breed. Biotech5(4):344~353 doi:10.9787/PBB.2017.5.4.344

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. (2017) The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications  doi:10.1038/s41467-017-01491-7

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. (2017) Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/1.  Genome Announcements doi:10.1128/genomeA.01105-17

Yerramsetty PK, Agar EM, Yim WC, Cushman JC, Berry JO (2017) 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

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 (2017) Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. The Plant Journal DOI:10.1111/tpj.13630

Yim WC* & Cushman JC (2017) Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments.  PeerJ doi:10.7717/peerj.3486

Yobi A, Schlauch KA, Tillett RL, Yim WC, Espinoza C, Wone BWM, Cushman JC, Oliver MJ (2017) Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics. BMC Plant Biol doi: 10.1186/s12870-017-1013-7
.


2016-2007

Chiang C, Yim WC, Sun Y, Ohnishi M, Mimura T, Cushman JC, Yen HE. (2016) 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

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, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith, JAC, Cushman JC, Paull RE, Yu, Q. (2015) The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47: 1435–1442

Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JAC, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, Ming R, Schlauch KA, Abraham P, Stewart JR, Guo H-B, Albion RA, Ha J, Lim SD, Wone BWM, Yim WC, Garcia T, Mayer JA, Petereit J, Nair SS, Casey E, Hettich RL, Ceusters J, Ranjan P, Palla KJ, Yin H, Reyes-García C, Andrade JL, Freschi L, Beltran JD, Dever LV, Boxall SF, Waller J, Davies J, Bupphada P, Kadu N, Winter K, Sage RF, Aguilar CN, Schmutz J, Jenkins J, Holtum, JAC.  (2015) A roadmap for research on crassulacean acid metabolism to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytologist.  207: 491–504.

Song K, Kim JH, Yoon GY, Kim HC, Shin S, Yim WC, Kim K-H, Lee B-M (2015) Distribution of Genetic Variants in Korean Soybeans. The Korean Journal of Crop Science 60: 224–230

Moon J-C, Yim WC, Lim SD, Song K, Lee B-M (2014) Differentially expressed genes and in silico analysis in response to ozone (O3) stress of soybean leaves. Australian Journal of Crop Science

Song K, Yim WC, Jung G-H, Kim SL, Kwon Y-U, Lee B-M (2013) Relationship of Transformation Efficiency and Metabolites Induced in Korean Soybean Cotyledons Treated with Sonication. Korean Journal of Crop Science 58: 119–127

Moon J-C, Lim SD, Yim WC, Song K, Lee B-M (2013) Characterization of Expressed Genes Under Ozone Stress in Soybean. Plant Breeding and Biotechnology 1: 270–276

Yim WC, Yu Y, Song K, Jang CS, Lee B-M (2013) PLANEX: the plant co-expression database. BMC Plant Biology 13: 83

Moon J-C, Yim WC, Lee J-E, Kwon Y-U, Song K, Lee B-M (2012) Transcriptome analysis in response to UV-B stress in soybean [Glycine max (L.) Merr.]. Australian Journal of Crop Science

Kim DS, Lee KJ, Yim WC, Kim J-B, Ha B-K, Kim SH, Kang S-Y (2012) Transcriptional network analysis of the tryptophan-accumulating rice mutant during grain filling. Mol Genet Genomics 287: 699–709

Yim WC, Lee B-M, Kwon Y (2012) Cross-experimental analysis of microarray gene expression datasets for in silico risk assessment of TiO2 nanoparticles. Mol Cell Toxicol 8: 229–239

Yim WC, Min K, Jung D, Lee B-M, Kwon Y (2011) Cross experimental analysis of microarray gene expression data from volatile organic compounds treated targets. Mol Cell Toxicol 7: 233–241

Wang HW, Kwon HJ, Yim WC, Lim SD, Moon J-C, Lee B-M, Seo YW, Kim W, Jang CS (2010) Expressional diversity of wheat nsLTP genes: evidence of subfunctionalization via cis-regulatory divergence. Genetica 138: 843–852

Yim WCKeum C, Kim S, Cho Y, Lee B-M, Kwon Y (2010a) Identification of novel 17B-estradiol (E2) target genes using cross-experiment gene expression datasets. Toxicol Environ Health Sci 2: 25–38

Yim WCKeum C, Kim S, Jang CS, Lee B-M (2010b) Identification of the Housekeeping Genes Using Cross Experiments via in silico Analysis. Korean Journal of Crop Science

Lim SD, Yim WC, Moon J-C, Kim DS, Lee B-M, Jang CS (2009) A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol Biol 72: 369–380

Yim WC, Kim DS, Moon J-C, Jang CS, Lee B-M (2009a) A Genome-wide Approach for Functional Analysis Using Rice Mutant. Korean Journal of Crop Science

Yim WC, Lee B-M, Jang CS (2009b) Expression diversity and evolutionary dynamics of rice duplicate genes. Mol Genet Genomics 281: 483–493

Jang CS, Yim WC, Moon J-C, Jung JH, Lee TG, Lim SD, Cho SH, Lee KK, Kim W, Seo YW, et al (2008) Evolution of non-specific lipid transfer protein (nsLTP) genes in the Poaceae family: their duplication and diversity. Mol Genet Genomics 279: 481–497

Jang CS, Jung JH, Yim WC, Lee B-M, Kim YWS and W (2007) Divergence of Genes Encoding Non-specific Lipid Transfer Proteins in the Poaceae Family. Molecules and Cells 24: 215–223

Yim WC, Jang CS (2007) Discovery of gene regulatory networks via in silico analysis and their application in abiotic stress responses. Korean Journal of Breeding Science

Yim WC, Kang MS, Kwon Y-U, Jang CS, Seo YW, Lim SD, Kim K-H, Moon J-C, Lee S-K, Lee B-M (2007) Evaluation of genetic diversity among Korean wheat using RAPD and ISSR analysis. Korean Journal of Breeding Science 39: 309–315