PUBLICATIONS

2020
  • Kim TM, Yoo JS, Moon HW, Hur KJ, Choi JB, Hong SH, Lee JY, Ha US. Distinct mutation profiles between primary bladder cancer and circulating tumor cells warrant the use of circulating tumors cells as cellular resource for mutation follow-up. BMC Cancer. 2020 Dec 7;20(1):1203. doi: 10.1186/s12885-020-07684-6. PMID: 33287735 Pubmed

  • Liu JJ, Ho JY, Lee JE, Hur SY, Yoo J, Kim KR, Ryu D, Kim TM*, Choi YJ*. (*co-correspondence) Genomic, transcriptomic, and viral integration profiles associated with recurrent/metastatic progression in high-risk human papillomavirus cervical carcinomas. Cancer Med. 2020 Oct 5. doi: 10.1002/cam4.3426. PMID: 33017516 Pubmed

  • Kim HR, Kang HN, Yun MR, Ju KY, Choi JW, Jung DM, Pyo KH, Hong MH, Ahn MJ, Sun JM, Kim HS, Kim J, Yoo J, Kim KR, Koh YW, Kim SH, Choi EC, Yoon SO, Shim HS, Paik S, Kim TM*, Cho BC*. (*co-correspondence) Mouse-human co-clinical trials demonstrate superior anti-tumour effects of buparlisib (BKM120) and cetuximab combination in squamous cell carcinoma of head and neck. Br J Cancer. 2020 Sep 23. doi: 10.1038/s41416-020-01074-2. PMID: 32963347 Pubmed

  • Hong MH, Heo SG, Lee YG, Kim HS, Park KU, Kim HG, Ko YH, Chung IJ, Min YJ, Kim MK, Kim KR, Yoo J, Kim TM*, Kim HR*, Cho BC*. (*co-correspondence) Phase 2 study of afatinib among patients with recurrent and/or metastatic esophageal squamous cell carcinoma. Cancer. 2020 Aug 4. doi: 10.1002/cncr.33123. PMID: 32749686 Pubmed

  • Kim TM, Yang IS, Seung BJ, Lee S, Kim D, Ha YJ, Seo MK, Kim KK, Kim HS, Cheong JH, Sur JH, Nam H, Kim S. Cross-species oncogenic signatures of breast cancer in canine mammary tumors. Nat Commun. 2020 Jul 17;11(1):3616. doi: 10.1038/s41467-020-17458-0. PMID: 32680987 Free PMC article. Pubmed

  • Lee SH, Yoo J, Song YS, Lim CH, Kim TM. Mutation Analysis of Colorectal and Gastric Carcinomas Originating from Adenomas: Insights into Genomic Evolution Associated with Malignant Progression. Cancers (Basel). 2020 Jan 31;12(2). PubMed

2019
  • Lee HH, Kim SY, Jung ES, Yoo J, Kim TM. Mutation heterogeneity between primary gastric cancers and their matched lymph node metastases. Gastric Cancer. 2019 Mar;22(2):323-334. PubMed

  • Kim TM, Ko YH, Ha SJ, Lee HH. Impact of in vitro driven expression signatures of CD133 stem cell marker and tumor stroma on clinical outcomes in gastric cancers. BMC Cancer. 2019 Feb 4;19(1):119 PubMed

2018
  • Kim K, Jeon S, Kim TM*, Jung CK*. (*co-correspondence) Immune Gene Signature Delineates a Subclass of Papillary Thyroid Cancer with Unfavorable Clinical Outcomes. Cancers (Basel). 2018 Dec 5;10(12). PubMed

  • Rhee JK, Yoo J, Kim KR, Kim J, Lee YJ, Cho BC, Kim TM. Identification of local clusters of mutation hotspots in cancer-related genes and their biological relevance. IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar 16. doi: 10.1109/TCBB.2018.2813375. PMID: 29993813 PubMed

  • Rhee JK, Kim TM. Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes. BMC Med Genomics. 2018 Apr 20;11(Suppl 2):29PMID: 29697365 PubMed

  • Rhee JK, Jung YC, Kim KR, Yoo J, Kim J, Lee YJ, Ko YH, Lee HH, Cho BC, Kim TM. Impact of tumor purity on immune gene expression and clustering analyses across multiple cancer types. Cancer Immunol Res. 2018 Jan;6(1):87-97. PubMed

~ 2017
  • Kim M, Rhee JK, Choi H, Kwon A, Kim J, Lee GD, Jekarl DW, Lee S, Kim Y, Kim TM. Passage-dependent accumulation of somatic mutations in mesenchymal stromal cells during in vitro culture revealed by whole genome sequencing. Sci Rep. 2017 Nov 6;7(1):14508. PubMed

  • Cortes-Ciriano I, Lee S, Park WY, Kim TM*, Park PJ*. A molecular portrait of microsatellite instability across multiple cancers. Nat Commun. 2017 Jun 6;8:15180. (*co-correspondence) PubMed

  • Kim HR, Kang HN, Shim HS, Kim EY, Kim J, Kim DJ, Lee JG, Lee CY, Hong MH, Kim SM, Kim H, Pyo KH, Yun MR, Park HJ, Han JY, Youn HA, Ahn MJ, Paik S*, Kim TM*, Cho BC*. Co-clinical trials demonstrate predictive biomarkers for dovitinib, an FGFR inhibitor, in lung squamous cell carcinoma. Ann Oncol. 2017 Jun 1;28(6):1250-1259. (*co-correspondence) PubMed

  • Rhee JK, Lee S, Park WY, Kim YH, Kim TM. Allelic imbalance of somatic mutations in cancer genomes and transcriptomes. Sci Rep. 2017 May 10;7(1):1653. PubMed

  • Jung YC and Kim TM. Aneuploidy meets network analysis: leveraging copy number alterations to identify molecular pathways disrupted in high-grade serous ovarian carcinomas. Translational Cancer Research, In press.

  • Rhee JK, Lee JH, Yang HK, Kim TM*, Yoon KH*. DNA Methylation Profiles of Blood Cells Are Distinct between Early-Onset Obese and Control Individuals. Genomics Inform. 2017 Mar;15(1):28-37. PMID: 28416947 (*co-correspondence) PubMed

  • Kim HS, Jung M, Kang HN, Kim H, Park CW, Kim SM, Shin SJ, Kim SH, Kim SG, Kim EK, Yun MR, Zheng Z, Chung KY, Greenbowe J, Ali SM*, Kim TM*, Cho BC*. Oncogenic BRAF fusions in mucosal melanomas activate the MAPK pathway and are sensitive to MEK/PI3K inhibition or MEK/CDK4/6 inhibition. Oncogene. 2017 Jan 16. doi: 10.1038/onc.2016.486. [Epub ahead of print] PMID: 28092667. (*co-correspondence) PubMed

  • Choi YJ, Rhee JK, Hur SY, Kim MS, Lee SH, Chung YJ, Kim TM*, Lee SH*. Intraindividual genomic heterogeneity of high-grade serous carcinoma of the ovary and clinical utility of ascitic cancer cells for mutation profiling. J Pathol. 2017 Jan;241(1):57-66. PMID: 27741368. (*co-correspondence) PubMed

  • Lim CH, Cho YK, Kim SW, Choi MG, Rhee JK, Chung YJ, Lee SH, Kim TM. The chronological sequence of somatic mutations in early gastric carcinogenesis inferred from multiregion sequencing of gastric adenomas. Oncotarget, 2016 Jun 28;7(26):39758-39767. PMID: 27175599. PubMed

  • Young-Ho Kim, Eun-Kyung Hong, Sun-Young Kong, Sung-Sik Han, Seoung-Hoon Kim, Je-Keun Rhee, Soo-Kyung Hwang, Sang-Jae Park, Tae-Min Kim. Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations. Oncotarget, 2016 Apr 26;7(17):23825-36. PMID: 27009864. PubMed

  • Huang KK, Jang KW, Kim S, Kim HS, Kim SM, Kwon HJ, Kim HR, Yun HJ, Ahn MJ, Park KU, Ramnarayanan K, McPherson JR, Zhang S, Rhee JK, Vettore AL, Das K, Ishimoto T, Kim JH, Koh YW, Kim SH, Choi EC, Teh BT, Rozen SG, Kim TM*, Tan P*, Cho BC*. Exome sequencing reveals recurrent REV3L mutations in cisplatin-resistant squamous cell carcinoma of head and neck. Sci Rep. 2016 Jan 21;6:19552. doi: 038/srep19552. PubMed PMID: 26790612; PubMed Central PMCID: PMC4726344. (*co-correspondence) PubMed

  • Kim TM, An CH, Rhee JK, Jung SH, Lee SH, Baek IP, Kim MS, Lee SH, Chung YJ. Clonal origins and parallel evolution of regionally synchronous colorectal adenoma and carcinoma. Oncotarget. 2015 Sep 29;6(29):27725-35. doi: 10.18632/oncotarget.4834. PubMed PMID: 26336987; PubMed Central PMCID: PMC4695021. PubMed

  • Kim TM, Jung SH, An CH, Lee SH, Baek IP, Kim M, Park SW, Rhee JK, Lee SH, Chung YJ. Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity. Clin Cancer Res. 2015 Oct 1;21(19):4461-72. PubMed

  • Park RW*, Kim TM*, Kasif S, Park PJ. Identification of rare germline copy number variations over-represented in five human cancer types. Mol Cancer. 2015 Feb 3;14(1):25. (*equal contribution) PubMed

  • Kim TM, Park PJ. A genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies. Cancer Res. 2014 Nov 15;74(22):6377-6382. PubMed

  • Kim TM, Jung SH, Kim MS, Baek IP, Park SW, Lee SH, Lee HH, Kim SS, Chung YJ, Lee SH. The mutational burdens and evolutionary ages of early gastric cancers are comparable to those of advanced gastric cancers. J Pathol. 2014 Nov;234(3):365-74 PubMed

  • Kim TM, Jung SH, Baek IP, Lee SH, Choi YJ, Lee JY, Chung YJ, Lee SH. Regional Biases in Mutation Screening Due to Intratumoral Heterogeneity of Prostate Cancer. J Pathol. 2014 Aug;233(4):425-35 PubMed

  • Kim TM, Laird PW, Park PJ. The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes. Cell. 2013 Nov 7;155(4):858-68 PubMed

  • Kim TM, Lee SH, Chung YJ. Clinical applications of next-generation sequencing in colorectal cancers. World J Gastroenterol. 2013 Oct 28;19(40):6784-6793 PubMed

  • Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 2013 Feb; 23(2):217-27 PubMed

  • Kim TM, Ramires V, Barrera-Chimal J, Bobadilla NA, Park PJ, Vaidya VS. Gene expression analysis reveals the cell cycle and kinetochore genes participating in renal ischemia reperfusion injury and early development in kidney. PLoS One. 2011;6(9):e25679. Epub 2011 Sep 28. PubMed

  • Kim TM, Ha SA, Kim HK, Yoo J, Kim S, Yim SH, Jung SH, Kim DW, Chung YJ, Kim JW. Gene expression signatures associated with the in vitro resistance to two tyrosine kinase inhibitors, nilotinib and imatinib. Blood Cancer Journal (2011) 1, e32; doi:10.1038/bcj.2011.32 PubMed

  • Kim TM, Huang W, Park R, Park PJ, Johnson MD. A developmental taxonomy of glioblastoma defined and maintained by microRNAs. Cancer Res. 2011 May 1;71(9):3387-99. Epub 2011 Mar 8. Pubmed

  • Kim TM, Park PJ Advances in analysis of transcriptional regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 2011 Jan-Feb;3(1):21-35. PubMed

  • Kim TM, Luquette LJ, Xi R, Park PJ rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics. 2010; 11:432. PubMed

  • Yim SH, Kim TM*, Hu HJ, Kim JH, Kim BJ, Lee JY, Han BG, Shin SH, Jung SH, Chung YJ (* equally contributed) Copy number variations in East-Asian population and their evolutionary and functional implications. Hum Mol Genet. 2010; 19(6):1001-8. PubMed

  • Kim TM, Yim SH, Jeoung YB, Jung YC, Chung YJ PathCluster: a framework for gene set-based hierarchical clustering. Bioinformatics. 2008; 24:1957-8 PubMed

  • Kim TM, Yim SH, Jung YC, Park CK, Choi JY, Park WS, Kwon MS, Fiegler H, Carter NP, Rhyu MG, Chung YJ. Clinical implication of recurrent copy number alterations in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q. Int J Cancer. 2008; 123(12):2808-15 PubMed

  • Kim TM, Yim SH, Chung YJ. Copy number variations in the human genome: potential source for the individual diversity and disease association studies (Review). Genomics and Informatics. 2008; 6(1):1-7 Journal Link

  • Kim TM, Jung YC, Rhyu MG, Jung MH, Chung YJ. GEAR: Genomic Enrichment Analysis of Regional DNA copy number changes. Bioinformatics. 2008; 24:420 PubMed

  • Kim TM, Chung YJ, Rhyu MG, Jung MH. Inferring biological functions and associated transcriptional regulators using Gene Set Expression Coherence Analysis (GSECA).  BMC Bioinformatics. 2007; 8:453 PubMed

  • Kim TM, Chung YJ, Rhyu MG, Jung MH. Genome-wide germline methylation patterns inferred from local nucleotide frequency of repetitive sequences in human genome. Mamm Genome. 2007 Apr;18(4):277-85. PubMed

  • Kim TM, Jung MH. Identification of transcriptional regulators using Binding Site Enrichment Analysis (BSEA). In Silico Biol. 2006. 6:0049. PubMed

  • Chung YJ*, Kim TM*, Kim DW, Namkoong H, Kim HK, Ha SA, Kim S, Shin SM, Kim JH, Lee YJ, Kang HM, Kim JW. (*equally contributed) Gene expression signatures associated with the resistance to imatinib. Leukemia. 2006 Sep;20(9):1542-50. PubMed

  • Kim TM, Yim SH, Lee JS, Kwon MS, Ryu JW, Kang HM, Fiegler H, Carter NP, Chung YJ. Genome-wide screening of genomic alterations and their clinicopathologic implications in non-small cell lung cancers. Clin Cancer Res. 2005 Dec 1;11(23):8235-42. PubMed

  • Kim TM, Jung YC, Rhyu MG. Alu and L1 retroelements are correlated with the tissue extent and peak rate of gene expression, respectively. J Korean Med Sci. 2004 Dec;19(6):783-92. PubMed

  • Kim TM, Hong SJ, Rhyu MG. Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate. J Korean Med Sci. 2004 Apr;19(2):177-85. PubMed