Bioinformatics and Genomics Lab

Publications

37. Splicing-guided aggregation of somatic mutations in human complex disease
Seonggyun and Younghee Lee*
Manuscript in preparation


36. Identification of epigenetic interactions between miRNA and DNA methylation associated with alternative splicing as potential prognostic markers in bladder cancer
Authors TBD including Seonggyun Han and Younghee Lee*
Manuscript in preparation


35. Adaptation of Aymara population to high altitude through alternative splicing mechanism
Jihyun Song+, Seonggyun Han+, Josef Prchal* and Younghee Lee* (+ equal contribution)
Manuscript in preparation


34. Proteogenomics study of alternative splicing variants in breast cancer for precision medicine
Authors TBD including Dongwook Kim and Younghee Lee*
Manuscript in preparation


33. Crosstalk between hypo-methylation and alternative splicing in cancer
Dongwook Kim, Seonggyun Han, Jeremy Wood, Ji-young Lee, Olufunmilayo I. Olopade, Dokyoon Kim and Younghee Lee*
Manuscript in preparation


32. Landscape of alternative splicing in HIV-infected CD4+ T-cells
Seyoun Byun, Seonggyun Han, Yue Zheng, Vicente Planelles, and Younghee Lee*
Manuscript in preparation


31. IMAS: Integrative analysis of Multi-omics data for Alternative Splicing
Seonggyun Han, Heyim Jung, Dongwook Kimi, Dokyoon Kim and Younghee Lee*
Manuscript in preparation


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*
Conditionally accepted.


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 (Accepted).


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 Genomcs 2018


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
Will be published


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* (*Corresponding author)
PLoS One. 2018


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*, and Younghee Lee* (*Corresponding author)
Molecular Cancer Research. 2018


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, and Younghee Lee* (*Corresponding author)
Nature Scientific Reports. 2017


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 Kim (*First author)
BMC Biomedical Genomics. 2017


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 Genomics 2014. 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 Am
Med Inform Assoc. 2012. 19(2):306-16

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. Context-constrain molecular interaction networks uncover shared biological pathways among breast cancer signature

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 Informatics 2002


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