Image Place holder

Youngchul Kim, PhD

Academic Rank: Assistant Member

Overview


Discipline

    • Biostatistics and Bioinformatics
    • Cancer Biology and Evolution Program

Education & Training

Fellowship:

  • Seoul National University, PhD - Statistics
  • Seoul National University, Fellow - Bioinformatics and Biostatistics
Research

My primary research interest is in biostatistics and statistical bioinformatics which are interdisciplinary fields that develop statistical methods and software tools for analyzing high-throughput biological data and medical data. I have developed multi-gene signature-based prediction models for predicting chemotherapeutic response in recurrent ovarian cancer patients and bladder cancer patients. I have been developing CONCORD technique that uses gene signatures concordantly co-expressed between cancer cell lines and cancer patients not only for predicting response to cancer therapy but also for cancer drug repositioning. Recent researches have been focused on molecular cancer biomarker discovery, high-throughput Ribosome Footprint data analysis, metagenomic sequencing data analysis, and genetic association in cancer diagnosis and prognosis. I am leading a team for supporting basic science collaborations at the Department of Biostatistics and Bioinformatics.

Publications

  • Yuan Z, Naghavi AO, Tang D, Kim Y, Ahmed KA, Dhillon J, Giuliano AR, Spiess PE, Johnstone PA. The relationship between HPV status and chemoradiotherapy in the locoregional control of penile cancer. World J Urol. 2018 Sep;36(9):1431-1440. Pubmedid: 29589134.
  • Nerlakanti N, Yao J, Nguyen DT, Patel AK, Eroshkin AM, Lawrence HR, Ayaz M, Kuenzi BM, Agarwal N, Chen Y, Gunawan S, Karim RM, Berndt N, Puskas J, Magliocco AM, Coppola D, Dhillon J, Zhang J, Shymalagovindarajan S, Rix U, Kim Y, Perera R, Lawrence NJ, Schonbrunn E, Mahajan K. Targeting the BRD4-HOXB13 Co-regulated Transcriptional Networks with Bromodomain-Kinase Inhibitors to Suppress Metastatic Castration-Resistant Prostate Cancer. Mol Cancer Ther. 2018 Sep. Pubmedid: 30242092.
  • Perez MC, de Pinho FR, Holstein A, Oliver DE, Naqvi SMH, Kim Y, Messina JL, Burke E, Gonzalez RJ, Sarnaik AA, Cruse CW, Wuthrick EJ, Harrison LB, Sondak VK, Zager JS. Resection Margins in Merkel Cell Carcinoma: Is a 1-cm Margin Wide Enough?. Ann Surg Oncol. 2018 Oct;25(11):3334-3340. Pubmedid: 30073600.
  • Naghavi AO, Echevarria MI, Strom TJ, Abuodeh YA, Venkat PS, Ahmed KA, Demetriou S, Frakes JM, Kim Y, Kish JA, Russell JS, Otto KJ, Chung CH, Harrison LB, Trotti A, Caudell JJ. Patient choice for high-volume center radiation impacts head and neck cancer outcome. Cancer Med. 2018 Oct;7(10):4964-4979. Pubmedid: 30175512. Pmcid: PMC6198196.
  • Hill KS, Roberts ER, Wang X, Marin E, Park TD, Son S, Ren Y, Fang B, Yoder S, Kim S, Wan L, Sarnaik AA, Koomen JM, Messina JL, Teer JK, Kim Y, Wu J, Chalfant CE, Kim M. PTPN11 plays oncogenic roles and is a therapeutic target for BRAF wild-type melanomas. Mol Cancer Res. 2018 Oct. Pubmedid: 30355677.
  • Baksh K, Prithviraj G, Kim Y, Hoffe S, Shridhar R, Coppola D, Centeno B, Pimiento J, Meredith K, Almhanna K. Correlation Between Standardized Uptake Value in Preneoadjuvant and Postneoadjuvant Chemoradiotherapy and Tumor Regression Grade in Patients With Locally Advanced Esophageal Cancer. Am J Clin Oncol. 2018 Mar;41(3):254-258. Pubmedid: 26703814.
  • Chen YZ, Kim Y, Soliman H, Ying G, Lee JK. Single drug biomarker prediction for ER- breast cancer outcome from chemotherapy. Endocr Relat Cancer. 2018 Jun;25(6):595-605. Pubmedid: 29599124. Pmcid: PMC5920016.
  • Kim Y, Dillon PM, Park T, Lee JK. CONCORD biomarker prediction for novel drug introduction to different cancer types. Oncotarget. 2018 Jan;9(1):1091-1106. Pubmedid: 29416679. Pmcid: PMC5787421.
  • Altazi BA, Fernandez DC, Zhang GG, Hawkins S, Naqvi SM, Kim Y, Hunt D, Latifi K, Biagioli M, Venkat P, Moros EG. Investigating multi-radiomic models for enhancing prediction power of cervical cancer treatment outcomes. Phys Med. 2018 Feb;46:180-188. Pubmedid: 29475772.
  • Perez MC, Miura JT, Naqvi SMH, Kim Y, Holstein A, Lee D, Sarnaik AA, Zager JS. Talimogene Laherparepvec (TVEC) for the Treatment of Advanced Melanoma: A Single-Institution Experience. Ann Surg Oncol. 2018 Dec;25(13):3960-3965. Pubmedid: 30298318.
  • Abbott AM, Doepker MP, Kim Y, Perez MC, Gandle C, Thomas KL, Choi J, Shridhar R, Zager JS. Hepatic Progression-free and Overall Survival After Regional Therapy to the Liver for Metastatic Melanoma. Am J Clin Oncol. 2018 Aug;41(8):747-753. Pubmedid: 28059929.
  • Kim Y, Pierce CM, Robinson LA. Impact of viral presence in tumor on gene expression in non-small cell lung cancer. BMC Cancer. 2018 Aug;18(1):843. Pubmedid: 30134863. Pmcid: PMC6106745.
  • Sreeraman Kumar R, Thapa R, Kim Y, Khushalani NI, Sondak VK, Reed DR. Higher than reported adolescent and young adult clinical trial enrollment during the "Golden Age" of melanoma clinical trials. Cancer Med. 2018 Apr;7(4):991-996. Pubmedid: 29478277. Pmcid: PMC5911596.
  • Naghavi AO, Gonzalez RJ, Scott JG, Mullinax JE, Abuodeh YA, Kim Y, Binitie O, Ahmed KA, Bui MM, Saini AS, Zager JS, Biagioli MC, Letson D, Harrison LB, Fernandez DC. Implications of staged reconstruction and adjuvant brachytherapy in the treatment of recurrent soft tissue sarcoma. Brachytherapy. 2017 Jul;15(4):495-503. Pubmedid: 27180128.
  • Naghavi AO, Gonzalez RJ, Scott JG, Kim Y, Abuodeh YA, Strom TJ, Echevarria M, Mullinax JE, Ahmed KA, Harrison LB, Fernandez DC. Staged reconstruction brachytherapy has lower overall cost in recurrent soft-tissue sarcoma. J Contemp Brachytherapy. 2017 Feb;9(1):20-29. Pubmedid: 28344600. Pmcid: PMC5346606.
  • O'Donoghue C, Perez MC, Mullinax JE, Hardman D, Sileno S, Naqvi SMH, Kim Y, Gonzalez RJ, Zager JS. Isolated Limb Infusion: A Single-Center Experience with Over 200 Infusions. Ann Surg Oncol. 2017 Dec;24(13):3842-3849. Pubmedid: 29019175.
  • Ahmed KA, Berglund AE, Welsh EA, Naghavi AO, Kim Y, Yu M, Robinson TJ, Eschrich SA, Johnstone PA, Torres-Roca JF. The radiosensitivity of brain metastases based upon primary histology utilizing a multigene index of tumor radiosensitivity. Neurooncol. 2017 Aug;19(8):1145-1146. Pubmedid: 28379582. Pmcid: PMC5570253.
  • Naghavi AO, Echevarria MI, Grass GD, Strom TJ, Abuodeh YA, Ahmed KA, Kim Y, Trotti AM, Harrison LB, Yamoah K, Caudell JJ. Having Medicaid insurance negatively impacts outcomes in patients with head and neck malignancies. Cancer. 2016 Nov;122(22):3529-3537. Pubmedid: 27479362.
  • Kim DW, Wu N, Kim YC, Cheng PF, Basom R, Kim D, Dunn CT, Lee AY, Kim K, Lee CS, Singh A, Gazdar AF, Harris CR, Eisenman RN, Park KS, MacPherson D. Genetic requirement for Mycl and efficacy of RNA Pol I inhibition in mouse models of small cell lung cancer. Gene Dev. 2016 Jun;30(11):1289-1299. Pubmedid: 27298335. Pmcid: PMC4911928.
  • Freeman-Keller M, Kim Y, Cronin H, Richards A, Gibney G, Weber J. Nivolumab in Resected and Unresectable Metastatic Melanoma: Characteristics of Immune-Related Adverse Events and Association with Outcomes. Clin Cancer Res. 2016 Feb;22(4):886-894. Pubmedid: 26446948. Pmcid: PMC4755809.
  • Ahmed KA, Abuodeh YA, Echevarria MI, Arrington JA, Stallworth DG, Hogue C, Naghavi AO, Kim S, Kim Y, Patel BG, Sarangkasiri S, Johnstone PA, Sahebjam S, Khushalani NI, Forsyth PA, Harrison LB, Yu M, Etame AB, Caudell JJ. Clinical outcomes of melanoma brain metastases treated with stereotactic radiosurgery and anti-PD-1 therapy, anti-CTLA-4 therapy, BRAF/MEK inhibitors, BRAF inhibitor, or conventional chemotherapy. Ann Oncol. 2016 Dec;27(12):2288-2294. Pubmedid: 27637745.
  • Abuodeh Y, Naghavi AO, Ahmed KA, Venkat PS, Kim Y, Kis B, Choi J, Biebel B, Sweeney J, Anaya DA, Kim R, Malafa M, Frakes JM, Hoffe SE, El-Haddad G. Prognostic value of pre-treatment F-18-FDG PET-CT in patients with hepatocellular carcinoma undergoing radioembolization. World J Gastroenterol. 2016 Dec;22(47):10406-10414. Pubmedid: 28058021. Pmcid: PMC5175253.
  • Ma Z, Kim Y, Hu F, Lee JK. Point success rate for patient therapeutic response prediction by continuous biomarker scores. Stat Methods Med Res. 2016 Aug;25(4):1638-1647. Pubmedid: 23839122.
  • Sung H, Kanchi KL, Wang X, Hill KS, Messina JL, Lee JH, Kim Y, Dees ND, Ding L, Teer JK, Yang S, Sarnaik AA, Sondak VK, Mulé JJ, Wilson RK, Weber JS, Kim M. Inactivation of RASA1 promotes melanoma tumorigenesis via R-Ras activation. Oncotarget. 2016 Apr;7(17):23885-23896. Pubmedid: 26993606. Pmcid: PMC5029671.
  • Kim Y, Guntupalli SR, Lee SJ, Behbakht K, Theodorescu D, Lee JK, Diamond JR. Retrospective analysis of survival improvement by molecular biomarker-based personalized chemotherapy for recurrent ovarian cancer. PLoS One. 2014 Feb;9(2):e86532. Pubmedid: 24505259. Pmcid: PMC3914805.
  • Trimble A, Gochuico BR, Markello TC, Fischer R, Gahl WA, Lee JK, Kim Y, Burdick MD, Strieter RM, Mehrad B. Circulating fibrocytes as biomarker of prognosis in Hermansky-Pudlak syndrome. Am J Respir Crit Care Med. 2014 Dec;190(12):1395-1401. Pubmedid: 25347450. Pmcid: PMC4299649.
  • Choi HS, Kim Y, Cho KH, Park T. Integrative analysis of time course microarray data and DNA sequence data via log-linear models for identifying dynamic transcriptional regulatory networks. Int J Data Min Bioinform. 2013 Feb;7(1):38-57. Pubmedid: 23437514.
  • Shen K, Song N, Kim Y, Tian C, Rice SD, Gabrin MJ, Symmans WF, Pusztai L, Lee JK. A systematic evaluation of multi-gene predictors for the pathological response of breast cancer patients to chemotherapy. PLoS One. 2012 Nov;7(11):e49529. Pubmedid: 23185353. Pmcid: PMC3504014.
  • Ferriss JS, Kim Y, Duska L, Birrer M, Levine DA, Moskaluk C, Theodorescu D, Lee JK. Multi-gene expression predictors of single drug responses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resistance. PLoS One. 2012 Jul;7(2):e30550. Pubmedid: 22348014. Pmcid: PMC3277593.
  • Sharma R, Sharma PR, Kim YC, Leitinger N, Lee JK, Fu SM, Ju ST. IL-2-controlled expression of multiple T cell trafficking genes and Th2 cytokines in the regulatory T cell-deficient scurfy mice: implication to multiorgan inflammation and control of skin and lung inflammation. J Immunol. 2011 Jan;186(2):1268-1278. Pubmedid: 21169543. Pmcid: PMC3136806.
  • Lee JK, Coutant C, Kim YC, Qi Y, Theodorescu D, Symmans WF, Baggerly K, Rouzier R, Pusztai L. Prospective comparison of clinical and genomic multivariate predictors of response to neoadjuvant chemotherapy in breast cancer. Clin Cancer Res. 2010 Jan;16(2):711-718. Pubmedid: 20068086. Pmcid: PMC2807997.
  • Kim Y, Bekiranov S, Lee JK, Park T. Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. Bioinformatics. 2009 Oct;25(19):2486-2491. Pubmedid: 19667080. Pmcid: PMC2800349.
  • Lee SY, Chung Y, Elston RC, Kim Y, Park T. Log-linear model-based multifactor dimensionality reduction method to detect gene gene interactions. Bioinformatics. 2007 Oct;23(19):2589-2595. Pubmedid: 17872915.
  • Lee JH, Kim SH, Wang LH, Choi YL, Kim YC, Kim JH, Park TS, Hong YC, Shin YK. Clinical significance of CD99 down-regulation in gastric adenocarcinoma. Clin Cancer Res. 2007 May;13(9):2584-2591. Pubmedid: 17473187.
  • Park T, Kim Y, Bekiranov S, Lee JK. Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays. Nucleic Acids Res. 2007 Jun;35(9):e69. Pubmedid: 17430969. Pmcid: PMC1888820.
  • Wang LH, Kim SH, Lee JH, Choi YL, Kim YC, Park TS, Hong YC, Wu CF, Shin YK. Inactivation of SMAD4 tumor suppressor gene during gastric carcinoma progression. Clin Cancer Res. 2007 Jan;13(1):102-110. Pubmedid: 17200344.
  • Namkung J, Kim Y, Park T. Whole-genome association studies of alcoholism with loci linked to schizophrenia susceptibility. BMC Genet. 2005 Dec;6 Suppl 1:S9. Pubmedid: 16451705. Pmcid: PMC1866690.