Bioinformatics and Computational Biology Lab

Papers

2023


2022


2021


2006~2020

- Kanga S. Ye L.Yu, Cho SY, and Park SY. Prevalence of pathogenic variants in actionable genes in advanced ovarian cancer: a next-generation sequencing analysis of a nationwide registry study. Eur J Cancer. 2020 Dec;141:185-192.

- Lee EY, Yu JY, Paek AR, Lee SH, Jang H, Cho SY, Kim JH, Kang HG, Yun T, Oh SE, Park SY, and  You HJ. Targeting TJP1 attenuates cell–cell aggregation and modulates chemosensitivity against doxorubicin in leiomyosarcoma. Journal of Molecular Medicine volume 98, pages761–773(2020) 

- Hamed Haselimashhadi, Jeremy C Mason, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole Babalola, Elif F Acar, Vivek Kumar, Jacqui White, Ann M Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E Christianson, Chih-Wei Hsu, Corey L Reynolds, Denise G Lanza, Isabel Lorenzo, Jennie R Green, Juan J Gallegos, Ritu Bohat, Rodney C Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmult Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Cho SY, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T Reilly, Nadine Spielmann, Holger Maier, Valerie Gailus-Durner, Tania Sorg, Masuya Hiroshi, Obata Yuichi, Jason D Heaney, Mary E Dickinson, Wurst Wolfgang, Glauco P Tocchini-Valentini, Kevin C Kent Lloyd, Colin McKerlie, Je Kyung Seong, Herault Yann, Martin Hrabé de Angelis, Steve D M Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen Parkinson, Terrence F Meehan. Soft windowing application to improve analysis of high-throughput phenotyping data. Bioinformatics,  March 2020, 36(5):1492–1500,

- Hyung D, Ann-Marie Mallon, Kyung DS, Cho SY, and Seong JK. TarGo: network based target gene selection system for human disease related mouse models. Laboratory Animal Research volume 35, Article number: 23 (2019) 

- Park C, Yoon K, Kim J, Park IH, Park SJ, Kim MK, Jang W, Cho SY, Park B, Kong SY, and Lee ES. Integrative molecular profiling identifies a novel cluster of estrogen receptor‐positive breast cancer in very young women. Cancer Sci. 2019 May; 110(5): 1760–1770.

- Cho SY. Identification of ERBB Pathway-Activated Cells in Triple-Negative Breast Cancer. Genomics Inform. 2019 Mar; 17(1): e3.

- Kim J, Kim JH, Kang HG, Park SY, YU JY, Lee EY, Oh SE, Kim YH, Yun T, Park C, Cho SY, You HJ. Integrated molecular characterization of adult soft tissue sarcoma for therapeutic targets. BMC Medical Genetics 2018, 19(Suppl 1):0. (Co-Corresponding Author)

- Yang H, Hong D, Cho SY, Park YS, Ko WR, Kim JH, Hur H, Lee J, Kim SJ, Kwon SY, Lee JH, Park DY, Song KS, Chang H, Ryu MH, Cho KS, Kang JW, Kook MC, Thiessen N, He A, Mungall A, Han SU, Kim HK. RhoGAP domain-containing fusions and PPAPDC1A fusions are recurrent and prognostic in diffuse gastric cancer. Nat Commun. 2018 Oct 25;9(1):4439. doi: 10.1038/s41467-018-06747-4. (Co-First)

- Woo JK, Shin JH, Lee SH, Park HM, Cho SY, Sung YM, Kim IY, Seong JK. Essential role of Ahnak in adipocyte differentiation leading to the transcriptional regulation of Bmpr1α expression. Cell Death Dis. 2018 Aug 28;9(9):864.

- Kyung DS, Sung HR, Kim YJ, Kim KD, Cho SY, Choi JH, Lee YH, Kim IY, Seong JK. Global transcriptome analysis identifies weight regain-induced activation of adaptive immune responses in white adipose tissue of mice. Int J Obes (Lond). 2018 Apr;42(4):755-764

- Chung M, Cho SY, Lee YS. Construction of a Transcriptome-Driven Network at the Early Stage of Infection with Influenza A H1N1 in Human Lung Alveolar Epithelial Cells. Biomol Ther. 2018 Feb 5. (Co-First)

- IMPC Consortium. Identification of genetic elements in metabolism by high throughput mouse phenotyping. Nat Commun. 2018 Jan 18;9(1):288.

- Hyung D, Kim J, Cho SY, Park C. ASpedia: a comprehensive encyclopedia of human alternative splicing. Nucleic Acids Res. 2018 Jan 4;46(D1):D58-D63. (Co-Corresponding Author)

- Woo JK1, Jung HJ, Park JY, Kang JH, Lee BI, Shin D, Nho CW, Cho SY, Seong JK, Oh SH. Daurinol blocks breast and lung cancer metastasis and development by inhibition of focal adhesion kinase (FAK). Oncotarget. 2017 Jul 4;8(34):57058-57071.

- Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N; International Mouse Phenotyping Consortium, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet. 2017 Jun 26. doi: 10.1038/ng.3901.

- Cho SY, Park JW, Liu Y, Park YS, Kim JH, Yang H, Um H, Ko WR, Lee BI, Kwon SY, Ryu SW, Kwon CH, Park DY, Lee J-H, Lee SI, Song KS, Hur H, Han S-U, Chang H, Kim SJ, Kim B-S, Yook J-H, Yoo M-W, Kim B-S, Lee I-S, Kook M-C, Thiessen N, He A, Stewart C, DunfordA, Kim J, Shih J, Saksena G, Cherniack AD, Schumacher S, Weiner A-T, Rosenberg M, Getz G, Yang EG, Ryu MH, Bass AJ, Kim HK. Sporadic Early-onset Diffuse Gastric Cancers Have High Frequency of Somatic CDH1 Alterations but Low Frequency of Somatic RHOA Mutations Compared with Late-onset Cancers. Gastroenterology. 2017, doi: 10.1053/j.gastro.

- SH Park, HS Sim, HI Kim, DC Jeong, G Wu, SY Cho, YS Lee, HJ Kwon, KW Lee. CD11b Regulates Antibody Class Switching via Induction of AID. Mol Immunol. 2017 Apr 10. 87, 47-59. 

- Cho SY, Choi MY, Ban HJ, Lee CH, Park SJ, Kim HK, Kim YS, Lee YS, Lee JY. Cervical small cell neuroendocrine tumor mutation profiles via whole exome sequencing. Oncotarget. 2017 Jan 31;8(5):8095-8104. 

- Lee ST, Lee JC, Kim JW, Cho SY, Seong JK, Moon MH. Global Changes in Lipid Profiles of Mouse Cortex, Hippocampus, and Hypothalamus Upon p53 Knockout. Sci Rep. 2016 Nov 7;6:36510.

- Park SM, Byeon SK, Sung H, Cho SY, Seong JK, Moon MH. Lipidomic Perturbations in Lung, Kidney, and Liver Tissues of p53 Knockout Mice Analyzed by Nanoflow UPLC-ESI-MS/MS. J Proteome Res. 2016 Oct 7;15(10):3763-3772.

-Shin JH, Lee SH1, Kim YN, Kim IY, Kim YJ, Kyeong DS, Lim HJ, Cho SY, Choi J, Wi YJ, Choi JH, Yoon YS, Bae YS, Seong JK1. AHNAK deficiency promotes browning and lipolysis in mice via increased responsiveness to β-adrenergic signalling. Sci Rep. 2016 Mar 18;6:23426. doi: 10.1038/srep23426.

- Shin JH, Kim IY, Kim YN, Shin SM, Roh KJ, Lee SH, Sohn M, Cho SY, Lee SH, Ko CY, Kim HS, Choi CS, Bae YS, Seong JK. Obesity Resistance and Enhanced Insulin Sensitivity in Ahnak-/- Mice Fed a High Fat Diet Are Related to Impaired Adipogenesis and Increased Energy Expenditure. PLoS One. 2015 Oct 14;10(10):e0139720. doi: 10.1371/journal.pone.0139720. eCollection 2015.

- YH Lee, YS Lee, SY Cho, HJ Kwon. Perspective of Peptide Vaccine Composed of Epitope Peptide, CpG-DNA, and Liposome Complex Without Carriers. Advances in Protein Chemistry and Structural Biology. doi:10.1016/bs.apcsb.2015.03.004

- MS Park, Rukhsana Kausar, MW Kim, SY Cho, YSeek Lee, MA Lee. Tcf7l1-mediated transcriptional regulation of Krüppellike factor 4 gene. Animal Cells and Systems, 19:1, 16-29, DOI:10.1080/19768354.2014.991351

- Noh H, Park C, Park S, Lee YS, Cho SY, Seo H. Prediction of miRNA-mRNA associations in Alzheimer's disease mice using network topology. BMC Genomics. 2014 Aug 3;15(1):644. (Co-Corresponding Author)

-Park D, Lee SC, Park JW, Cho SY, Kim HK. Overexpression of miR-17 in gastric cancer is correlated with proliferation-associated oncogene amplification. Pathol Int. 2014 Jul;64(7):309-14.

-Lee SY, Kim JM, Cho SY, Kim HS, Shin HS, Jeon JY, Kausar R, Jeong SY, Lee YS, Lee MA. TIMP-1 Modulates Chemotaxis of Human Neural Stem Cells Through CD63 and Integrin Signaling. Biochem J. 2014 May 1;459(3):565-76.

- Kang H, Choi I, Cho SY, Ryu D, Lee S, Kim W. gsGator: an integrated web platform for cross-species gene set analysis. BMC Bioinformatics. 2014 Jan 14;15(1):13.

- Cho SY, Chai JC, Park SJ, Seo H, Sohn CB, Lee YS. EPITRANS: A database that integrates epigenome and transcriptome data. Mol Cells. 2013 Nov;36(5):472-5.

-Kim SH, Jung KH, Kim SK, Kim SJ, Kim JC, Cho SY, Chai JC, Lee YS, Kim YK, Hwang HC, Ryu SG, Chai YG. Genetic diversity of Korean Bacillus anthracis isolates from soil evaluated with a single nucleotide repeat analysis. J Vet Sci. 2013;14(4):457-65. Epub 2013 Jun 30.

- Kim YN, Kim SG, Kim IY, Shin JH, Cho SY, Yi SS, Kim WK, Kim KS, Lee SH, Seong JK. Transcriptomic Analysis of Insulin-Sensitive Tissues from Anti-Diabetic Drug Treated ZDF Rats, a T2DM Animal Model. PLos One. 2013;8(7); e69624. doi:10.1371/journal.pone.0069624

- Chai JC, Park SJ, Seo HM, Cho SY, Lee YS. Identification of cancer-specific biomarkers by using microarray gene expression profiling. BioChip J. 2013; 7(1): 57-62. (Co-Corresponding Author)

- Kim SC, Jung Y, Park J, Cho SY, Seo C, Kim J, Kim P, Park J, Seo J, Kim J, Park S, Jang I, Kim N, Yang JO, Lee B, Rho K, Jung Y, Keum J, Lee J, Han J, Kang S, Bae S, Choi SJ, Kim S, Lee JE, Kim W, Kim J, Lee S. A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers. PLoS One. 2013;8(2):e55596. doi: 10.1371/journal.pone.0055596. Epub 2013 Feb 6. (Co-first Author)

- Cho SY, Jang I, Jun Y, Yoon S, Ko M, Kwon Y, Choi I, Jang H, Ryu D, Lee B, Kim VN, Kim W, Lee S. miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucl Acids Res. 2013 Jan 1;41(D1):D252-7

- Jung KH, Kim SH, Kim SK, Cho SY, Chai JC, Lee YS, Kim JC, Kim SJ, Oh HB, Chai YG. Genetic populations of Bacillus anthracis isolates from Korea. J Vet Sci. 2012 Dec;13(4):385-93.

-Cho SY, Park SH, Chai JC, Lee SY. Knowledge based construction of functional modules for genetic network in Saccharomyces Cerevisiae. BioChip J. 2011 June 5(2): 146-151

-Cho SY, Jun Y, Lee S, Choi HS, Jung S, Jang Y, Park C, Kim S, Lee S, Kim W. miRGator v2.0 : an integrated system for functional investigation of microRNAs. Nucl. Acids Res. 2011 Jan 39: D158-D162

- Lee SH, Cho SY, Frances S, Jun F and Danny R. The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements. PLoS One. 2010 Jun 29;5(6):e11353

- Lee SH, Preethi E, Cho SY, Danny R. Control of chicken CR1 retrotransposons is independent of Dicer-mediated RNA interference pathway. BMC Biology 2009, 7:53

-Cai CM, Van KJ, Kim MY, Jun TH, Shin JH, Cho SY, Lee YS, Lee SH. SNP discovery, linkage analysis and microsynteny in tentative consensus sequences derived from roots cDNA in a supernodulating soybean mutant. Euphytica. 2008 November:164:189-197

- Cho SY, Chung M, Park M, Park S, Lee YS. ZIFIBI: Prediction of DNA binding sites for zinc finger proteins. Biochem Biophys Res Commun. 2008 May:369(3):845-8

- Choi HJ, Chung TW, Kim SJ, Cho SY, Lee YS, Lee YC, Ko JH, Kim CH. The AP-2{alpha} The AP-2alpha transcription factor is required for the ganglioside GM3-stimulated transcriptional regulation of a PTEN gene. Glycobiology. 2008 May;18(5):395-407.

- Kang NY, Kang SK, Lee YC, Choi HJ, Lee YS, Cho SY, Kim YS, Ko JH, Kim CH. Transcriptional regulation of the human GD3 synthase gene expression in Fas-induced Jurkat T cells: a critical role of transcription factor NF-kappaB in regulated expression. Glycobiology. 2006 May;16(5):375-89