Lab of Bioinformatics and Molecular Design

Publications

β-catenin/TCF activity regulates IGF-1R tyrosine kinase inhibitor sensitivity in colon cancer.
Hani Lee, Nayoung Kim, Young Ji Yoo, Hyejin Kim, Euna Jeong, SeokGyeong Choi, Sung Ung Moon, Seung Hyun Oh, Gordon B.Mills, Sukjoon Yoon, Woo-young Kim

Oncogene. Epub ahead of print. (2018)

QSurface: Fast identification of surface expression markers in cancers.
Yourae Hong, choa Park, Nayoung Kim, Juyeon Cho, Sung Ung Moon, Jongmin Kim, Euna Jeong, Sukjoon Yoon

BMC Syst Biol. 12(Suppl2), 12-17(2018)

Transcriptome modeling and phenotypic assays for cancer precision medicine.
Euna Jeong, Sung Ung Moon, Mee Song, Sukjoon Yoon

Arch Pharm Res. 40(8), 906-914(2017)

Patient sample-oriented analysis of gene expression highlights extracellular signatures in breast cancer progression.
Yourae Hong, Nayoung Kim, Chao Li, Euna Jeong, Sukjoon Yoon

Biochem Biophys Res Commun. 487(2), 307-312(2017)

Loss-of-function screens of druggable targetome against cancer stem-like cells.
Mee Song, Hani Lee, Myung-Hee Nam, Euna Jeong, Somin Kim, Yourae Hong, Nayoung Kim, Hwa Young Yim, Young-Ji Yoo, Jung Seok Kim, Jin-Seok Kim, Yong-Yeon Cho, Gordon B. Mills, Woo-Young Kim, Sukjoon Yoon

FASEB J. 31(2), 625-635(2017)

Cardiac glycosidesdisplay selective efficacy for STK11 mutant lung cancer.
Nayoung Kim, Hwa Young Yim, Ningning He, Cheol-Jung Lee, Ju Hyun Kim, Jin-Sung Choi, Hye Suk Lee, Somin Kim, Euna Jeong, Mee Song, Sang-Min Jeon, Woo-Young Kim, Gordon B. Mills, Yong-Yeon Cho, Sukjoon Yoon

Scientific Reports. 6, 29721(2016)

Glucose starvation induces mutation and lineage-dependent adaptive response in a large collection of cancer cell lines.
Ningning He, Nayoung Kim, Euna Jeong, Yiling Lu, Gordon B. Mills, Sukjoon Yoon

Int J oncol. 48, 62-72(2016)

Differential regulation and synthetic lethality of exclusive RB1 and CDKN2A mutations in lung cancer.
Nayoung Kim, Mee Song, Somin Kim, Yujeong Seo, Yonghwan Kim, Sukjoon Yoon

Int J oncol. 48, 367-375(2016)

Analysis of image-based phenotypic parameters for high throughput gene perturbation assays.
Mee Song, Euna Jeong, Tae-Kyu Lee, Yury Tsoy, Yong-Jun Kwon, Sukjoon Yoon

Comput Biol Chem. 58, 192-198(2015)

MACE: Mutation-oriented profiling of chemical response and gene expression in cancers.
Euna Jeong, Ningning He, Hyerin Park, Mee Song, Nayoung Kim, Seongjoon Lee, Sukjoon Yoon

Bioinformatics. 31(9), 1508-1514(2015)

Integrated analysis of transcriptomes of cancer cell lines and patient samples reveals STK11/LKB1-driven regulation of cAMP phosphodiesterase-4D (PDE4D).
Ningning He, Nayoung Kim, Mee Song, Choa Park, Somin Kim, Eun Young Park, Hwa Young Yim, Kyunga Kim, Jong Hoon Park, Keun Il Kim, Fan Zhang, Gordon B Mills, Sukjoon Yoon

Mol Cancer Ther. 13(10), 2463-2473(2014)

Dissecting the global variation of gene expression for the functional interpretation of transcriptome data.
Nayoung Kim, Euna Jeong, Xiaqi Wang, Sukjoon Yoon

Genomics. Vol. 104(4),279-286(2014)

Cell line modeling for systems medicine in cancers (Review).
Nayoung Kim, Ningning He, Sukjoon Yoon

International Journal of Oncology. 44(2) 371-376(2014)

Somatic Mutaome Profile in Human Cancer tissues.
Nayoung Kim, Yourae Hong, Doyoung Kwon, Sukjoon Yoon

Genomics & Informatics. 11(4), 289-244(2013)

3D shape-based analysis of cell line-specific compound response in cancers.
Ningning He, Xiaoqi Wang, Nayoung Kim, Jong-Seok Lim, Sukjoon Yoon

Journal of Molecular Graphics and Modelling. 43 ,41-46(2013)

Somatic mutation patterns and compound response in cancers.
Ningning He, Nayoung Kim and Sukjoon Yoon

BMB Reports. 46(2), 97-102(2013)

The Regulatory Mechanism of the LY6K Gene Expression in Human Breast Cancer Cells.
Hyun Kyung Kong, Sukjoon Yoon and Jong Hoon Park

Journal of Biological Chemistry. 287, 38889-38900(2012)

QCanvas: An advanced tool for data clustering and visualization of genomics data.
Nayoung Kim, Herin Park, Ningning He, Hyeon Young Lee and Sukjoon Yoon

Genomics & Informatics. 10(4), 263-265(2012)

Systematic analysis of genotype-specific drug responses in cancer.
Nayoung Kim, Ningning He, Changsik Kim, Fan Zhang, Yiling Lu, Qinghua Yu, Katherine Hale, Joel Greshock, Richard Wooster, Sukjoon Yoon, Gordon B Mills

Int. J. of Cancer. 131(10), 2456-2464(2012)

NDRG2 Is Involved in the Oncogenic Properties of Renal Cell Carcinoma and Its Loss Is a Novel Independent Poor Prognostic Factor After Nephrectomy.
Zhe Long Liang, Kyeongah Kang, Sukjoon Yoon, Song Mei Huang, Jae Sung Lim, Jin Man Kim, Jong-Seok Lim and Hyo Jin Lee.

Annals of Surgical Oncology. 19(8), 2763-2772(2012)

Gene Expression Signatures for Compound Response in Cancers.
Ningning He and Sukjoon Yoon.

Genomics & Informatics. 9(4), 173-180(2011)

Enrichment of virtual hits by progressive shape-matching and docking.
Jiwon Choi, Ningning He, Nayoung Kim, Sukjoon Yoon.

Journal of Molecular Graphics and Modelling. 32, 82-88(2011)

Sanguinarine is an allosteric activator of AMP-activated protein kinase.
Jiwon Choi, Ningning He, Mi-Kyung Sung, Young Yang and Sukjoon Yoon

Biochem Biophys Res Commun. 413(2), 259-263(2011)

1,3-Diphenyl-1H-pyrazole derivatives as a new series of potent PPARγ partial agonists.
Jiwon Choi, Yunsun Park, Hui Sun Lee, Young Yang and Sukjoon Yoon

Bioorganic & medicinal chemistry. 18(23), 8315-23 (2010)

Global analysis of microarray data reveals intrinsic properties of gene expression.
Changsik Kim, Jiwon Choi, Yanghee Jang, Hyunjin Park, Yunsun Park, Jungsun Park, Taesung Park, Young Yang and Sukjoon Yoon,

Bioinformatics. 26(14), 1723-30(2010)

Identification of (b-carboxyethyl)-rhodanine derivatives exhibiting peroxisome proliferator-activated receptor g activity: virtual screening and QSAR studies.
Jiwon Choi, Yoonae Ko, Huisun Lee, Yunsun Park, Young Yang, Kwang-Hwi Cho and Sukjoon Yoon,

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY. 45(1), 193-202(2010)

Integrative Analysis of Microarray Data with Gene Ontology to Select Perturbed Molecular Functions using Gene Ontology Functional Code.
Changsik Kim, Jiwon Choi and Sukjoon Yoon,

Genomics & Informatics 7(2), 122-130(2009)

NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation.
Changsik Kim, Jiwon Choi, Seong Joon Lee, William J. Welsh and Sukjoon Yoon,

Nucleic Acids Research. 1;37(Web Server issue), W469-473(2009)

Transposon Directed Base-Exchange Mutagenesis (TDEM): A Novel Method for Multiple-Nucleotides Substitution within a Target Gene.
Yun Cheoul Kim, Hui Sun Lee, Sukjoon Yoon and Sherie L. Morrison,

Biotechniques. 46(7), 534-42(2009)

Cyanobacterial glucokinase complements the glucose sensing role of Arabidopsis thaliana hexokinase 1.
Ryu JY, Jeong SW, Kim SY, Ko Y, Yoon S, Choi SB, Park YI.

Biochem Biophys Res Commun. 374(3), 454-459(2008)

Optimization of high throughput virtual screening by combining shape-matching and docking methods.
Huisun Lee, Jiwon Choi, Irina Kufareva, Ruben Abagyan, Anton Filikov, Young Yang and Sukjoon Yoon,

Journal of Chemical Information and Modeling. 48(3), 489-497(2008)

Microarray Data Analysis of Perturbed Pathways in Breast Cancer Tissues.
Changsik Kim, Jiwon Choi and Sukjoon Yoon,

Genomics & Informatics 6(4), 210-222(2008)

Evaluation of Advanced Structure-Based Virtual Screening Methods for Computer-Aided Drug Discovery.
Hui Sun Lee, Jiwon Shoi and Sukjoon Yoon

Genomics & Informatics 5(1), 24-29(2007)

CSSP2: An improved method for predicting contact-dependent secondary structure propensity.
Sukjoon Yoon, William J. Welsh, Heeyoung Jung and Young Do Yoo,

Computational Biology and Chemistry. 31(5-6), 373-377 (2007)

Qhelix: a computational tool for the improved measurement of inter-helical angles in proteins.
Huisun Lee and Sukjoon Yoon,

Protein J. 26(8), 556-561(2007)

Large scale data mining approach for the gene-specific standardization of microarray gene expression data.
Sukjoon Yoon and Young Yang, Jiwon Choi and Jeeweon Seong,

Bioinformatics. 22(23), 2898-904(2006)

GEDA: New Knowledge Base of Gene Expression in Drug Addiction.
Young Ju Suh, Moon Hee Yang, Sukjoon Yoon and Jong Hoon Park,

Journal of Biochemistry and Molecular Biology. 13(4), 441-447(2006)

Analysis of chameleon sequences by energy decomposition on a pairwise per-residue basis.
Sukjoon Yoon and Heeyoung Jung,

The Protein Journal. 25(5), 361-368(2006)

RASSF1A suppresses oncogenic H-Ras-induced c-Jun N-terminal kinase activation.
Yoo YA, Na AR, Lee MS, Yoon S, Kim JS, Yoo YD.

Int J Oncol. 29(6), 1541-1547(2006)

Tumor necrosis factor-alpha and interleukin-1beta increases CTRP1 expression in adipose tissue.
Kim KY, Kim HY, Kim JH, Lee CH, Kim DH, Lee YH, Han SH, Lim JS, Cho DH, Lee MS, Yoon S, Kim KI, Yoon DY, Yang Y.

FEBS Lett. 580(16), 3953-3960(2006)

Rapid assessment of contact-dependent secondary structure propensity: relevance to amyloidogenic sequences.
Sukjoon Yoon and William J. Welsh,

PROTEINS: Structure, Function and Bioinformatics. 60(1), 110-117(2005)

Improved method for predicting beta-turn using support vector machine,
Qidong Zhang, Sukjoon Yoon and William J. Welsh,

Bioinformatics. 21(10), 2370-2374, (2005)

Surrogate Docking: Structure-based virtual screening at high throughput speed.
Sukjoon Yoon, Andrew Smellie, Dave Hartsough and Anton Filikov

Journal of Computer-aided Molecular Design. 19(7),483-497(2005)

Computational identification of proteins for selectivity assays.
Sukjoon Yoon, Andrew Smellie, Dave Hartsough and Anton Filikov,

Journal of Computer-aided Molecular Design. 19(7), 483-497(2005)

Identification of minimal subset of receptor conformations for improved multiple conformation docking method and two-step scoring.
Sukjoon Yoon and William J. Welsh,

Journal of Chemical Information and Computer Sciences (JCICS). 44(1), 88-96(2004)

Detecting hidden sequence propensity for amyloid fibril formation, docking method and two-step scoring.
Sukjoon Yoon and William J. Welsh,

Protein Science. 13(8), 2149-2160(2004)

Analysis of morphology and protein expression pattern during microspore-derived embryogeneisis of Brassica napus.
Sukjoon Yoon, Sunghan Sohn and Kwang-Woong Lee,

Korean J. Bot. 36(4), 399-406(1993)