publication

Pubmed

Processing Papers

1. Ban HJ*, Seo J*, Choi JK, Kho GH, Lee S, Kim SC+ and Lee B+.(* 1st, +* Corresponding) STAS-seq: Statistical Analysis Suite for RNA-seq data. 

2. Lee KW, Shin SY, Kim SC, Ahn T, Joung JG, Hwang KB  iSURV: an integrated survival analysis platform with transcriptome sequencing data

2023

1.  Jeon K, Kim Y, Kang SK, Park U, Kim J, Park N, Koh J, Shim MS, Kim M, Rhee YJ, Jeong H, Lee S, Park D, Lim J, Kim H, Ha NY, Jo HY, Kim SC, Lee JH, Shon J, Kim H, Jeon YK, Choi YS, Kim HY, Lee WW, Choi M, Park HY, Park WY, Kim YS, Cho NH. Elevated IFNA1 and suppressed IL12p40 associated with persistent hyperinflammation in COVID-19 pneumonia. Front Immunol. 2023 Jan 27;14:1101808.

2022

2.  HY Jo, HH Seo, D G, YC Park, HJ Han, HW Han, RK Thimmulappa, SC Kim and JH Kim. Single-Cell RNA Sequencing of Human Pluripotent Stem Cell-Derived Macrophages for Quality Control of The Cell Therapy Product.  Frontiers in Genetics

3. S Lee, SC Kim & D Yu An efficient GPU-parallel coordinate descent algorithm for sparse precision matrix estimation via scaled lasso Computational Statistics (2022) 4 

4. Jo HY, SC Kim et al. Establishment of the large-scale longitudinal multi-omics dataset in COVID-19 patients: data profile and biospecimen.

5. Lee CK, Chon HJ, Kwon WS, Ban HJ, Kim SC, Kim H, Jeung HC, Chung J, Rha SY. The UGT1A9*22 genotype identifies a high-risk group for irinotecan toxicity among gastric cancer patients. Genomics & Informatics 2022; 20(3): e29.

2020

1. Seo HH,  Han HW, Lee, SE, Hong SH,  Cho SH, Kim SC, Koo, SK Kim JH. Modeling Toxoplasma gondii infection in human cerebral organoid, Emerg Microbes Infect (2020)

2. Cho SB, Jang JH, Chung MG, Kim SC Exome Chip Analysis of 14,026 Koreans Reve-als Known and Newly Discovered Genetic Loci Associated with Type 2 Diabetes Mellitus Diabetes Metab J (2020)

3. Kim KH*, Kim HS*, Kim SC*(co 1st), Kim DA, Kim YB, Chung HC, Rha SY. Gene Expression Profiling Identifies Akt as a Target for Radiosensitization in Gastric Cancer Cells. Frontiers in Oncology (2020)

4. Jo HY, Lee Y, Han HJ Han, Kwon A, Kim BY, Jo EH, Go GY, Ha HY, Kim SC, Kim JH, Kim YO, Koo SK and Park MH Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation Scientific Reports volume 10, Article number: 18582 (2020)

2019

1. Cho SB, Kim SC & Chung MG  Identification of novel population clusters with different susceptibilities to type 2 diabetes and their impact on the prediction of diabetes, Scientific Reports volume 9, Article number: 3329 (2019) 

2018

1. Oh SC, Sohn BH, Kim SB, Lee SH, Park YY, Lee HS, Jang HJ, Park ES, Kim SC, Heo J, Chu IS, Cheng JH, Jang YJ, Mok YJ, Jung WK, Kim BH, Kim A, Cho JY, Lim JY, Hayash Y, Elimova E, Shiozaki H, Lee JH, Bhutani MS, Liu Y, Liu W, Lee J, Kang WK, Kim S, Noh SH, Mills GB, Ajani JA and Lee JS. Clinical and genomic landscape of gastric cancer with a mesenchymal phenotype Nature Communications volume 9, Article number: 1777 (2018)

2. Kim SC, Yu D and Cho SB. COEX-seq: COnvert a variety of measurments of gene EXpression in RNA-seq. Genomics & Informatics, 2018 Dec;16(4):e36

2017

1. Jung H, Yoo HY, Lee SH, Shin S, Kim SC, Lee S, Joung JG, Nam JY, Ryu D, Yun JW, Choi JK, Kim KK, Kim SJ, Kim WS, Park WY, Ko YH. (2017)  The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP Oncotagert 10.18632/oncotarget.14928

2. Kim SC and Yu D. Identification of differentially expressed genes using tests based on multiple imputations. Quantitative Bio-Science vol. 36 No.1 : 23-31

3. Shin HT, Yun JY, Kim NK, Kim SY, Jeon HJ, Nam JY, Lee C, Ryu D, Kim SC, Park K, Lee J, Kim ST, Park K, Ahn MJ, Lee SH, Ahn JS, Kim HC, Lee WY, Oh BY, Lm YH, Park YH, Lee JE, Lee KH, Park PJ, Choi YL, Park WY. Accurate identification of low-allele-fraction variants in clinical samples Nature Communication. 8:1337

2016

1. Lee WJ, Kim SC, Yoon JH, Yoon SJ, Lim J, Kim YS, Kwon SW, Park JH. (2016) Meta-Analysis of Tumor Stem-like Breast Cancer Cells using Gene Set and Network Analysis PLOS One 11(2) e0148818

2. Choi EB, Yang AY, Kim SC, J Lee, Choi JK Kim MY (2016) PARP1 enhances lung adenocarcinoma metastasis by novel mechanisms independent of DNA repair Oncogene doi:10.1038/onc.2016.3

3. Nam JY*, Kim N KD*, Kim SC, Joung JG, Park PJ#, Park WY# Evaluation of somatic copy number variation calling tools using whole exome sequencing data. Briefings in Bioinformatics 2016 Mar;17(2):185-92.

4. Sohn BH, Shim JJ, Kim SB, Jang KY, Kim SM, Kim JH, Hwang JH, Jang HJ, Lee HS, Kim SC, Jeong W, Kim SS, Park ES, Heo J, Kim YJ, Kim DG, Leem SH, Kaseb AO, Hassan MM, Cha M, Chu IS, Johnson R, Park YY, and Lee JS,* (2016) Inactivation of Hippo pathway is significantly associated with poor prognosis in hepatocellular carcinoma Clinical Cancer Research Mar 1:22(5):1256-64

5. Woo HR, Koo HJ, Kim J, Jeong H, Yang JO, Lee IH, Jun JH, Choi SH, Park SJ, Kang B, Kim YW, Phee BK, Kim JH, Seo C, Park C, Kim SC, Park S, Lee B, Lee S, Hwang D, Nam HG (2016)  Programming of plant leaf senescence with temporal and inter-organellar coordination of transcriptome Plant Physiology 2016 Mar 10. pp 01929

6. Joung JG*, Bae JS*, Kim SC, Jung HC, Park WY, Song SY(* 1st)  (2016) Genomic characterization and comparison of multi-regional and pooled tumor biopsy specimens. PLOS One 11(3): e0152574

7. Lee KW,Lee SS, Hwang JE, Jang HJ, Lee HS, Oh SC, Lee SH, Sohn BH, Kim SB, Jeong W, Cheong JH, Cho JY, Lim JY, Park ES, Kim SC, Kang YK, Noh SH, Ajani JA, and Lee JS (2016) Development and Validation of a Six-Gene Recurrence Risk Score Assay for Gastric Cancer.  Clinical Cancer Research 2016 Sep 21

8. Jang HJ, Lee HS, Burt BM, Lee GK, Yoon KA, Park YY, Sohn BH, Kim SB, Kim MS, Lee JM, Joo J, Kim HK, Kim SC, Yun JS, Na KJ, Choi YL, Park JL, Kim SY, Lee K, Lee YS, Han Leng, Liang H, Zo JI, Shim YM, and Lee JS. (2016) Integrated Genomic Analysis of  Recurrence-Associated Small Non-Coding RNAs in Oesophageal Cancer.  Gut doi:10.1136/gutjnl-2015-311238

9.  Song KH, Park MS, Nandu TS, Gadad S, Kim SC, Kim MY. GALNT14 promotes lung-specific breast cancer metastasis by modulating self-renewal and interaction with the lung microenvironment. Nat Commun. 2016 Dec 16;7:13796

2015

1. Yu D*, Lee SJ*, Lee WJ,  Kim SC, Lim J and Kwon SW.(* 1st)  Classification of Spectral Data Using Fused Lasso Logistic Regression. Chemometrics and Intelligent Laboratory Systems Volume 142, 15 March 2015, Pages 70–77

2. Kim KT+, Lee HW+, Lee HO+, Kim SC, Seo YJ, Chung W, Eum HH, Nam DH, Kim J, Joo KM*, Park WY* Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells Genome Biology 2015, 16:127 

3. Kim K, Yang W, Lee KS, Bang H, Jang K, Kim SC, Yang JO, Park S, Park K, Choi JK. Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes. Nucleic Acids Res. 2015 Vol 42, 12 5716-5729

4. Larrainzar E*, Riely BK*, Kim SC, Carrasquilla-Garcia N, Yu HJ, Hwang HJ, Oh M, Kim GB, Surendrarao AK, Chasman D, Siahpirani AF, Penmetsa RV, Lee GS, Kim N, Roy S, Mun JH, Cook DR Deep sequencing of the Medicago truncatula root transcriptome reveals 32 a massive and early interaction between Nod factor and ethylene signals Plant Physiology 169(1):233-65

5. Bae JS, Kim NK, Lee C, Kim SC, Lee HR, Song HR, Park KB, Kim HW, Lee SH, Kim HY, Lee SC, Jeong C, Park MS, Yoo WJ, Chung CY, Choi IH, Kim OH, Park WY and Cho TJ (2015) Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing. Genet Med. 2015 Sep 24

2014

1. Lee WJ, Kim SC*, Lee SJ, Lee J, Park JH, Lim J, Kwon SW* (* corresponding) Investigation of different mechanisms of genotoxic carcinogens and non-genotoxic carcinogens by gene set analysis PLOS One January 2014 | Volume 9 | Issue 1 | e86700

2. Jeong W, Kim SB, Sohn BH, Park YY, Park ES, Kim SC, Kim SS, Johnson RL, Birrer M, Bowtell DS, Mills GB, Sood A, Lee JS. (2014) Activation of YAP1 Is Associated with Poor Prognosis and Response to Taxanes in Ovarian Cancer. Anticancer Res. 2014 Feb;34(2):811-7

3. Yoo HY*, Sung MK*, Lee SH, Kim S, Lee H, Park S, Kim SC, Lee B, Rho K, Lee JE, Cho KH, Kim W, Ju H, Kim J, Kim SJ, Kim WS, Lee S+, Ko YH+ (* 1st, + corresponding) A frequent inactivating mutation in RHOA GTPase in angioimmunoblastic T-cell lymphoma Nature Genetics 46, 371–375 (2014)

4. Yang JO*, Hwang S, Kim WY, Park SJ, Kim SC, Park K, Lee B*, The HUGO Pan-Asian SNP Consortium (2014) Identification of Ethnically Specific Genetic Variations in Pan-Asian Ethnos Genomics & Informatics 2014;12(1):42-47

5. Kim K*, Ban HJ*, Seo J, Lee K, Yavartanoo M, Kim SC, Park K, Cho SB, Choi JK.(* 1st) (2014) Genetic factors underlying discordance in chromatin accessibility between monozygotic twins Genome Biology 15:R72

6. Kim HJ, Ryu J, Woo HM, Sho SS, Sung MK, Kim SC, Rark MH, Park T, Koo SK Patterns of gene expression associated with Pten deficiency in the developing inner ear PLOS One June 2014 | Volume 9 | Issue 6 | e97544

7. Davis* CF, Ricketts* C, Wang* M, Yang* L, Cherniack AD, Shen H, Buhay C, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA, The Cancer Genome Atlas Research Network**, Matthew L. Meyerson, Raju Kucherlapati, Woong-Yang Park, A. Gordon Robertson, Peter W. Laird, Elizabeth P. Henske, David J. Kwiatkowski, Peter J. Park, Margaret Morgan, Brian Shuch, Donna Muzny, David A. Wheeler, W. Marston Linehan, Richard A. Gibbs, W. Kimryn Rathmell, Chad J. Creighton The somatic genomic landscape of chromophobe renal cell carcinoma Cancer Cell 26, 1–12, September 8, 2014

8. Kim SK*, Lee H*, Han K, Kim SC, Choi Y, Park SW, Bak G, Lee Y, Choi JK, Kim TK, Han YM+, and Lee D+ SET7/9 methylation of the pluripotency factor LIN28A is a nucleolar localization mechanism that blocks let-7 biogenesis in human ESCs Cell Stem Cell 15, 735–749

2013

1. Lee KB*, Kim SC*, Jung I*, Jahng J, Kim K, Jung DW, Lee S, Bogu GK, Seo J, Lee B, Choi JK. (* 1st) Genetic Architecture of Chromatin Regulation in Yeast. PLOS Genetics 9(2) e1003229

2. Park SJ, Yang JO, Kim SC, Kwon JK, Lee S, Lee B Inference of kinship coefficients from Korean SNP genotyping data. BMB Reports  Jun;46(6):305-9.

3. Lee WK, Kim N, Kim J, Moon J-K, Jeong N, Choi I-Y, Kim SC, Chung W-H, Kim HS, Lee S-H, Jeong S-C Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps THEORETICAL AND APPLIED GENETICS 126(4) 1103-1119

4. Kim SC*, Jung Y*, Park J*, Cho S*, 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 8(2) e55596

5. Kim HS, Shin SJ, Kim SC, An S, Rha SY, Ahn JB, Cho BC, Choi HJ, Sohn JH, Kim HS, Chung HC, Kim JH, Rho JK, Lee S. Randomized Controlled Trial of Standardized Education and Telemonitoring for Pain in Outpatients with Advanced Solid Tumors  Supportive Care in Cancer 21:1751-1759

6. Park YY, Lee SS, Lim JY, Kim SC, Kim SB, Sohn BH, Chu IS, Oh SC, Park ES, Jeong W, Kim SS, Kopetz S, Lee JS. Comparison of prognostic genomic predictors in colorectal cancer. PLoS One. 2013 Apr 23;8(4):e60778.

7. Kim SC, Lee SJ, Lee WJ, Yum YN, Kim JH, Sohn S, Park JH, Lee J, Lim J*, Kwon SW* Stouffer's Test in a Large Scale Simultaneous Hypothesis Testing. PLOS One 8(5): e63290

8. Lee SJ, Yum YN, Kim SC, Kim Y, Lim J, Lee WJ, Koo KH, Kim JH, Kim JE, Lee WS, Sohn S, Park SN, Park JH, Lee J, Kwon SW. Distinguishing between genotoxic and non-genotoxic hepatocarcinogens by gene expression profiling and bioinformatic pathway analysis. Sci Rep. 2013 Oct 3;3:2783

9.  

2012

• 1. Chai C*, Ju HK*, Kim SC, Park JH, Lim J, Kwon SW, Lee J.(* 1st)Determination of bioactive compounds in fermented soybean products using GC/MS and further investigation of correlation of their bioactivities Journal of Chromatography B, 880 (2012) 42- 492.

  2. Lim J, Kim J, Kim SC, Yu DH, Kim KA, Kim BS (2012) Detection of Differentially Expressed Gene Sets Using a Multivariate Test Statistic in a Partially Paired Microarray Data Set. Statistical Applications in Genetics and Molecular Biology, 11(3), 1-28

  3. Oh SC, Park YY, Lim JY, Kim SM, Kim SB, KIm J, Park ES, Kim SC, Chu IS, Smith JJ, Beauchamp RD, Yeatman TJ, Kopetz S, and Lee JS. Gene Expression Signature Associated with Two Molecularly Distinct Subtypes of Colorectal Cance GUT 61(9):1291-1298

  4. Kim SM, Leem SH, Chu IS, Park YY, Kim SC, Kim SB, Park ES, Lim JY, Heo J, Kim YJ, Kim DG, Kaseb A, Park YN, Wang XW, Thorgeirsson SS and Lee JS. 65-gene-based risk score classifier predicts recurrence and survival in hepatocellular carcinoma. hepatology 55(5) 1443-52

  5. Seo J, Kim SC, Salleh NLM, Lee HS, Han Y, Shon HJ, Kim JK, Chung I, Lee JH, Desai KV, Liu E, Kang ES, Kim JS & Choi JK Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells. NAR 2012 Jul;40(13):5965-74.

  6. Kim HS*, Kim SC*, Kim SJ, Park CH, Jeung HC, Kim YB, Ahn JB, Chung HC, Rha SY(* 1st).(2012) Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells BMC Genomics 13:348

  7. Park YY, Park ES, Kim SB, Kim SC, Sohn BH, Chu IS, Heo J, Lim JY, Kim Y, Leem SH, Mills GB, Byers LA, Lee JS. Development and Validation of a Prognostic Gene-Expression Signature for Lung Adenocarcinoma, PLOS One 7(9) e44225

2011

• 1. Sung CO, Kim SC, Karnan S, Karube K, Shin HJ, Nam DH, Suh Y-L, Kim S-H, Kim JY, Kim SJ, Kim WS, Seto M, and Ko Y-H. (2011). Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma. BLOOD 117(4), 1291-1300.

  2. Ban HJ*, Kim SC*, Seo J*, Kang HB, Choi JK. (* 1st) (2011). Genetic and metabolic characterization of insomnia. PLOS One 6(4): e18455

  3. Kim SC and Choi JK Controlling transcriptional programs for cellular adaptation by chromatin regulation. Molecular BioSystems 2011, 7, 1713-1719

2010

• 1. Kim SC, Lim J. (2010). Note on the equality of variances in two sample t-test. Korean Communication in Statistics 17(1): 79-88.

  2. Lee JS, Leem SH, Lee SY, Kim SC, Park ES, Kim SB, Kim SK, Kim YJ, Kim WJ and Chu IS. (2010). Expression signature of E2F1 and its associated genes predicts superficial-to-invasive progression of bladder tumors. Journal of Clinical Oncology 28(16), 2660--2667. (4/26)

2009

• 1. Kim SC, Lee J-H, Kim BS (2009). A Concordance Study of the Preprocessing Orders in Microarray Data. The Korean Journal of Applied Statistics. 22(3): 585-594

  2. Kim BS, Jang JS, Kim SC, Lim J. (2009). A Report on the Inter-Gene Correlations in cDNA Microarray Data Sets. The Korean Journal of Applied Statistics 22(3): 617-626.

  3. Rha SY, Jeung HC, Seo MY, Kim SC, Yang WI, Moon YW, Chung HC. (2009). Prediction of high-risk patients by genome-wide copy number alterations from remaining cancer after neoadjuvant chemotherapy and surgery. Int J Oncol.  34(3): 837-46.

  4. Kim BS and Kim SC (2009). A penalized spline based method for detecting the DNA copy number alternation in an array-CGH experiment. The Korean Journal of Applied Statistics 22(1), 115-127.