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Youngchul Kim, PhD

Program: Biostatistics and Bioinformatics

Overview


Associations

    • Biostatistics and Bioinformatics
    • Cancer Biology and Evolution Program
    • Melanoma Research Center of Excellence
    • Cancer Biology and Evolution Program

Education & Training

Fellowship:

  • 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

  • Rubino S, Kim Y, Zhou J, Dhillon J, Li R, Spiess P, Poch M, Manley BJ, Pow-Sang J, Gilbert S, Sexton W, Zhang J. Positive Ki-67 and PD-L1 expression in post-neoadjuvant chemotherapy muscle-invasive bladder cancer is associated with shorter overall survival: a retrospective study. World J Urol. 2021 May.39(5):1539-1547. Pubmedid: 32656671.
  • Vogelbaum MA, Kroll D, Etame A, Tran N, Liu J, Ford A, Sparr E, Kim Y, Forsyth P, Sahebjam S, Mokhtari S, Peguero E, Macaulay R. A Prospective Validation Study of the First 3D Digital Exoscope for Visualization of 5-ALA-Induced Fluorescence in High-Grade Gliomas. World Neurosurg. 2021 May.149:e498-e503. Pubmedid: 33561551.
  • Egan KM, Kim Y, Bender N, Hodge JM, Coghill AE, Smith-Warner SA, Rollison DE, Teras LR, Grimsrud TK, Waterboer T. Prospective investigation of polyomavirus infection and the risk of adult glioma. Sci Rep. 2021 May.11(1):9642. Pubmedid: 33953301. Pmcid: PMC8100283.
  • Chakiryan NH, Hajiran A, Kim Y, Aydin AM, Zemp L, Katende E, Nguyen J, Fan W, Cheng CH, Lopez-Blanco N, Chahoud J, Spiess PE, Fournier M, Dhillon J, Wang L, Moran-Segura C, Mulé J, Du D, Yoder SJ, Berglund A, Teer JK, Manley BJ. Correlating Immune Cell Infiltration Patterns with Recurrent Somatic Mutations in Advanced Clear Cell Renal Cell Carcinoma. Eur Urol Focus. 2021 May. Pubmedid: 33994165.
  • Zaman S, Hajiran A, Coba GA, Robinson T, Madanayake TW, Segarra DT, Chobrutskiy BI, Boyle TA, Zhou JM, Kim Y, Mulé JJ, Teer JK, Manley BJ. Aberrant Epidermal Growth Factor Receptor RNA Splice Products Are Among the Most Frequent Somatic Alterations in Clear Cell Renal Cell Carcinoma and Are Associated with a Poor Response to Immunotherapy. Eur Urol Focus. 2021 Mar.7(2):373-380. Pubmedid: 31901438. Pmcid: PMC7771328.
  • Yuan Z, Fernandez D, Dhillon J, Abraham-Miranda J, Awasthi S, Kim Y, Zhang J, Jain R, Serna A, Pow-Sang JM, Poch M, Li R, Manley B, Fink A, Naghavi A, Torres-Roca JF, Grass GD, Kim S, Latifi K, Hunt D, Johnstone PAS, Yamoah K. Proof-of-principle Phase I results of combining nivolumab with brachytherapy and external beam radiation therapy for Grade Group 5 prostate cancer: safety, feasibility, and exploratory analysis. Prostate Cancer P D. 2021 Mar.24(1):140-149. Pubmedid: 32651467. Pmcid: PMC7882397.
  • Kamal Y, Dwan D, Hoehn HJ, Sanz-Pamplona R, Alonso MH, Moreno V, Cheng C, Schell MJ, Kim Y, Felder SI, Rennert HS, Melas M, Lazaris C, Bonner JD, Siegel EM, Shibata D, Rennert G, Gruber SB, Frost HR, Amos CI, Schmit SL. Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse. Oncoimmunology. 2021 Mar.10(1):1862529. Pubmedid: 33763292. Pmcid: PMC7951964.
  • Lacson JCA, Doyle SH, Qian L, Del Rio J, Forgas SM, Valavanis S, Carvajal R, Gonzalez-Calderon G, Kim Y, Roetzheim RG, Sutton SK, Vadaparampil ST, Kanetsky PA. A Randomized Trial of Precision Prevention Materials to Improve Primary and Secondary Melanoma Prevention Activities among Individuals with Limited Melanoma Risk Phenotypes. Cancers (Basel). 2021 Jun.13(13). Pubmedid: 34201795. Pmcid: PMC8267659.
  • Li R, Berglund A, Zemp L, Dhillon J, Putney R, Kim Y, Jain RK, Grass GD, Conejo-Garcia J, Mulé JJ. The 12-CK Score: Global Measurement of Tertiary Lymphoid Structures. Front Immunol. 2021 Jun.12:694079. Pubmedid: 34267760. Pmcid: PMC8276102.
  • Broman KK, Hughes T, Dossett L, Sun J, Kirichenko D, Carr MJ, Sharma A, Bartlett EK, Nijhuis AAG, Thompson JF, Hieken TJ, Kottschade L, Downs J, Gyorki DE, Stahlie E, van Akkooi A, Ollila DW, Frank J, Song Y, Karakousis G, Moncrieff M, Nobes J, Vetto J, Han D, Farma JM, Deneve JL, Fleming MD, Perez MC, Lowe MC, Olofsson Bagge R, Mattsson J, Lee AY, Berman RS, Chai H, Kroon HM, Teras J, Teras RM, Farrow NE, Beasley G, Hui JYC, Been L, Kruijff S, Kim Y, Naqvi SMH, Sarnaik AA, Sondak VK, Zager JS. Active surveillance of patients who have sentinel node positive melanoma: An international, multi-institution evaluation of adoption and early outcomes after the Multicenter Selective Lymphadenectomy Trial II (MSLT-2). Cancer. 2021 Jul.127(13):2251-2261. Pubmedid: 33826754.
  • Chakiryan NH, Kimmel GJ, Kim Y, Johnson JO, Clark N, Hajiran A, Chang A, Aydin AM, Zemp L, Katende E, Chahoud J, Ferrall-Fairbanks MC, Spiess PE, Francis N, Fournier M, Dhillon J, Park JY, Wang L, Mulé JJ, Altrock PM, Manley BJ. Geospatial Cellular Distribution of Cancer-Associated Fibroblasts Significantly Impacts Clinical Outcomes in Metastatic Clear Cell Renal Cell Carcinoma. Cancers (Basel). 2021 Jul.13(15). Pubmedid: 34359645. Pmcid: PMC8345222.
  • Hodge JM, Coghill AE, Kim Y, Bender N, Smith-Warner SA, Gapstur S, Teras LR, Grimsrud TK, Waterboer T, Egan KM. Toxoplasma gondii infection and the risk of adult glioma in two prospective studies. Int J Cancer. 2021 Jan. Pubmedid: 33427315.
  • Ruiz-Deya G, Matta J, Encarnación-Medina J, Ortiz-Sanchéz C, Dutil J, Putney R, Berglund A, Dhillon J, Kim Y, Park JY. Differential DNA Methylation in Prostate Tumors from Puerto Rican Men. Int J Mol Sci. 2021 Jan.22(2). Pubmedid: 33450964. Pmcid: PMC7828429.
  • Siegel EL, Whiting J, Kim Y, Sun W, Laronga C, Lee MC. Effect of surgical complications on outcomes in breast cancer patients treated with mastectomy and immediate reconstruction. Breast Cancer Res Treat. 2021 Aug.188(3):641-648. Pubmedid: 33939063.
  • Hajiran A, Chakiryan N, Aydin AM, Zemp L, Nguyen J, Laborde JM, Chahoud J, Spiess PE, Zaman S, Falasiri S, Fournier M, Teer JK, Dhillon J, McCarthy S, Moran-Segura C, Katende EN, Sexton WJ, Koomen JM, Mulé J, Kim Y, Manley B. Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response. Clin Exp Immunol. 2021 Apr.204(1):96-106. Pubmedid: 33346915. Pmcid: PMC7944355.
  • Cote DJ, Smith-Warner SA, Creed JH, Furtado J, Gerke T, Wang M, Kim Y, Stampfer MJ, Egan KM. Circulating lipids and glioma risk: results from the UK Biobank, Nurses' Health Study, and Health Professionals Follow-Up Study. Cancer Causes Control. 2021 Apr.32(4):347-355. Pubmedid: 33484419.
  • Chakiryan NH, Kimmel GJ, Kim Y, Hajiran A, Aydin AM, Zemp L, Katende E, Nguyen J, Lopez-Blanco N, Chahoud J, Spiess PE, Fournier M, Dhillon J, Wang L, Moran-Segura C, El-Kenawi A, Mulé J, Altrock PM, Manley BJ. Spatial clustering of CD68+ tumor associated macrophages with tumor cells is associated with worse overall survival in metastatic clear cell renal cell carcinoma. PLoS One. 2021 Apr.16(4):e0245415. Pubmedid: 33882057. Pmcid: PMC8059840.
  • Patel SY, Trona N, Alford B, Laborde JM, Kim Y, Li R, Manley BJ, Gilbert SM, Sexton WJ, Spiess PE, Poch MA. Preoperative immunonutrition and carbohydrate loading associated with improved bowel function after radical cystectomy. Nutr Clin Pract. 2021 Apr. Pubmedid: 33900647.
  • Jain RK, Skelton Iv WP, Pond GR, Naqvi M, Kim Y, Curran C, Freeman D, Nuzzo PV, Alaiwi SA, Nassar AH, Jain RK, Sonpavde G. Angiotensin Blockade Modulates the Activity of PD1/L1 Inhibitors in Metastatic Urothelial Carcinoma. Clin Genitourin Cancer. 2021 Apr. Pubmedid: 34011489.
  • Li R, Sundi D, Zhang J, Kim Y, Sylvester RJ, Spiess PE, Poch MA, Sexton WJ, Black PC, McKiernan JM, Steinberg GD, Kamat AM, Gilbert SM. Systematic Review of the Therapeutic Efficacy of Bladder-preserving Treatments for Non-muscle-invasive Bladder Cancer Following Intravesical Bacillus Calmette-Guérin. Eur Urol. 2020 Sep.78(3):387-399. Pubmedid: 32143924. Pmcid: PMC7771323.
  • Kim KB, Kim Y, Rivard CJ, Kim DW, Park KS. FGFR1 Is Critical for RBL2 Loss-Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer. Cancer Res. 2020 Nov.80(22):5051-5062. Pubmedid: 32973083. Pmcid: PMC7669587.
  • Berglund A, Amankwah EK, Kim YC, Spiess PE, Sexton WJ, Manley B, Park HY, Wang L, Chahoud J, Chakrabarti R, Yeo CD, Luu HN, Pietro GD, Parker A, Park JY. Influence of gene expression on survival of clear cell renal cell carcinoma. Cancer Med. 2020 Nov.9(22):8662-8675. Pubmedid: 32986937. Pmcid: PMC7666730.
  • Kim Y, Kim D, Cao B, Carvajal R, Kim M. PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients. BMC Bioinformatics. 2020 Jul.21(1):288. Pubmedid: 32631229. Pmcid: PMC7336455.
  • Rizk VT, Naghavi AO, Brohl AS, Joyce DM, Binitie O, Kim Y, Hanna JP, Swank J, Gonzalez RJ, Reed DR, Druta M. Chemotherapy improves distant control in localized high-grade soft tissue sarcoma of the extremity/trunk. Clin Sarcoma Res. 2020 Jul.10:11. Pubmedid: 32670544. Pmcid: PMC7350709.
  • Eroglu Z, Eatrides J, Naqvi SMH, Kim Y, Rich J, Babacan NA, Brohl AS, Markowitz J, Sarnaik A, Zager J, Khushalani NI, Sondak VK, Messina J. Neoadjuvant BRAF-targeted therapy in regionally advanced and oligometastatic melanoma. Pigment Cell Melanoma Res. 2020 Jan.33(1):86-95. Pubmedid: 31329344. Pmcid: PMC6928428.
  • Yang G, Mills M, Kim Y, Figura NB, Doyle C, Oliver D, Grass GD, Robinson T, Chavez J, Kim S. Enhancement of the Follicular Lymphoma International Prognostic Index (FLIPI) with lymphopenia (FLIPI-L): a predictor for overall survival and histologic transformation. Blood Cancer J. 2020 Jan.9(12):104. Pubmedid: 31894139. Pmcid: PMC6938796.
  • Naghavi AO, Kim Y, Yang GQ, Ahmed KA, Caudell JJ. Alterations in genetic pathways following radiotherapy for head and neck cancer. Head Neck. 2020 Feb.42(2):312-320. Pubmedid: 31833149. Pmcid: PMC7771332.
  • Carr MJ, Sun J, Kroon HM, Miura JT, Beasley GM, Farrow NE, Mosca PJ, Lowe MC, Farley CR, Kim Y, Naqvi SMH, Kirichenko DA, Potdar A, Daou H, Mullen D, Farma JM, Henderson MA, Speakman D, Serpell J, Delman KA, Smithers BM, Coventry BJ, Tyler DS, Thompson JF, Zager JS. Oncologic Outcomes After Isolated Limb Infusion for Advanced Melanoma: An International Comparison of the Procedure and Outcomes Between the United States and Australia. Ann Surg Oncol. 2020 Dec.27(13):5107-5118. Pubmedid: 32918177. Pmcid: PMC7674259.
  • Yao J, Chen Y, Nguyen DT, Thompson ZJ, Eroshkin AM, Nerlakanti N, Patel AK, Agarwal N, Teer JK, Dhillon J, Coppola D, Zhang J, Perera R, Kim Y, Mahajan K. The Homeobox gene, HOXB13, Regulates a Mitotic Protein-Kinase Interaction Network in Metastatic Prostate Cancers. Sci Rep. 2019 Jul.9(1):9715. Pubmedid: 31273254. Pmcid: PMC6609629.
  • 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. 2019 Feb.17(2):583-593. Pubmedid: 30355677. Pmcid: PMC6386183.
  • Chatzkel J, Mocha J, Smith J, Zhou JM, Kim Y, El-Haddad G, Zhang J. Circulating tumor cells and γH2AX as biomarkers for responsiveness to radium-223 in advanced prostate cancer patients. Future Sci OA. 2019 Dec.6(1):FSO437. Pubmedid: 31915536. Pmcid: PMC6920735.
  • Miura JT, Kroon HM, Beasley GM, Mullen D, Farrow NE, Mosca PJ, Lowe MC, Farley CR, Kim Y, Naqvi SMH, Potdar A, Daou H, Sun J, Farma JM, Henderson MA, Speakman D, Serpell J, Delman KA, Mark Smithers B, Coventry BJ, Tyler DS, Thompson JF, Zager JS. Long-Term Oncologic Outcomes After Isolated Limb Infusion for Locoregionally Metastatic Melanoma: An International Multicenter Analysis. Ann Surg Oncol. 2019 Aug.26(8):2486-2494. Pubmedid: 30911949. Pmcid: PMC7771312.
  • Miura JT, Dossett LA, Thapa R, Kim Y, Potdar A, Daou H, Sun J, Sarnaik AA, Zager JS. Robotic-Assisted Pelvic Lymphadenectomy for Metastatic Melanoma Results in Durable Oncologic Outcomes. Ann Surg Oncol. 2019 Apr.27(1):196-202. Pubmedid: 30949862. Pmcid: PMC7771311.
  • Naqvi SMH, Kim Y. Epigenetic modification by galactic cosmic radiation as a risk factor for lung cancer: real world data issues. Transl Lung Cancer Res. 2019 Apr.8(2):116-118. Pubmedid: 31106121. Pmcid: PMC6504655.
  • Weitman ES, Perez MC, Lee D, Kim Y, Fulp W, Sondak VK, Sarnaik AA, Gonzalez RJ, Cruse CW, Messina JL, Zager JS. Re-biopsy of partially sampled thin melanoma impacts sentinel lymph node sampling as well as surgical margins. Melanoma Manag. 2019 Apr.6(2):MMT17. Pubmedid: 31406562. Pmcid: PMC6688556.
  • 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. Pmcid: PMC7771321.
  • 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. Pmcid: PMC7771268.
  • 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.
  • 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. Pmcid: PMC7810133.
  • 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. Pmcid: PMC7771366.
  • 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 Coregulated Transcriptional Networks with Bromodomain-Kinase Inhibitors to Suppress Metastatic Castration-Resistant Prostate Cancer. Mol Cancer Ther. 2018 Dec.17(12):2796-2810. Pubmedid: 30242092. Pmcid: PMC6528782.
  • 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. Pmcid: PMC7771271.
  • 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. Pmcid: PMC7771287.
  • 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. Pmcid: PMC7771533.
  • 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. Pmcid: PMC7771340.
  • 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. Pmcid: PMC7810134.
  • Ahmed KA, Stallworth DG, Kim Y, Johnstone PA, Harrison LB, Caudell JJ, Yu HH, Etame AB, Weber JS, Gibney GT. Clinical outcomes of melanoma brain metastases treated with stereotactic radiation and anti-PD-1 therapy. Ann Oncol. 2016 Mar.27(3):434-441. Pubmedid: 26712903.
  • 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. Pmcid: PMC7771551.
  • 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.
  • 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. 2013 May.7(11):e49529. Pubmedid: 23185353. Pmcid: PMC3504014.
  • 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.
  • 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.