Jae Lee, PhD

Where You Are:
Jae K. Lee, PhD

Senior Member

Education And Training
  • PhD, University of Wisconsin, 1995 - Computational Statistics & Statistical Genetics
  • MS, Seoul National University, 1987 - Statistics


Dr. Lee obtained his PhD in Statistics at the University of Wisconsin at Madison. He then completed postdoctoral training in computational biology and statistical genetics at the University of Southern California and worked as a Research Scientist in the Laboratory of Molecular Pharmacology at the National Cancer Institute (NCI). 

  • McKown RL, Coleman Frazier EV, Zadrozny KK, Deleault AM, Raab RW, Ryan DS, Sia RK, Lee JK, Laurie GW. A Cleavage-potentiated Fragment of Tear Lacritin Is Bactericidal. J Biol Chem. 2014 Aug;289(32):22172-22182. Pubmedid: 24942736.
  • Zhao Q, Wu CZ, Lee JK, Zhao SR, Li HM, Huo Q, Ma T, Zhang J, Hong YS, Liu H. Anticancer Effects of the Hsp90 Inhibitor 17-Demethoxy-Reblastatin in Human Breast Cancer MDA-MB-231 Cells. J Microbiol Biotechnol. 2014 Jun;24(7):914-920. Pubmedid: 24705874.
  • Maluf DG, Dumur CI, Suh JL, Lee JK, Cathro HP, King AL, Gallon L, Brayman KL, Mas VR. Evaluation of molecular profiles in calcineurin inhibitor toxicity post-kidney transplant: input to chronic allograft dysfunction. Am J Transplant. 2014 May;14(5):1152-1163. Pubmedid: 24698514.
  • Kelly BN, Haverstick DM, Lee JK, Thorner MO, Vance ML, Xin W, Bruns DE. Circulating microRNA as a biomarker of human growth hormone administration to patients. Drug Test Anal. 2014 Mar;6(3):234-238. Pubmedid: 23495241.
  • Maluf DG, Dumur CI, Suh JL, Scian MJ, King AL, Cathro H, Lee JK, Gehrau RC, Brayman KL, Gallon L, Mas VR. The urine microRNA profile may help monitor post-transplant renal graft function. Kidney Int. 2014 Feb;85(2):439-449. Pubmedid: 24025639. Pmcid: PMC3946645.
  • Haggart CR, Ames EG, Lee JK, Holmes JW. Effects of stretch and shortening on gene expression in intact myocardium. Physiol Genomics. 2014 Jan;46(2):57-65. Pubmedid: 24302644. Pmcid: PMC3921349.
  • 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;9(2):e86532. Pubmedid: 24505259. Pmcid: PMC3914805.
  • Newhook TE, Blais EM, Lindberg JM, Adair SJ, Xin W, Lee JK, Papin JA, Parsons JT, Bauer TW. A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest. PLoS One. 2014;9(9):e105631. Pubmedid: 25180633.
  • Elagib KE, Rubinstein JD, Delehanty LL, Ngoh VS, Greer PA, Li S, Lee JK, Li Z, Orkin SH, Mihaylov IS, Goldfarb AN. Calpain 2 activation of P-TEFb drives megakaryocyte morphogenesis and is disrupted by leukemogenic GATA1 mutation. Dev Cell. 2013 Dec;27(6):607-620. Pubmedid: 24369834. Pmcid: PMC3892434.
  • Ma Z, Kim Y, Hu F, Lee JK. Point success rate for patient therapeutic response prediction by continuous biomarker scores. Stat Methods Med Res. 2013 Jul. Pubmedid: 23839122.
  • Dominguez CL, Floyd DH, Xiao A, Mullins GR, Kefas BA, Xin W, Yacur MN, Abounader R, Lee JK, Wilson GM, Harris TE, Purow BW. Diacylglycerol kinase α is a critical signaling node and novel therapeutic target in glioblastoma and other cancers. Cancer Discov. 2013 Jul;3(7):782-797. Pubmedid: 23558954. Pmcid: PMC3710531.
  • Wang N, Zimmerman K, Raab RW, McKown RL, Hutnik CM, Talla V, Tyler MF, Lee JK, Laurie GW. Lacritin rescues stressed epithelia via rapid forkhead box O3 (FOXO3)-associated autophagy that restores metabolism. J Biol Chem. 2013 Jun;288(25):18146-18161. Pubmedid: 23640897. Pmcid: PMC3689958.
  • 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.
  • Zhang Y, Farenholtz KE, Yang Y, Guessous F, Dipierro CG, Calvert VS, Deng J, Schiff D, Xin W, Lee JK, Purow B, Christensen J, Petricoin E, Abounader R. Hepatocyte growth factor sensitizes brain tumors to c-MET kinase inhibition. Clin Cancer Res. 2013 Mar;19(6):1433-1444. Pubmedid: 23386689. Pmcid: PMC3602223.
  • Walters DM, Stokes JB, Adair SJ, Stelow EB, Borgman CA, Lowrey BT, Xin W, Blais EM, Lee JK, Papin JA, Parsons JT, Bauer TW. Clinical, molecular and genetic validation of a murine orthotopic xenograft model of pancreatic adenocarcinoma using fresh human specimens. PLoS One. 2013;8(10):e77065. Pubmedid: 24204737. Pmcid: PMC3799939.
  • 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.
  • Alexander MR, Moehle CW, Johnson JL, Yang Z, Lee JK, Jackson CL, Owens GK. Genetic inactivation of IL-1 signaling enhances atherosclerotic plaque instability and reduces outward vessel remodeling in advanced atherosclerosis in mice. J Clin Invest. 2012 Jan;122(1):70-79. Pubmedid: 22201681. Pmcid: PMC3248279.
  • Cheng F, Theodorescu D, Schulman IG, Lee JK. In vitro transcriptomic prediction of hepatotoxicity for early drug discovery. J Theor Biol. 2011 Dec;290:27-36. Pubmedid: 21884709. Pmcid: PMC3386613.
  • Williams PD, Owens CR, Dziegielewski J, Moskaluk CA, Read PW, Larner JM, Story MD, Brock WA, Amundson SA, Lee JK, Theodorescu D. Cyclophilin B expression is associated with in vitro radioresistance and clinical outcome after radiotherapy. Neoplasia. 2011 Dec;13(12):1122-1131. Pubmedid: 22241958. Pmcid: PMC3257187.
  • Paige M, Burdick MD, Kim S, Xu J, Lee JK, Shim YM. Pilot analysis of the plasma metabolite profiles associated with emphysematous Chronic Obstructive Pulmonary Disease phenotype. Biochem Bioph Res Co. 2011 Oct;413(4):588-593. Pubmedid: 21925153. Pmcid: PMC3199021.
  • Smith SC, Baras AS, Dancik G, Ru Y, Ding KF, Moskaluk CA, Fradet Y, Lehmann J, Stöckle M, Hartmann A, Lee JK, Theodorescu D. A 20-gene model for molecular nodal staging of bladder cancer: development and prospective assessment. Lancet Oncol. 2011 Feb;12(2):137-143. Pubmedid: 21256081. Pmcid: PMC3613042.
  • Smith SC, Havaleshko DM, Moon K, Baras AS, Lee J, Bekiranov S, Burke DJ, Theodorescu D. Use of yeast chemigenomics and COXEN informatics in preclinical evaluation of anticancer agents. Neoplasia. 2011 Jan;13(1):72-80. Pubmedid: 21253455. Pmcid: PMC3023847.
  • 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.
  • Nagji AS, Cho SH, Liu Y, Lee JK, Jones DR. Multigene expression-based predictors for sensitivity to Vorinostat and Velcade in non-small cell lung cancer. Mol Cancer Ther. 2010 Oct;9(10):2834-2843. Pubmedid: 20713531. Pmcid: PMC2953585.
  • Smith SC, Baras AS, Lee JK, Theodorescu D. The COXEN principle: translating signatures of in vitro chemosensitivity into tools for clinical outcome prediction and drug discovery in cancer. Cancer Res. 2010 Mar;70(5):1753-1758. Pubmedid: 20160033. Pmcid: PMC2831138.
  • Little KM, Lee JK, Ley K. ReSASC: a resampling-based algorithm to determine differential protein expression from spectral count data. Proteomics. 2010 Mar;10(6):1212-1222. Pubmedid: 20058246.
  • 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.
  • Cheng F, Cho SH, Lee JK. Multi-gene expression-based statistical approaches to predicting patients' clinical outcomes and responses. Methods Mol Biol. 2010;620:471-484. Pubmedid: 20652516.
  • Havaleshko DM, Smith SC, Cho H, Cheon S, Owens CR, Lee JK, Liotta LA, Espina V, Wulfkuhle JD, Petricoin EF, Theodorescu D. Comparison of global versus epidermal growth factor receptor pathway profiling for prediction of lapatinib sensitivity in bladder cancer. Neoplasia. 2009 Nov;11(11):1185-1193. Pubmedid: 19881954. Pmcid: PMC2767220.
  • 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.
  • Overdevest JB, Theodorescu D, Lee JK. Utilizing the molecular gateway: the path to personalized cancer management. Clin Chem. 2009 Apr;55(4):684-697. Pubmedid: 19246616.
  • Arnold RS, Sun CQ, Richards JC, Grigoriev G, Coleman IM, Nelson PS, Hsieh CL, Lee JK, Xu Z, Rogatko A, Osunkoya AO, Zayzafoon M, Chung L, Petros JA. Mitochondrial DNA mutation stimulates prostate cancer growth in bone stromal environment. Prostate. 2009 Jan;69(1):1-11. Pubmedid: 18850577. Pmcid: PMC2753601.
  • Williams PD, Lee JK, Theodorescu D. Genomancy: predicting tumour response to cancer therapy based on the oracle of genetics. Curr Oncol. 2009 Jan;16(1):56-58. Pubmedid: 19229372. Pmcid: PMC2644622.
  • Sung SY, Hsieh CL, Law A, Zhau HE, Pathak S, Multani AS, Lim S, Coleman IM, Wu LC, Figg WD, Dahut WL, Nelson P, Lee JK, Amin MB, Lyles R, Johnstone PA, Marshall FF, Chung LW. Coevolution of prostate cancer and bone stroma in three-dimensional coculture: implications for cancer growth and metastasis. Cancer Res. 2008 Dec;68(23):9996-10003. Pubmedid: 19047182. Pmcid: PMC3105756.
  • Chung HK, Pise-Masison CA, Radonovich MF, Brady J, Lee JK, Cheon SY, Markham P, Cristillo A, Pal R. Cellular gene expression profiles in rhesus macaques challenged mucosally with a pathogenic R5 tropic simian human immunodeficiency virus isolate. Viral Immunol. 2008 Dec;21(4):411-423. Pubmedid: 19115930. Pmcid: PMC2952136.
  • Williams PD, Lee JK, Theodorescu D. Molecular credentialing of rodent bladder carcinogenesis models. Neoplasia. 2008 Aug;10(8):838-846. Pubmedid: 18670642. Pmcid: PMC2481571.
  • Yi SG, Park T, Lee JK. Response projected clustering for direct association with physiological and clinical response data. BMC Bioinformatics. 2008 Apr;9:76. Pubmedid: 18237428. Pmcid: PMC2275250.
  • Lee JK, Williams PD, Cheon S. Data mining in genomics. Clin Lab Med. 2008 Mar;28(1):145-66, viii. Pubmedid: 18194724. Pmcid: PMC2253491.
  • Aiyar SE, Cho H, Lee J, Li R. Concerted transcriptional regulation by BRCA1 and COBRA1 in breast cancer cells. Int J Biol Sci. 2008 Feb;3(7):486-492. Pubmedid: 18071589. Pmcid: PMC2096739.
  • Cho H, Smalley DM, Theodorescu D, Ley K, Lee JK. Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry. Proteomics. 2007 Oct;7(20):3681-3692. Pubmedid: 17879999.
  • Lee JK, Havaleshko DM, Cho H, Weinstein JN, Kaldjian EP, Karpovich J, Grimshaw A, Theodorescu D. A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc Natl Acad Sci U S A. 2007 Aug;104(32):13086-13091. Pubmedid: 17666531. Pmcid: PMC1941805.
  • 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.
  • Cho HJ, Shashkin P, Gleissner CA, Dunson D, Jain N, Lee JK, Miller Y, Ley K. Induction of dendritic cell-like phenotype in macrophages during foam cell formation. Physiol Genomics. 2007 Apr;29(2):149-160. Pubmedid: 17244792.
  • Shankavaram UT, Reinhold WC, Nishizuka S, Major S, Morita D, Chary KK, Reimers MA, Scherf U, Kahn A, Dolginow D, Cossman J, Kaldjian EP, Scudiero DA, Petricoin E, Liotta L, Lee JK, Weinstein JN. Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther. 2007 Mar;6(3):820-832. Pubmedid: 17339364.
  • Havaleshko DM, Cho H, Conaway M, Owens CR, Hampton G, Lee JK, Theodorescu D. Prediction of drug combination chemosensitivity in human bladder cancer. Mol Cancer Ther. 2007 Feb;6(2):578-586. Pubmedid: 17308055.
  • Jain N, Cho H, O'Connell M, Lee JK. Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data. BMC Bioinformatics. 2006 Mar;6:187. Pubmedid: 16042779. Pmcid: PMC1187876.
  • Wu Z, Siadaty MS, Riddick G, Frierson HF, Lee JK, Golden W, Knuutila S, Hampton GM, El-Rifai W, Theodorescu D. A novel method for gene expression mapping of metastatic competence in human bladder cancer. Neoplasia. 2006 Mar;8(3):181-189. Pubmedid: 16611411. Pmcid: PMC1578518.
  • Soukup M, Cho H, Lee JK. Robust classification modeling on microarray data using misclassification penalized posterior. Bioinformatics. 2005 Jun;21 Suppl 1:i423-i430. Pubmedid: 15961487.
  • Park T, Yi SG, Lee S, Lee JK. Diagnostic plots for detecting outlying slides in a cDNA microarray experiment. Biotechniques. 2005 Mar;38(3):463-471. Pubmedid: 15786811.
  • Mullins IM, Slingluff CL, Lee JK, Garbee CF, Shu J, Anderson SG, Mayer ME, Knaus WA, Mullins DW. CXC chemokine receptor 3 expression by activated CD8+ T cells is associated with survival in melanoma patients with stage III disease. Cancer Res. 2004 Nov;64(21):7697-7701. Pubmedid: 15520172.
  • Cho H, Lee JK. Bayesian hierarchical error model for analysis of gene expression data. Bioinformatics. 2004 Sep;20(13):2016-2025. Pubmedid: 15044230.
  • Wooten GF, Currie LJ, Bovbjerg VE, Lee JK, Patrie J. Are men at greater risk for Parkinson's disease than women?. J Neurol Neurosur Ps. 2004 Apr;75(4):637-639. Pubmedid: 15026515. Pmcid: PMC1739032.
  • Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau JP, Shankavaram U, Lababidi S, Smith LH, Gottesman MM, Weinstein JN. Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol. 2004 Mar;4(12):R82. Pubmedid: 14659019. Pmcid: PMC329421.
  • Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, Waltham M, Kouros-Mehr H, Bussey KJ, Lee JK, Espina V, Munson PJ, Petricoin E, Liotta LA, Weinstein JN. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A. 2003 Nov;100(24):14229-14234. Pubmedid: 14623978. Pmcid: PMC283574.
  • Jain N, Thatte J, Braciale T, Ley K, O'Connell M, Lee JK. Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics. 2003 Oct;19(15):1945-1951. Pubmedid: 14555628.
  • Nishizuka S, Chen ST, Gwadry FG, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee JK, Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN. Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling. Cancer Res. 2003 Sep;63(17):5243-5250. Pubmedid: 14500354.
  • Lankford AR, Byford AM, Ashton KJ, French BA, Lee JK, Headrick JP, Matherne GP. Gene expression profile of mouse myocardium with transgenic overexpression of A1 adenosine receptors. Physiol Genomics. 2002 Oct;11(2):81-89. Pubmedid: 12388787.
  • Weinstein JN, Scherf U, Lee JK, Nishizuka S, Gwadry F, Bussey AK, Kim S, Smith LH, Tanabe L, Richman S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC. The bioinformatics of microarray gene expression profiling. Cytometry. 2002 Jan;47(1):46-49. Pubmedid: 11774349.
  • Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A. 2001 Sep;98(19):10787-10792. Pubmedid: 11553813. Pmcid: PMC58553.
  • Lee JK. Analysis issues for gene expression array data. Clin Chem. 2001 Aug;47(8):1350-1352. Pubmedid: 11468221.
  • Lee JK, Thomas DC. Performance of Markov chain-Monte Carlo approaches for mapping genes in oligogenic models with an unknown number of loci. Am J Hum Genet. 2000 Nov;67(5):1232-1250. Pubmedid: 11032787. Pmcid: PMC1288565.
  • Woodfolk JA, Sung SS, Benjamin DC, Lee JK, Platts-Mills TA. Distinct human T cell repertoires mediate immediate and delayed-type hypersensitivity to the Trichophyton antigen, Tri r 2. J Immunol. 2000 Oct;165(8):4379-4387. Pubmedid: 11035075.
  • Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. A gene expression database for the molecular pharmacology of cancer. Nat Genetics. 2000 Mar;24(3):236-244. Pubmedid: 10700175.
  • Tanabe L, Scherf U, Smith LH, Lee JK, Hunter L, Weinstein JN. MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques. 1999 Dec;27(6):1210-4, 1216. Pubmedid: 10631500.
  • Lee JK, Lascoux M, Newton MA, Nordheim EV. A study of deleterious gene structure in plants using Markov chain Monte Carlo. Biometrics. 1999 Jun;55(2):376-386. Pubmedid: 11318190.
  • Lascoux M, Lee JK. One step beyond lethal equivalents: characterization of deleterious loci in the rapid cycling Brassica rapa L. base population. Genetica. 1998 Oct;104(2):161-170. Pubmedid: 16220375.
  • Lee JK, Dancík V, Waterman MS. Estimation for restriction sites observed by optical mapping using reversible-jump Markov Chain Monte Carlo. J Comput Biol. 1998;5(3):505-515. Pubmedid: 9773346.
  • Lee JK, Lascoux M, Nordheim EV. Number of lethal equivalents in human populations: how good are the previous estimates?. Heredity (Edinb). 1996 Aug;77 ( Pt 2):209-216. Pubmedid: 8760402.
  • Kallmes DF, O E, Roy SS, Piccolo RG, Marx WF, Lee JK, Jensen ME. Radiation dose to the operator during vertebroplasty: prospective comparison of the use of 1-cc syringes versus an injection device. Ajnr Am J Neuroradiol. 24(6):1257-1260. Pubmedid: 12812967.
  • Shi LM, Fan Y, Lee JK, Waltham M, Andrews DT, Scherf U, Paull KD, Weinstein JN. Mining and visualizing large anticancer drug discovery databases. J Chem Inf Comput Sci. 40(2):367-379. Pubmedid: 10761142.
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