Yeong C. Kim, Ph.D.


Yeong C. Kim, Ph.D.Dept. of Genetics Cell Biology & Anatomy
College of Medicine, University of Nebraska Medical Center

B.S. in Biology, Yonsei University
M.S. in Biology, Yonsei University
M.S. in Computer Science, Illinois Institute of Technology
Ph.D. in Computer Science, Illinois Institute of Technology
Postdoctoral training in Bioinformatics, Northwestern University

Phone: 402-559-4640
Fax: 402-559-7328

Research Interest

My research area is computational cancer genomics using next-generation sequencing at the whole genome, exome, and transcriptome level. I am currently involved in studies of various cancers, such as familial breast cancer, colorectal cancer, leukemia, lung cancer, and other diseases such as diabetes. Previously, we developed a tag-based genome-wide mapping technique called DGS(Ditag Genome Scanning) that greatly facilitates identifying genetic aberrations and abnormalities in cancers and inherited diseases, at resolutions that were not easily detectable by using normal methods. In addition to finding cancer variations on coding regions, my current research focuses on applying next-generation sequencing analysis to study cancer mutations on non-coding and gene regulatory regions, especially promoters, and on developing algorithms and software tools for fully automated large-scale genomic data analysis to accelerate cancer genomics research.

Recent Publications

1. Angulo-Ibanez M, Rovira-Clave X, Granados-Jaen A, Downs B, Kim YC, Wang SM, Reina M, Espel E. (2015) Erk5 contributes to maintaining the balance of cellular nucleotide levels and erythropoiesis. Cell Cycle (in press).

2. Zhang Y, Huo W, Talmon G, Kim YC, Wang SM, Wang J. (2015) Pyruvate dehydrogenase kinase 4 mediates drug resistance in colorectal cancer. Oncotarget (in press).

3. Downs B, Kim YC, Xiao F, Snyder C, Chen P, Fleissner EA, Becirovic D, Wen H, Sherman S, Cowan KH, (2015) Two PALB2 germline mutations found in both BRCA1+ and BRCAx familial breast cancer. Breast Cancer Res Treat 151(1):219-24.

4. Wen H, Kim YC, Snyder C, Xiao F, Fleissner EA, Becirovic D, Luo J, Downs B, Sherman S, Cowan KH, Lynch H, Wang SM. (2014) Family-specific, novel, deleterious germline variants provide a rich resource to identify genetic predispositions for BRCAx familial breast cancer. BMC Cancer 14(1):470.

5. Xiao F, Kim YC, Snyder C, Wen H, Chen PX, Luo J, Becirovic D, Downs B, Cowan KH, Lynch H, Wang SM. (2014) Genome instability in blood cells of a BRCA1+ breast cancer family. BMC Cancer 14(1):342.

6. Xiao F, Kim YC, Wen H, Luo J, Chen PX, Cowan KH, Wang SM. (2013) The genome of polymorphonuclear neutrophils maintains normal coding sequences. PLoS One 8(11):e78685.

7. Lynch H, Wen H, Kim YC, Snyder C, Kinarsky Y, Chen PX, Xiao F, Goldgar D, Cowan KH, Wang SM. (2013) Can Unknown predisposition in familial breast cancer be family-specific? Breast J. 19(5):520-8.

8. COMPLEXO, Southey MC, Park DJ, Nguyen-Dumont T, Campbell I, Thompson E, Trainer AH, Chenevix-Trench G, Simard J, Dumont M, Soucy P, Thomassen M, Jønson L, Pedersen IS, Hansen TV, Nevanlinna H, Khan S, Sinilnikova O, Mazoyer S, Lesueur F, Damiola F, Schmutzler R, Meindl A, Hahnen E, Dufault MR, Chris Chan T, Kwong A, Barkardóttir R, Radice P, Peterlongo P, Devilee P, Hilbers F, Benitez J, Kvist A, Törngren T, Easton D, Hunter D, Lindstrom S, Kraft P, Zheng W, Gao YT, Long J, Ramus S, Feng BJ, Weitzel JN, Nathanson K, Offit K, Joseph V, Robson M, Schrader K, Wang SM, Kim YC, Lynch H, Snyder C, Tavtigian S, Neuhausen S, Couch FJ, Goldgar DE. (2013) COMPLEXO: identifying the missing heritability of breast cancer via next generation collaboration. Breast Cancer Res. 15(3):402.

9. Wen H, Li Y, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Rowley JD, Zhang MQ, Wang SM. (2012) New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS One. 7(12):e51203.

10. Chen J, Kim YC, Wang SM. (2012) DGS (Ditag Genome Scanning) – A restriction-based paired-end sequencing approach for genome structural analysis. In Tag-Based Next Generation Sequencing (Harbers M & Kahl G, eds; Wiley-Blackwell; ISBN:978-352732892) 2012:277-285.

11. Xu J, Wang D, Zhang C, Song J, Liang T, Kim YC, Jin WR, Wang SM, Hou GH. (2011) Alternatively expressed genes identified in the CD4+ T cells of skin allograft rejection mice. Cell Transplantation 20:333-50.

12. Kim YC, Jung YC, Chen J, Alhasan AH, Kaewsaard P, Zhang Y, Ma S, Rosen S, Wang SM. (2010) Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia. BMC Research Notes 3:341.

13. Huang X, Guo H, Tammana S, Jung YC, Mellgren E, Bassi P, Cao Q, Tu ZJ, Kim YC, Ekker SC, Wu X, Wang SM, Zhou X. (2010) Gene transfer efficiency and genome-wide integration profiling of sleeping beauty, Tol2 and PiggyBac transposons in human primary T cells. Molecular Therapy 18:1803-1813.

14. Kim YC, Wu Q, Chen J, Xuan Z, Jung YC, Zhang MQ, Rowley JD, Wang SM. (2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. PNAS 106(20):8278-8283.

15. Jung YC, Xu J, Chen J, Kim YC, Wang SM. (2009) Simplified DGS procedure for large-scale genome structural study. Biotechniques 47(5):969-971.

16. Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu C-I, Wang SM. (2008) Poly A- transcripts expressed in HeLa cells. PLoS ONE 3(7):e2803.

17. Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. (2008) Scanning the human genome at kilobase resolution. Genome Res. 18(5):751-762.

18. Lee S, Hwang J, Ulaszek J, Kim YC, Dong H, Kim HS, Seok JW, Suh BK, Yim SJ, Johnson D, Choe NH, Chang KT, Ryoo Zy, Tseng CC, Wickrema A, Wang SM. (2007) Stable transcriptional status in the apoptotic erythroid genome. Biochem Biophys Res Commun. 359(3):556-562.

19. Kim YC, Jung YC, Xuan Z, Dong H, Zhang MQ, Wang SM. (2006) Pan-genome Isolation of low abundance transcripts using SAGE tag. FEBS Lett. 580(28-29):6721-6729.

20. Lee S, Chen J, Zhou G, Shi RZ, Bouffard G, Kocherginsky M, Ge X, Sun M, Jayathilaka N, Kim YC, Emmanuel N, Bohlander S, Minden M, Kline J, Ozer O, Larson R, LeBeau M, Green E, Trent J, Karrison T, Liu P, Wang SM, Rowley JD. (2006) Gene expression profiles in acute myeloid leukemia with common translocations using SAGE. PNAS 103(4):1030-1035.

21. Lee S, Chen JJ, Zhou GL, Shi R, Kocherginsky M, Karrison TG, Kim YC, Ge XJ, Jayathialaka N, Neilly MB, Bouffard G, Young A, Komblau S, Bloomfield C, Bohlander S, Liu PP, Sun M, Wang SM, Rowley JD. (2005) Gene Expression Profiles in Acute Myeloid Leukemia (AML): From Diagnosis to Prognosis. Blood 106(11):839A-840A.

22. Lee S, Johnson D, Dunbar K, Dong H, Ge X, Kim YC, Wing C, Jayathilaka N, Emmanuel N, Zhou CQ, Gerber HL, Tseng CC, Wang SM. (2005) 2.45 GHz radiofrequency fields alter gene expression in cultured human cells. FEBS Lett. 579(21):4829-4836.

23. Lee S, Bao JY, Zhou GL, Shapiro J, Xu JH, Shi RZ, Lu XM, Clark T, Johnson D, Kim YC, Wing C, Tseng C, Sun M, Lin W, Wang J, Yang HM, Du W, Wu CI, Zhang XQ, Wang SM. (2005) Detecting novel low-abundant transcripts in Drosophila. RNA 11(6):939-46.

24. Lee S, Chen JJ, Zhou GL, Touma E, Shi R, Sun M, Kocherginsky M, Karrison TG, Kim YC, Ge XJ, Jayathialaka N, Emmanuel N, Bouffard G, Dietrich N, Young A, Green E, Liu PP, Li XM, Wang SM, Rowley JD. (2004) Gene Expression Profiles in Acute Myeloid Leukemia (AML): A Novel Approach Using SAGE and Custom Microarray. Blood 104(11):60A-61A.

* Underlined authors contributed equally.