67 Publications (Page 1 of 3)
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, HeejoonLee, SangseonSeo, SeokjunJung, DaekyoungChang, HyeonsookNephew, 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, BenjaminLim, SangsooChae, HeejoonSeo, SeokjunLee, SunwonKang, JaewooSun, 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, InukAhn, HongryulShin, Seon-JuKim, JukonKwon, Hawk-BinJung, 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 MinLee, SangseonChae, HeejoonKim, RyongNamKwon, Mi JeongOh, EnselChoi, Yoon-LaKim, 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, KyuriJung, InukMoon, 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, JinwooHur, BenjaminRhee, SungminLim, SangsooKim, Min-SuKim, KwangsooHan, 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, YoungjunePark, YoungjuneLim, SangsooLim, SangsooNam, Jin WuNam, Jin-WuKim, 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, JusangJo, KyuriLee, SunwonKang, 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, SPark, YHur, BKim, MHan, 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-suHur, 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, HeejoonLee, SangseonNephew, Kenneth PSun, Kim and Kim, Sun
BMC systems biology, vol. 10, pp. 116, December 23, 2016. | Journal Article
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.
Chae, HeejoonRhee, SungminNephew, 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, ShailaYerrapragada, ShailaShukla, AnimeshShukla, AnimeshHallsworth-Pepin, KymberlieHallsworth-Pepin, KymberlieChoi, KwangminChoi, KwangminWollam, AyeWollam, AyeClifton, SandraClifton, SandraQin, XiangQin, XiangMuzny, DonnaMuzny, DonnaRaghuraman, SriramRaghuraman, SriramAshki, HalehAshki, HalehUzman, AkifUzman, AkifHighlander, Sarah KHighlander, Sarah KFryszczyn, Bartlomiej GFryszczyn, Bartlomiej GFox, George EFox, George ETirumalai, Madhan RTirumalai, Madhan RLiu, YameiLiu, YameiKim, SunKim, SunKehoe, David MKehoe, David MWeinstock, George M and Weinstock, George M
Genome announcements, vol. 3, (no. 3), 2015. | Journal Article
A multifunctional protein EWS regulates the expression of Drosha and microRNAs
Kim, KHwang, YJung, M-kChoe, JKim, YKim, SLee, C-jAhn, HLee, JKowall, NKim, YKim, J-iLee, 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, JaehyunKim, KwangsooChae, 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, InukPark, 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, KyuriKwon, Hawk-Bin and Kim, Sun
Methods, vol. 67, (no. 3), pp. 372, 2014-06-01. | Journal Article
Bio and health informatics meets cloud : BioVLab as an example.
Chae, HeejoonJung, InukLee, HyungroMarru, SureshLee, 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, HeejoonPark, JinwooLee, Seong-WhanNephew, 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, XEvans, JChae, HPilrose, JKim, SYan, PHuang, R-LLai, H-CLin, HLiu, YMiller, DRhee, J-KHuang, Y WGu, FGray, J WHuang, Th-M and Nephew, K P
Oncogene, vol. 32, (no. 38), pp. 4519-4528, September 19, 2013. | Journal Article
An, J.Kim, K.Rhee, S-MChae, H.Nephew, Ken and Kim, S.
Journal of Bioinformatics and Computational Biology, vol. 11, (no. 3), pp. 1341003-1-20, 2013. | Journal Article
An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells
Nam, SeungyoonLong, XinghuaKwon, ChangHyukKim, 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, SeungyoonLong, XinghuaKwon, ChanghyukKim, 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, YoungikYang, YoungikNephew, KennethNephew, KennethKim, 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, HyungroYang, YoungikChae, HeejoonNam, SeungyoonChoi, DonghoonTangchaisin, PatanachaiHerath, ChathuraMarru, SureshNephew, Ken and Kim, Sun
IEEE transactions on nanobioscience, vol. 11, (no. 3), pp. 266-72, 2012/Sep. | Journal Article