Bioinformatics and Genomics Lab

Publications

DNA methylations are coupled with splicing regulatory elements for exon expression
(In Preparation)

Development of a new Pharmacogenomics database combining genetic variants, DNA methylation, and exon expression data

(In Preparation)


Uncovering an overlooked impact of exon skipping in miRNA target sites in 3'UTR

(In Preparation)


Development of R-package for RNA-seq data analysis and identifying novel exon skipping and intron retention.

(In Preparation)


24. 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)
(Under Review)


23. Racial differences in intron retention and DNA methylation in breast cancer subtypes
Dongwook Kim, Manu Shivakumar, Michael S Sinclair, Youngji Lee, Dokyoon Kim*, and Younghee Lee* (*Corresponding author)
(Under Review)


22. Evidence of selection on splicing-associated loci in human populations and disease loci mapping
Eric Gamazon, Nancy J Cox, and Younghee Lee* (*Corresponding author)
(Under Review)


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