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40. ADAS-viewer: Web-based analysis and visualization of alternative splicing in alzheimer's disease

Seonggyun Han, Jaehang Shin, Habtamu Minassie Aycheh, andYounghee Lee*

NPJ Systemps Biology and Applications. (In press) (*Corresponding author)

39. Differential alternative splicing between hepatocellular carcinoma with normal and elevated serum alpha-fetoprotein level

Young-Joo Jin, John Chamberlin, Seonggyun Han, Jaehang Shin, Habtamu Minassie Aycheh, Seyoun Byun, andYounghee Lee*

BMC Med Genomics. 2020. (*Corresponding author)

38.Gene Expression in Torn Rotator Cuff Tendons Determined by RNA Sequencing

Robert Z Tashjian , Ian Lock , Erin K Granger , Yangliang Wang ,Younghee Lee, Peter N Chalmers , Kevin B Jones

Orthop J Sports Med. 2020.

37.Sex-specific alternative splicing regulation of alzheimer’s risk variants in CLU

Seonggyun Han, Kwangsik Nho* andYounghee Lee*

Int J. Mol. Sci. 2020. (*Corresponding author)

36.Personal Health Information Inference Using Machine Learning on RNA Expression Data from Patients With Cancer: Algorithm Validation Study

Solbi Kweon, Jeong Hoon Lee,Younghee Lee and Yu Rang Park*

JMed Internet Res. 2020..

35.Functional impact of alternative splicing on pathogen life cycle in human foreskin fibroblasts infected with Trypanosoma cruzi

Hyeim Jung, Seonggyun Han, andYounghee Lee*

Nature Scientific Report. 2020. (*Corresponding author)

34.An exome-wide rare variant analysis of Korean men identifies three novel genes predisposing to prostate cancer.

D Jong Jin Oh, Manu Shivakumar, Jason Miller, Shefali Verma , Hakmin Lee, Younghee Lee, Sung Kyu Hong , Sang Eun Lee, Dokyoon Kim*, Seok-Soo Byun*

Nature Scientific Report. 2019.

33.Differential alternative splicing regulation among hepatocellular carcinoma with different risk factors

Young-Joo Jin, Seyoun Byun, Dongwook Kim, Seonggyun Han, John Chamberlin, Min Jung Kim, andYounghee Lee*

BMC Medical Genomics. 2019.

32.Landscape of alternative splicing in HIV-infected CD4+ T-cells

Seyoun Byun, Seonggyun Han, Yue Zheng, Vicente Planelles, andYounghee Lee*

BMC Medical Genomics 2019. (*Corresponding author)

31.IMAS: Integrative analysis of Multi-omics data for Alternative Splicing

Seonggyun Han, Heyim Jung, Dongwook Kimi, andYounghee Lee*

https://bioconductor.org/packages/release/bioc/html/IMAS.html

30.Identification of exon skipping events associated with in Alzheimer’s disease in the human hippocampus

Seonggyun Han, Jason E Miller, Seyoun Byun, dokyoon Kim, Shannon L. Risacher, Andrew J Saykin,Younghee Lee*and Kwangsik Nho*

BMC Medical Genomics. 2019. (*Corresponding author)

29.Genetic variation affecting exon skipping contributes to hippocampal atrophy in Alzheimer’s disease

Younghee Lee, Seonggyun Han, Dongwook Kim, Dokyoon Kim, Emrin Horgousluoglu, Shannon L. Risacher, Andrew J Saykin, and Kwangsik Nho*.

The AMIA SUMMIT. 2018. (*First author)

28.CAS-viewer: Web-based analysis and visualization of alternative splicing in cancer

Seonggyun Han, Dongwook Kim, Youngjun Kim, Kanghoon Choi, Jason E. Miller, Dokyoon Kim,Younghee Lee*.

BMC Medical Genomics. 2018. (*Corresponding author)

27.Rare variants in the Splicing Regulatory Elements of EXOC3L4 are associated with brain glucose metabolism in Alzheimer’s disease

Jason Miller, Manu Shivakumar,Younghee Lee, Kwangsik Nho, and Dokyoon Kim

BMC Medical Genomics. 2018.

26.The effects of alternative splicing on miRNA binding sites on miRNA binding sites in bladder cancer

Seonggyun Han, Dongwook Kim, Manu Shivakumar, Young-Ji Lee, Tullika Garg, Jason E. Miller, Juhan Kim, Dokyoon Kim*, and Younghee Lee.

PLoS One. 2018. (*Corresponding author)

25.Population-dependent intron retention and DNA methylation in breast cancer

Dongwook Kim, Manu Shivakumar, Seonggyun Han, Michael S Sinclair, Youngji Lee, Zheong Yonglan, Olufunmilayo I. Olopade, Dokyoon Kim*, andYounghee Lee*

Molecular Cancer Research. 2018. (*Corresponding author)

24.Evidence of selection on loci affecting splicing in human populations and application to disease loci mapping

Eric R. Gamazon*, Anuar Konkashbaev, Eske M. Derks, Nancy J. Cox, andYounghee Lee*.

Scientific Report 2017. (*Correponding author)

23. Identification of epigenetic interactions between miRNA and DNA methylation associated with gene expression as potential prognostic markers in bladder cancer

Manu Shivakumar*,Younghee Lee*, Lisa Bang, Tullika Gary, Kyong-ah Sohn, and Dokyoon Kiim.

BMC Biomedical Genomics. 2017. (*Co-first author)

22. Dietary Management Software for Chronic Kidney Disease: Current Status and Open Issues

Xiaorui Chen, Maureen A. Murtaugh, Corinna Koebnick, Srinivasan Beddhu, Jennifer H. Garvin, Mike Conway,Younghee Lee, Ramkiran Gouripeddi, Gang Luo.

Health Information Science. 2016.

21.Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

H. Li, I. Achour, J. Berghout, V. Gardeux, J. Li, L. Bastarache,Younghee Lee,L. Pesce, X. Yang, K. S. Ramos, I. Foster, J. C. Denny, J. H. Moore, and Y. A. Lussier.

Nature Genomic Medicine.2016.

20. A variant at 9p21.3 functionally implicates CDKN2B in the etiology of pediatric B-cell precursor acute lymphoblastic leukemia

Eric A Hungate, Sapana R Vora, Eric R Gamazon, Heng Xu, Timothy Best, Imge Hülür,Younghee Lee, Eva Ellinghaus, Laurent Orsi, Jacqueline Clavel, Elizabeth Milne, Mignon L Loh, Jun J Yang, Nancy J Cox, Andrew D Skol, and Kenan Onel.

Nature Communications.2016.

19. Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony–forming cells

Nutan Prasain, Man Ryul Lee, Sasidhar Vemula, Jonathan Luke Meador, Momoko Yoshimoto, Michael J. Ferkowicz, Alexa Fett, Manav Gupta, Michael Ginsberg, Brian M. Rapp, Reza Saadatzadeh,Younghee Lee, Michael P. Murphy, Sherry L. Voytik-Harbin, Shahin Rafii, Hal E. Broxmeyer, and Mervin C. Yoder.

Nature Biotechnology.2014. doi:10.1038/nbt.3048

18. In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stromal targeting therapy assessment

X. Yang, Y. Huang,Younghee Lee, V. Gardeus, I. Achour, K. Regan, E. Rebman, H. Li, and Y. Lussier.

BMC Medical Genomics2014.7(Suppl 1):S2

17. Curation-free biomodules mechanisms in prostate cancer predict recurrent disease

J. L. Chen, A. Hsu, X. Yang, J. Li,Younghee Lee, G. Parinandi, H. Li, Y. A. Lussier.

BMC Medical Genomics.2013. 6(Suppl 2):S4.

16. Network models of GWAS establish the centrality of protein interactions in complex disease traits

Younghee Lee,H. Li, J. Li, E. Rebman, E. J. Gamazon, N. J. Cox, and Y. A. Lussier.J

Am Med Inform Assoc.2013

15. Hidden Dangers: A cryptic exon disrupts BRCA2 mRNA

J. D. Fackenthal,Younghee Lee, and O.I.

Olopade.Clinical Cancer Res.2012. 18(18):4865-7

14. Variants affecting exon skipping contribute to complex traits

Younghee Lee*,E. J. Gamazon, E. Rebman, Y. Lee, S. Lee, M.E. Dolan, N. J. Cox, and Y. A. Lussier.PLoS

Genetics.2012. 8(10):e1002998. (*Corresponding authors)

13. Complex disease networks of trait-associated SNPs unveiled by information theory.

H. Li*,Younghee Lee*, J. Li, J. L. Chen, E. Rebman, K. Regan, and Y. A. Lussier.J

Am Med Inform Assoc.2012.19(2):295-305. (*Co-first authors)

12. Translating mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants

K. Wang, K. Regan, E. Doughty, H. Li, J. Li,Younghee Lee, M. Kann, Y. A. Lussier. J

AmMed Inform Assoc.2012.19(2):306-1611. MicroRNA expression characterizes oligometastase

11. MicroRNA expression characterizes oligometastase

Y. A. L., J. K. Salama, N. Khodarev, H. R. Xing, Y. Huang, M. D. Hasselle, Q. Zhang, R. Malik, T. E Darg, H. Fan, S. Perakis, M. Filippo, X. Yang, Younghee Lee, S. J. Chmura, S. Hellman, R. R. Weichselbaum.

PLoS ONE. 2011. 6(12):e28650

10. GO-Module: Functional synthesis and improved interpretation of gene ontology patterns

X. Yang, J. Li,Younghee Lee, and Y. A. Lussier.

Bioinformatics. 2011.27(10):1444-6

9. Biomolecular systems of disease buried across multiple GWAS unveiled by information theory and ontology

Younghee Lee, J. Li, E. Gamazon, J. L. Chen, A. Tikhomirov, N. J. Cox, and Y. A. Lussier.

Proceedings of the 2010 AMIA STBI. 2011.2010:31

8. Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis

Younghee Lee, X. Yang, Y. Huang1, H. Fan, Q. Zhang, Y. Wu, J. Li, R. Hasina, C. Cheng, M. Lingen, M. Gerstein, R. Weichselbaum, H. R. Xing, and Yves A. Lussier.

PLoS Comput Biol.2010.6(4):e1000730

7. Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models.

X. Yang*,Younghee Lee*,Y. Huang, J. L. Chen, H.R. Xing, and Y. A. Lussier.

BMC Bioinformatics.2010. 11: Suppl 9:S11. (*Co-first authors)

6. CProtein Interaction Network Underpins Concordant Prognosis Among Heterogeneous Breast Cancer Signatures

J. L. Chen, L. Sam, Y. Huang,Younghee Lee, J. Li, Y. Liu, H. R. Xing, and Y. A. Lussier.

J Biomed Inform.2010.43(3):385-96

5. Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancer

X. Yang,Younghee Lee, H. Fan, X. Sun, and Y. A. Lussier.

Chin. Sci. Bull.2009.55(31): 3576-3589

4. ECgene: an alternative splicing database update.

Y.S. Lee*,Younghee Lee*, B.J. Kim*, Y.A. Shin, S.Y. Nam, P.R. Kim, N.S. Kim, W.H. Chung, J.S. Kim, and S.H. Lee.

Nucleic Acids Res.2007.35(Database issue): D99–D103. (*Co-first authors)

3. ECgene: genome annotation for alternative splicing

P.R. Kim*, N.S. Kim*,Younghee Lee*, B.J. Kim*, Y.A. Shin, and S.H. Lee.

Nucleic Acids Res.2005.33(Database issue): D75-9. (*Co-first authors)

2. A secondary database for journal search based on experimental materials and methods in Alzheimer disease research

Younghee Lee, B.J. Kim, and I.S. Koh.

Genome Informatics2002

1. Mitochondrial dysfunction and oxidative stress in cytotoxicity induced by amyloid peptide

J.H. Song, J.S. Park, J.Y. Chio,Younghee Lee,and B.G. Han.

The Kor J of Gerontol.2000