67 Publications (Page 1 of 3)
2016
BioVLAB-mCpG-SNP-EXPRESS : A System for Multi-level and Multi-perspective Analysis and Exploration of DNA Methylation, Sequence Variation (SNPs), and Gene Expression from Multi-omics Data.
Chae, Heejoon⋅Lee, Sangseon⋅Seo, Seokjun⋅Jung, Daekyoung⋅Chang, Hyeonsook⋅Nephew, Kenneth P and Kim, Sun
Methods (San Diego, Calif.), July 28, 2016. | Journal Article
 
CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments.
Hur, Benjamin⋅Lim, Sangsoo⋅Chae, Heejoon⋅Seo, Seokjun⋅Lee, Sunwon⋅Kang, Jaewoo⋅Sun, Kim and Kim, Sun
Biology direct, vol. 11, (no. 1), pp. 57, October 24, 2016. | Journal Article
 
Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice.
Jung, Inuk⋅Ahn, Hongryul⋅Shin, Seon-Ju⋅Kim, Jukon⋅Kwon, Hawk-Bin⋅Jung, Woosuk and Kim, Sun
BMC systems biology, vol. 10, pp. 115, December 23, 2016. | Journal Article
 
Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis.
Jeong, Hae Min⋅Lee, Sangseon⋅Chae, Heejoon⋅Kim, RyongNam⋅Kwon, Mi Jeong⋅Oh, Ensel⋅Choi, Yoon-La⋅Kim, Sun and Shin, Young Kee
Epigenomics, vol. 8, (no. 8), pp. 1061-1077, August 2016. | Journal Article
 
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways.
Jo, Kyuri⋅Jung, Inuk⋅Moon, Ji Hwan and Kim, Sun
Bioinformatics (Oxford, England), vol. 32, (no. 12), pp. i128-i136, June 15, 2016. | Journal Article
 
Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms.
Park, Jinwoo⋅Hur, Benjamin⋅Rhee, Sungmin⋅Lim, Sangsoo⋅Kim, Min-Su⋅Kim, Kwangsoo⋅Han, Wonshik and Kim, Sun
Journal of bioinformatics and computational biology, vol. 14, (no. 5), pp. 1644002, October 2016. | Journal Article
 
Measuring intratumor heterogeneity by network entropy using RNA-seq data.
Park, Youngjune⋅Park, Youngjune⋅Lim, Sangsoo⋅Lim, Sangsoo⋅Nam, Jin Wu⋅Nam, Jin-Wu⋅Kim, Sun and Kim, Sun
Scientific reports, vol. 6, pp. 37767, November 24, 2016. | Journal Article
 
Prioritizing biological pathways by recognizing context in time-series gene expression data.
Lee, Jusang⋅Jo, Kyuri⋅Lee, Sunwon⋅Kang, Jaewoo and Kim, Sun
BMC bioinformatics, vol. 17, pp. 477, December 23, 2016. | Journal Article
 
Protein Interaction Network (PIN)-based Breast Cancer Subsystem Identification and Activation Measurement for Prognostic Modeling.
Lim, S⋅Park, Y⋅Hur, B⋅Kim, M⋅Han, W and Kim, S
Methods (San Diego, Calif.), June 18, 2016. | Journal Article
 
RDDpred: A condition-specific RNA-editing prediction model from RNA-seq data
Kim, Min-su⋅Hur, Benjamin and Kim, Sun
BMC genomics, vol. 17 Suppl 1, (no. 7), pp. 5, 2016-Jan-11. | Journal Article
 
Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines.
Chae, Heejoon⋅Lee, Sangseon⋅Nephew, Kenneth P⋅Sun, Kim and Kim, Sun
BMC systems biology, vol. 10, pp. 116, December 23, 2016. | Journal Article
2015
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.
Chae, Heejoon⋅Rhee, Sungmin⋅Nephew, Kenneth P and Kim, Sun
Bioinformatics (Oxford, England), vol. 31, (no. 2), pp. 265-267, January 15, 2015. | Journal Article
 
Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601.
Yerrapragada, Shaila⋅Yerrapragada, Shaila⋅Shukla, Animesh⋅Shukla, Animesh⋅Hallsworth-Pepin, Kymberlie⋅Hallsworth-Pepin, Kymberlie⋅Choi, Kwangmin⋅Choi, Kwangmin⋅Wollam, Aye⋅Wollam, Aye⋅Clifton, Sandra⋅Clifton, Sandra⋅Qin, Xiang⋅Qin, Xiang⋅Muzny, Donna⋅Muzny, Donna⋅Raghuraman, Sriram⋅Raghuraman, Sriram⋅Ashki, Haleh⋅Ashki, Haleh⋅Uzman, Akif⋅Uzman, Akif⋅Highlander, Sarah K⋅Highlander, Sarah K⋅Fryszczyn, Bartlomiej G⋅Fryszczyn, Bartlomiej G⋅Fox, George E⋅Fox, George E⋅Tirumalai, Madhan R⋅Tirumalai, Madhan R⋅Liu, Yamei⋅Liu, Yamei⋅Kim, Sun⋅Kim, Sun⋅Kehoe, David M⋅Kehoe, David M⋅Weinstock, George M and Weinstock, George M
Genome announcements, vol. 3, (no. 3), 2015. | Journal Article
2014
A multifunctional protein EWS regulates the expression of Drosha and microRNAs
Kim, K⋅Hwang, Y⋅Jung, M-k⋅Choe, J⋅Kim, Y⋅Kim, S⋅Lee, C-j⋅Ahn, H⋅Lee, J⋅Kowall, N⋅Kim, Y⋅Kim, J-i⋅Lee, S and Ryu, H
Cell Death and Differentiation, vol. 21, (no. 1), pp. 136-45, Jan 2014. | Journal Article
 
DegPack: a web package using a non-parametric and information theoretic algorithm to identify differentially expressed genes in multiclass RNA-seq samples.
An, Jaehyun⋅Kim, Kwangsoo⋅Chae, Heejoon and Kim, Sun
Methods (San Diego, Calif.), vol. 69, (no. 3), pp. 306-314, October 1, 2014. | Journal Article
 
piClust: a density based piRNA clustering algorithm.
Jung, Inuk⋅Park, Jong Chan and Kim, Sun
Computational biology and chemistry, vol. 50, pp. 60-67, June 2014. | Journal Article
 
Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress
Jo, Kyuri⋅Kwon, Hawk-Bin and Kim, Sun
Methods, vol. 67, (no. 3), pp. 372, 2014-06-01. | Journal Article
2013
Bio and health informatics meets cloud : BioVLab as an example.
Chae, Heejoon⋅Jung, Inuk⋅Lee, Hyungro⋅Marru, Suresh⋅Lee, Seong-Whan and Kim, Sun
Health information science and systems, vol. 1, pp. 6, 2013. | Journal Article
 
Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.
Chae, Heejoon⋅Park, Jinwoo⋅Lee, Seong-Whan⋅Nephew, Ken and Kim, Sun
Nucleic acids research, vol. 41, (no. 9), pp. 4783-91, 2013/May. | Journal Article
 
CpG island shore methylation regulates caveolin-1 expression in breast cancer.
Rao, X⋅Evans, J⋅Chae, H⋅Pilrose, J⋅Kim, S⋅Yan, P⋅Huang, R-L⋅Lai, H-C⋅Lin, H⋅Liu, Y⋅Miller, D⋅Rhee, J-K⋅Huang, Y W⋅Gu, F⋅Gray, J W⋅Huang, Th-M and Nephew, K P
Oncogene, vol. 32, (no. 38), pp. 4519-4528, September 19, 2013. | Journal Article
 
GENOME-WIDE ANALYSIS AND MODELING OF DNA METHYLATION SUSCEPTIBILITY IN 30 BREAST CANCER CELL LINES BY USING CpG FLANKING SEQUENCES
An, J.⋅Kim, K.⋅Rhee, S-M⋅Chae, H.⋅Nephew, Ken and Kim, S.
Journal of Bioinformatics and Computational Biology, vol. 11, (no. 3), pp. 1341003-1-20, 2013. | Journal Article
2012
An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells
Nam, Seungyoon⋅Long, Xinghua⋅Kwon, ChangHyuk⋅Kim, Sun and Nephew, Ken
BMC Genomics, vol. 13, (no. 1), pp. 732, 2012. | Journal Article
 
An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells.
Nam, Seungyoon⋅Long, Xinghua⋅Kwon, Changhyuk⋅Kim, Sun and Nephew, Ken
BMC genomics, vol. 13, pp. 732, 2012. | Journal Article
 
A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters
Yang, Youngik⋅Yang, Youngik⋅Nephew, Kenneth⋅Nephew, Kenneth⋅Kim, Sun and Kim, Sun
BMC bioinformatics, vol. 13 Suppl 3, (no. Suppl 3), pp. S15, 2012-Mar-21. | Journal Article
 
BioVLAB-MMIA: a cloud environment for microRNA and mRNA integrated analysis (MMIA) on Amazon EC2.
Lee, Hyungro⋅Yang, Youngik⋅Chae, Heejoon⋅Nam, Seungyoon⋅Choi, Donghoon⋅Tangchaisin, Patanachai⋅Herath, Chathura⋅Marru, Suresh⋅Nephew, Ken and Kim, Sun
IEEE transactions on nanobioscience, vol. 11, (no. 3), pp. 266-72, 2012/Sep. | Journal Article