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2010 – 2019
- 2016
[j12]Heejoon Chae, Sangseon Lee
, Kenneth P. Nephew, Sun Kim:
Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC Syst. Biol. 10(4): 433-443 (2016)- 2015
- [j11]Heejoon Chae, SungMin Rhee, Kenneth P. Nephew, Sun Kim:
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. Bioinform. 31(2): 265-267 (2015) - 2013
- [j10]Jaehyun An, Kwangsoo Kim, SungMin Rhee, Heejoon Chae, Kenneth P. Nephew, Sun Kim:
Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences. J. Bioinform. Comput. Biol. 11(3) (2013) - 2012
- [j9]Youngik Yang, Kenneth P. Nephew, Sun Kim:
A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. BMC Bioinform. 13(S-3): S15 (2012) - [j8]Pengyue Zhang, Raphaël Mourad, Yang Xiang, Kun Huang, Tim Hui-Ming Huang, Kenneth P. Nephew, Yunlong Liu, Lang Li:
A dynamic time order network for time-series gene expression data analysis. BMC Syst. Biol. 6(S-3): S9 (2012) - 2011
- [j7]Changyu Shen, Yi-Wen Huang, Yunlong Liu, Guohua Wang, Yuming Zhao, Zhiping Wang, Mingxiang Teng, Yadong Wang, David A. Flockhart, Todd C. Skaar, Pearlly Yan, Kenneth P. Nephew, Tim Hui-Ming Huang, Lang Li:
A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Syst. Biol. 5: 67 (2011) - [c6]Hyungro Lee, Youngik Yang, Heejoon Chae, Seungyoon Nam, Donghoon Choi, Patanachai Tangchaisin, Chathura Herath, Suresh Marru, Kenneth P. Nephew, Sun Kim:
BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis. BIBM 2011: 494-499 - [c5]Heng-Yi Wu, Yu Wang, Pengyue Zheng, Guanglong Jiang, Yunlong Liu, Tim Hui-Ming Huang, Kenneth P. Nephew, Lang Li:
An ERα/modulator regulatory network in the breast cancer cells. GENSiPS 2011: 5-8 - [c4]Mingxiang Teng, Yadong Wang, Yunlong Liu, Seongho Kim, Curtis Balch, Kenneth P. Nephew, Lang Li:
Empirical bayes model comparisons for differential methylation analysis. GENSiPS 2011: 9-12 - [c3]Suresh Marru, Heejoon Chae, Patanachai Tangchaisin, Sun Kim, Marlon E. Pierce, Kenneth P. Nephew:
Transitioning BioVLab cloud workbench to a science gateway. TG 2011: 40:1-40:2
2000 – 2009
- 2009
- [j6]Fuxiao Xin, Meng Li, Curtis Balch, Michael Thomson, Meiyun Fan, Yunlong Liu, Scott M. Hammond, Sun Kim, Kenneth P. Nephew:
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. Bioinform. 25(4): 430-434 (2009) - [j5]Huaxia Qin, Michael W. Y. Chan, Sandya Liyanarachchi, Curtis Balch, Dustin P. Potter, Irene J. Souriraj, Alfred S. L. Cheng, Francisco J. Agosto-Perez, Elena Nikonova, Pearlly Yan, Huey-Jen Lin, Kenneth P. Nephew, Joel H. Saltz, Louise C. Showe, Tim Hui-Ming Huang, Ramana V. Davuluri:
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. BMC Syst. Biol. 3: 73 (2009) - [j4]Seungyoon Nam, Meng Li, Kwangmin Choi, Curtis Balch, Sun Kim, Kenneth P. Nephew:
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res. 37(Web-Server-Issue): 356-362 (2009) - 2008
- [j3]Meng Li, Hyun-il Henry Paik, Curtis Balch, Yoosung Kim, Lang Li, Tim Hui-Ming Huang, Kenneth P. Nephew, Sun Kim:
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. Bioinform. 24(16): 1745-1748 (2008) - [c2]Sun Kim, Meng Li, Hyun-il Henry Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim Hui-Ming Huang:
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. Pacific Symposium on Biocomputing 2008: 315-326 - 2007
- [c1]Guohua Wang, Xin Wang, Lang Li, Kenneth P. Nephew, Howard J. Edenberg, Feng Zhou, Yunlong Liu:
Identification of Transcription Factor and microRNA Binding Sites from Array-derived Gene Expression Data. BIOCOMP 2007: 657-663 - 2006
- [j2]Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim Hui-Ming Huang, Kenneth P. Nephew:
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinform. 22(18): 2210-2216 (2006) - 2005
- [j1]Lang Li, Huidong Shi, Constantin T. Yiannoutsos, Tim Hui-Ming Huang, Kenneth P. Nephew:
Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System. J. Comput. Biol. 12(3): 370-390 (2005)
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