Published Books

Optimization in Medicine and Biology. Editors: EK Lee, G Limo, Taylor and Francis, Auerbach Publications, 564 pages, 2008.

Computing and Optimization in Medicine and Life Sciences, Volume 2. Editors: EK Lee, A Sofer, Springer Netherlands, Computer Science Series, 270 pages, 2006.

Computing and Optimization in Medicine and Life Sciences, Volume 1. Editors: EK Lee, A Sofer, Springer Science, Kluwer Academic Publishers, 301 pages, 2003.

Refereed Published Book Chapters

EK Lee, K Gupta, Algorithms for genomics analysis. In Encyclopedia of Optimization, 2nd edition. Editors: CA Floudas, and PM Pardalos. Springer, The Netherlands 2009. ISBN: 978-0-387-74760- 6.

EK Lee, TL Wu, Disease diagnosis: optimization based methods. In Encyclopedia of Optimization, 2nd edition. Editors: CA Floudas, and PM Pardalos. Springer, The Netherlands 2009. ISBN: 978-0-387-74760-6.

EK Lee, J Mitchell, Integer programming: branch-and-bound methods. In Encyclopedia of Optimization, 2nd edition. Editors: CA Floudas, and PM Pardalos. Springer, The Netherlands 2009. ISBN: 978-0-387-74760-6.

EK Lee, TLWu, Classification and disease prediction via mathematical programming. In Handbook in Optimization in Medicine, Chapter 12. Springer Optimization and Its Application, Vol 26. Editors: PM Pardalos and HE Romeijn. 2009. ISBN: 978-0-387-09769-5.

EK Lee, K Gupta, Algorithms for genomics analysis. In Handbook in Optimization in Medicine, Chapter 9. Springer Optimization and Its Application, Vol 26. Editors: PM Pardalos and HE Romeijn. 2009. ISBN: 978-0-387-09769-5.

EK Lee, TL Wu, Classification and disease prediction via mathematical programming. In Optimization in Medicine and Biology, Chapter 1, 3-60. Editors: EK Lee, G Limo, Taylor and Francis, Auerbach Publications, 2008.

EK Lee, K Gupta, Algorithms for genomics analysis. In Optimization in Medicine and Biology, Chapter 12, 355-393. Editors: EK Lee, G Limo, Taylor and Francis, Auerbach Publications, 2008.

EK Lee, D Lewis, Integer programming for telecommunications. In Handbook of Optimization in Telecommunications, Chapter 3, 67-102. Editors: GC Resende and PM Pardalos. Kluwer Academic Publishers, 2005.

EK Lee, M Zaider, Optimization and decision support in brachytherapy treatment planning. In Operations Research and Health Care: A Handbook of Methods and Applications, Chapter 28. (International Series in Operations Research & Management Science) Editors: M Bandeau, F Sainfort, WP Pierskalla. Kluwer Academic Publishers, Hillier International Series in OR/MS. 2004.

M Zaider, EK Lee, Treatment planning for low dose rate and high dose rate brachytherapy. In Basic and Advanced Techniques in Prostate Brachytherapy, Chapter 12. Editors: A Dicker, GS Merrick, LG Gomella, RK Valicenti, F Waterman, Gomella. 1-84184-298-2, CRC Press, 2004.

EK Lee, Branch-and-bound methods. In Handbook of Applied Optimization, Chapter 3, Section 2. Editors: Mauricio G. C. Resende and Panos M. Pardalos. Oxford University Press 2001, ISBN 0-19-512594-0. Honorable mention by the Association of American Publishers’ Outstanding Professional and Scholarly Titles of 2002 in Computer Science.

EK Lee, J Mitchell, Branch-and-bound methods for integer programming. In Encyclopedia of Optimization, Volume II, 509-519. Editors: Chris A. Floudas, and Panos M. Pardalos. Kluwer Academic Publishers, The Netherlands 2001.

JJ Sturm, DA Hirsh, EK Lee, R Massey, B Weselman, HK Simon, Practice characteristics that influence emergency department utilization. Academic Pediatrics. Submitted.

EK Lee, M Zaider, Operations research advances cancer therapeutics. Interfaces -- 2007 Franz Edelman Prize Special Issue, 38(1):5-25, 2008.

A Jayashankar, U Udayasankar, S Sebastian, M Kalra, EK Lee, W Small, MDCT of Thoraco-Abdominal Trauma: An Evaluation of the Success and Limitations of Primary Interpretation Using Multiplanar Reformatted Images versus Axial Images. Emergency Radiology, 15(1):29-34, 2008.

PK Mehta, L Simpson, EK Lee, TA Lyle, ME McConnell, WM Book, Endothelin receptor antagonists improve exercise tolerance and oxygen saturations in patients with Eisenmenger syndrome and congenital heart defects. Texas Heart Institute Journal 35(3):256-261, 2008.

Y Mei, L Wang, and SE Holte, A comparison of methods for determining HIV viral set point. Statistics in Medicine (accepted, July 2007).

JT Wu, S Riley, GM Leung, Spatial considerations for the allocation of pre-pandemic influenza vaccination in the United States.. Proceedings of the Royal Society B: Biological Sciences 274, 2811-7, 2007.

S Riley, JT Wu, GM Leung, Optimizing the dose of pre-pandemic influenza vaccines to reduce the infection attack rate. PLoS Medicine 4, e218, 2007.

EK Lee, Large-scale optimization-based classification models in medicine and biology. Annals of Biomedical Engineering -- Systems Biology, Bioinformatics, and Computational Biology 35(6):1095-1109, 2007.

EK Lee, TL Wu, Classification and disease prediction via mathematical programming. In Data Mining, Systems Analysis, and Optimization in Biomedicine. Editors: O Seref, OE Kundakcioglu and P Pardalos. AIP Conference Proceedings 953:1-42, 2007.

EK Lee, Optimization-Based Predictive Models in Medicine and Biology. Optimization in Medicine, Springer Netherlands, Springer Series in Optimization and Its Application, 12: 127-151, 2007.

EK Lee, KD Cha, JO Deasy, Robust optimization to accommodate effects of systematic treatment uncertainties. In Proceedings for International Conference on The Use of Computers in Radiation Therapy. 6256:1-5, 2007.

EK Lee, KD Cha, T Bortfeld, JO Deasy, 4D-Image-Guided treatment planning optimization for managing organ motion in radiotherapy planning. Proceedings for International Conference on The Use of Computers in Radiation Therapy. 6205:1-5, 2007.

EK Lee, T Easton, K Gupta, Novel evolutionary models and applications to sequence alignment problems. Annals of Operations Research, Operations Research in Medicine -- Computing and Optimization in Medicine and Life Sciences, 148: 167-187, 2006.

J. Burke, E. Small, G. Wilding, Carducci, D.C. Yu, P. Husak, J.T. Wu, J. Aimi, N. Ramesh, F. Borellini, P. Working, D. Ando, D. Kirn. A Phase I Trial of Intravenous Replication-Selective Oncolytic Adenovirus CG7870: Viral, Immunologic and Clinical Correlates. To appear in Molecular Therapy.

JT Wu, S Riley, C Fraser, GM Leung. Reducing the impact of the next influenza pandemic using household-based public health interventions, PLoS Medicine 3, e361, 2006.

EK Lee, DP Lewis, KD Cha, Fast Generation of Integer-Valued Beam Profiles for Intensity Modulated Radiation Therapy. Medical Physics. Currently in revision.

EK Lee, T Fox, I Crocker, Simultaneous beam geometry and intensity map optimization in intensity-modulated radiation therapy. International Journal of Radiation Oncology, Biology and Physics, 64(1): 301-320, 2006.

EK Lee, JO Deasy, Optimization in intensity-modulated radiation therapy. SIAG/OPT Views-and-News, Optimization in Medicine, 17(2): 20-32, 2006.

J Deasy, EK Lee, T Bortfeld, M Langer, K Zakarian, J Alaly, Y Zhang, H Liu, R Mohan, R Ahuja, A Pollack, J Purdy, R Rardin, A collaboratory for radiation therapy treatment planning optimization research, Annals of Operations Research, Operations Research in Medicine -- Computing and Optimization in Medicine and Life Sciences, 148: 55-63, 2006.

L Simpson, EK Lee, BJ Hott, DJ Vega and WM Book, Long-term results of angioplasty versus stenting in cardiac transplant recipients with allograft vasculopathy. The Journal of Heart and Lung Transplantation, 24(9): 1211-1217, 2005.

JT Wu, DH Kirn and LM Wein. Analysis of a Three-way Race Between Tumor Growth, a Replication-competent Virus and an Immune Response. Bulletin of Mathematical Biology, 66:605-625, 2004.

EK Lee, M Zaider, Intra-Operative Dynamic Dose Optimization in Permanent Prostate Implants. International Journal of Radiation Oncology, Biology and Physics, 56(3):854-861, 2003.

EK Lee, J Deasy, M Langer, R Rardin, J Deye, F Mahoney, Final report -- NCI/NSF workshop on operations research applied to radiation therapy, Washington, DC, February 7-9, 2002. Annals of Operations Research -- Optimization in Medicine 119:143-146, 2003.

EK Lee, T Fox, I Crocker, Integer programming applied to Intensity-modulated radiation therapy treatment planning. Annals of Operations Research -- Optimization in Medicine 119:165-181, 2003.

EK Lee, M Zaider, Mixed Integer Programming Approaches to Treatment Planning for Brachytherapy -- Application to Permanent Prostate Implants. Annals of Operations Research -- Optimization in Medicine, 119: 147-163, 2003.

JC Landry, M Koshy, JD Lawson, N Esiashivilli, CA Staley, JY Ting, R Howell, S Ghavidel, EK Lee, LW Davis, Intensity modulated radiation therapy (IMRT) for retroperitoneal sarcoma: A case for dose escalation and organ at risk (OAR) toxicity reduction. Proceedings of American Society of Clinical Oncology, 22: 297, 2003.

LM Wein, JT Wu and DH Kirn. Validation and Analysis of a Mathematical Model of a Replication-competent Virus for Cancer Treatment: Implications for Design and Delivery. Cancer Research, 63:1317-1324, 2003.

LM Wein, JT Wu, AG Ianculescu and RK Puri. A Mathematical Model of the Impact of Infused Targeted Cytotoxic Agents on Brain Tumors: Implications for Detection, Design and Delivery. Cell Proliferation, 35:343-361, 2002.

M Langer, EK Lee, JO Deasy, R Rardin, J Deye, Operations research applied to radiotherapy, an NCI-NSF - sponsored workshop February 7-9, 2002. International Journal of Radiation Oncology, Biology, Physics 57(3):762-768, 2003.

EK Lee, AYC Fung, JP Brooks, M Zaider, Automated Tumor Volume Contouring in Soft-Tissue Sarcoma Adjuvant Brachytherapy Treatment, Physics in Medicine and Biology, 47(11):1891-1910, 2002.

EK Lee, M Zaider, Determining an Effective Planning Volume for Permanent Prostate Implants. International Journal of Radiation Oncology, Biology and Physics, 49(4):1197-1206, 2001

LM Wein and JT Wu. Estimation of Replicative Senescence via a Population Dynamics Model of Cells in Culture. Experimental Gerontology, 36:79-88, 2001.

JT Wu, HM Byrne, DH Kirn and LM Wein. Modeling and Analysis of a Virus that Replicates Selectively in Tumor Cells. Bulletin of Mathematical Biology, 63:731-768, 2001.

LM Wein, JE Cohen and JT Wu. Dynamic Optimization of a Linear Quadratic Model with Incomplete Repair and Volume-Dependent Sensitivity and Repopulation. International Journal of Radiation Oncology, Biology and Physics, 47:1073-1083, 2000.

EK Lee, T Fox, I Crocker, Optimization of Radiosurgery Treatment Planning via Mixed Integer Programming. Medical Physics, 27(5):995-1004, 2000.

M Zaider, M Zelefsky, EK Lee, K Zakian, HA Amols, J Dyke, J Koutcher, Treatment Planning for Prostate Implants Using MR Spectroscopy Imaging. International Journal of Radiation Oncology, Biology and Physics, 47(4):1085-96, 2000.

CS Wuu, RD Ennis, PB Schiff, EK Lee, M Zaider, Dosimetric and Volumetric Criteria for Selecting a Source Type I-125 or Pd-103 and Source Activity in the Presence of Irregular Seed Placement in Permanent Prostate Implants. International Journal of Radiation Oncology, Biology and Physics, 47: 815-820, 2000.

EK Lee, RJ Gallagher, M Zaider, Planning implants of radionuclides for the treatment of prostate cancer: an application of mixed integer programming. Optima (Mathematical Programming Society Newsletter), feature article, 61: 1-10, 1999.

EK Lee, RJ Gallagher, D Silvern, CS Wuu, M Zaider, Treatment Planning for Brachytherapy: An Integer Programming Model, Two Computational Approaches and Experiments with Permanent Prostate Implant Planning. Physics in Medicine and Biology, 44(1):145-165, 1999.

EK Lee, D Silvern, R Gallagher, LG Stabile, RD Ennis, CR Moorthy, M Zaider, Treatment planning for permanent prostate implants: genetic algorithm versus integer programming. Medical & Biological Engineering & Computing 35: Supplement Part 2, 1997.

RJ Gallagher, EK Lee, Mixed Integer Programming Optimization Models for Brachytherapy Treatment Planning. In: Daniel R. Masys, Ed. Proceedings of the 1997 American Medical Informatics Association Annual Fall Symposium, 278-282, 1997.

EK Lee, CH Chen, F Pietz, B Benecke, Modeling and optimizing the public health infrastructure for emergency response. Interfaces -- 2008 Wagner Prize Special Issue, 2008. To appear Sep 2009.

EK Lee, HK Smalley, Y Zhang, F Pietz, B Benecke. Facility location and multi-modality mass dispensing strategies and emergency response for biodefense and infectious disease outbreaks. In-ternational Journal on Risk Assessment and Management -- Biosecurity Assurance in a Threatening World: Challenges, Explorations, and Breakthroughs. 12(2/3/4):311-351, 2009.

EK Lee, S Maheshwary, J Mason, W Glisson, Large-scale dispensing for emergency response to bioterrorism & infectious disease outbreak. Interfaces -- OR Applications for Homeland Defense, 36(6): 591-607, 2006.

EK Lee, S Maheshwary, J Mason, Emergency response decision support system for infectious disease outbreak and biodefense. Annals of Operations Research, Computing and Optimization in Medicine and Life Sciences, 148: 25-53, 2006.

EK Lee, S Maheshwary, J Mason, Emergency treatment response and real-time staff allocation for bioterrorism and infectious disease outbreak. The INFORMS William Pierskalla Best Paper Award on research excellence in HealthCare and Management Science, Nov 2005.

EK Lee, S Maheshwary, J Mason, Real-Time staff allocation for emergency treatment response of biologic threats and infectious disease outbreak. Medical Decision Making, Jul 2005. In review.

JT Wu, LM Wein and AS Perelson. Optimization of Influenza Vaccine Strain Selection. Operations Research 63, 1317-1324, 2004.

EK Lee, GS Galis, Fingerprinting native and angiogenic microvascular networks through pattern recognition and discriminant analysis of functional perfusion data. AAAS's Science Translational Medicine. Submitted.

MT McCabe, EK Lee, PM Vertino, A multifactorial signature of DNA sequence and polycomb binding predicts aberrant CpG island methylation. Cancer Research 69(1):282-291, 2009.

TD Querec, R Akondy, EK Lee, W Cao, HI Nakaya, D Teuwen, A Pirani, K Gernert, J Deng, B Marzolf, K Kennedy, H Wu, S Bennouna, H Olouch, J Miller, RZ Vencio, M Mulligan, A Aderem, R Ahmed, B Pulendran, Systems biology approach predicts the immunogenicity of the yellow fever vaccine in humans. Nature Immunology 10:116-125, 2009.

MT McCabe, EK Lee, PM Vertino, DNA sequence elements and polycomb binding predict aberrant CpG island methylation in human cancer. Nature Genetics. Submitted 2008.

Q Ling, C Pu, EK Lee, A model-driven approach to manage clinical data in relational databases. IEEE Bioinformatics and Biomedicine, Workshop on Biomedical and Health Informatics. 2008.

H Wu, M Yuan, S Kaech, M Halloran. A Statistical Analysis of Memory CD8 T Cell Differentiation: An Application of a Hierarchical State Space Model to a Short Time Course Microarray Experiment, Annals of Applied Statistics, 1(2), 442-458, 2007.

EK Lee, Large-scale optimization-based classification models in medicine and biology. Annals of Biomedical Engineering -- Systems Biology, Bioinformatics, and Computational Biology 35(6):1095-1109, 2007.

EK Lee, Large-scale optimization-based classification models in medicine and biology. Annals of Biomedical Engineering, Systems Biology and Bioinformatics 35(6): 1095-1109, 2007.

EK Lee, TL Wu, Classification and disease prediction via mathematical programming. In Data Mining, Systems Analysis, and Optimization in Biomedicine. Editors: O Seref, OE Kundakcioglu and P Pardalos. AIP Conference Proceedings 953:1-42, 2007.

EK Lee, Optimization-Based Predictive Models in Medicine and Biology. Optimization in Medicine, Springer Netherlands, Springer Series in Optimization and Its Application, 12: 127-151, 2007.

EK Lee, T Easton, K Gupta, Novel evolutionary models and applications to sequence alignment problems. Annals of Operations Research, Operations Research in Medicine -- Computing and Optimization in Medicine and Life Sciences, 148: 167-187, 2006.

FA Feltus, EK Lee, JF Costello, C Plass, PM Vertino, DNA motifs associated with aberrant CpG island methylation. Genomics 87:572-579, 2006.

M Yuan, C Kendziorski. Hidden Markov Models for Microarray Time Course Data under Multiple Biological Conditions (with discussion), Journal of the American Statistical Association, 101(476), 1323-1340, 2006.

M Yuan, C Kendziorski. A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification, Biometrics, 62(4), 1089-1098, 2006.

C Kendziorski, M Chen, M Yuan, H Lan, A Attie. Statistical Methods for Expression Trait Loci (eQTL) Mapping, Biometrics, 62(1), 19-27, 2006.

JP Brooks, Adele Wright, C Zhu, EK Lee, Discriminant analysis of motility and morphology data from human lung carcinoma cells placed on purified extracellular matrix proteins. IEEE Transactions on Biomedical Engineering 2005. In review.

EK Lee, S Jagannathan, C Johnson, GS Galis, Fingerprinting native and angiogenic microvascular networks through pattern recognition and discriminant analysis of functional perfusion data. Proceedings of the National Academy of Sciences, 2005. In review.

L Simpson, EK Lee, BJ Hott, DJ Vega and WM Book, Long-term results of angioplasty versus stenting in cardiac transplant recipients with allograft vasculopathy. The Journal of Heart and Lung Transplantation, 24(9): 1211-1217, 2005.

EK Lee, RJ Gallagher, A Campbell, M Prausnitz, Prediction of ultrasound-mediated disruption of cell membranes using machine learning techniques and statistical analysis of acoustic spectra. IEEE Transactions on Biomedical Engineering, 51(1): 1-9, 2004.

EK Lee, T Easton, EL Johnson, Combinatorial approach to the minimum weight common mutated sequence problem and its application to DNA sequencing problems. Discrete Applied Mathematics, 2004. In review.

L Simpson, PK Mehta, BJ Hott, JD Vega, EK Lee and WM Book, Long Term Results Of Angioplasty Versus Stenting In Cardiac Transplant Recipients With Allograft Vasculopathy, International society for heart and lung transplantation (ISHLT), 2004.

FA Feltus, EK Lee, JF Costello, C Plass, PM Vertino, Predicting Aberrant CpG Island Methylation, Dec 2002. Proceedings of the National Academy of Science, 100(21):12253-12258, 2003.

EK Lee, RJ Gallagher, D. Patterson, A Linear Programming Approach to Discriminant Analysis with a Reserved Judgment Region, INFORMS Journal on Computing, 15(1):23-41, 2003.

RJ Gallagher, EK Lee, D Patterson, Constrained Discriminant Analysis via 0/1 Mixed Integer Programming. Annals of Operations Research, Special Issue on Non-Traditional Approaches to Statistical Classification and Regression, 74, 65-88, 1997.

RJ Gallagher, EK Lee, D Patterson, An Optimization Model for Constrained Discriminant Analysis and Numerical Experiments with Iris, Thyroid, and Heart Disease Datasets In: Cimino JJ, Ed. Proceedings of the 1996 American Medical Informatics Association Annual Fall Symposium,209-213, 1996.

EK Lee, RJ Gallagher, Mixed integer programming models for machine learning and discriminant analysis, Proceedings of ICIAM 95.

JP Brooks, EK Lee, Solving a mixed integer programming multi-category classification model with misclassification constraints. INFORMS Journal on Computing. Submitted.

EK Lee, S Maheshwary, Facets of conflict hypergraphs. Annals of Operations Research -- In Memory of Peter Hammer. Submitted.

EK Lee, Machine learning framework for classification in medicine and biology. Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, 6th International Conference, CPAIOR 2009, Proceedings. WJ van Hoeve, JN Hooker (Eds). Lecture Notes in Computer Science 5547:1-7, Springer 2009.

EK Lee, CH Chen, F Pietz, B Benecke, Modeling and optimizing the public health infrastructure for emergency response. Interfaces -- 2008 Wagner Prize Special Issue, 2008. To appear Sep 2009.

EK Lee, HK Smalley, Y Zhang, F Pietz, B Benecke. Facility location and multi-modality mass dispensing strategies and emergency response for biodefense and infectious disease outbreaks. In-ternational Journal on Risk Assessment and Management -- Biosecurity Assurance in a Threatening World: Challenges, Explorations, and Breakthroughs. 12(2/3/4):311-351, 2009.

EK Lee, M Zaider, Operations Research Advances Cancer Therapeutics. Interfaces -- 2007 Franz Edelman Prize Special Issue, 38(1):5-25, 2008.

JP Brooks, EK Lee, Analysis of the consistency of a mixed integer programming-based multicategory constrained discriminant model, Annals of Operations Research on Data Mining. Accepted 2007. Early version appeared online 2008. In press.

EK Lee, Optimization-Based Predictive Models in Medicine and Biology. Optimization in Medicine, Springer Netherlands, Springer Series in Optimization and Its Application, 12: 127-151, 2007.

JP Brooks and EK Lee, Mixed integer programming constrained discrimination model for credit screening. In Proceedings of the 2007 Spring Simulation Multiconference, Business and Industry Symposium, 1-6, Norfolk, VA, Mar 2007. ACM Digital Library.

JP Brooks and EK Lee, Solving a mixed-integer programming formulation of a multi-category constrained discrimination model. In Proceedings of the 2006 INFORMS Workshop on Artificial Intelligence and Data Mining, 1-6, Pittsburgh, PA, November 2006.

EK Lee, S Maheshwary, J Mason, W Glisson, Large-scale dispensing for emergency response to bioterrorism & infectious disease outbreak. Interfaces -- OR Applications for Homeland Defense 36(6): 591-607, 2006.

EK Lee, S Maheshwary, J Mason, Emergency response decision support system for infectious disease outbreak and biodefense. Annals of Operations Research, Computing and Optimization in Medicine and Life Sciences, 148: 25-53, 2006.

EK Lee, S Maheshwary, Facets of conflict hypergraphs. Mathematics of Operations Research, 2006. In review.

JCC Tsai, VCP Chen, EK Lee, EL Johnson, Parallelization of the MARS value function approximation in a decision-making framework for wastewater treatment. Computational Statistics and Data Analysis 2005.

EK Lee, Generating cutting planes for mixed integer programming problems in a parallel computing environment. INFORMS Journal on Computing 16(1):3-26, 2004.

T Easton, K Hooker, EK Lee, Facets of the independent set polytope. Mathematical Programming B, 98: 177-199, 2003.

Bartholdi, J. J., III, D. Dave, EK. Lee, Computing optimal load plans in less-than-truckload freight networks. Advances in Manufacturing, Logistics, and Supply Chain Management: Proceedings of the International Workshop in IT-Enabled Manufacturing, Logistics, and Supply Chain Management, Bangalore, India, 1-22, 2003.

EK Lee, RJ Gallagher, D. Patterson, A Linear Programming Approach to Discriminant Analysis with a Reserved Judgment Region, INFORMS Journal on Computing, 15(1):23-41, 2003.

EK Lee, J Linderoth, M Savelsbergh, A parallel linear programming based heuristic for large scale set partition ing problems. INFORMS Journal on Computing 13: 191-209, 2001.

EK Lee, A linear-programming based parallel cutting plane algorithm for mixed integer programming problems. Proceeding for the Third Scandinavian Workshop on Linear Programming 22-31, 1999.

RE Bixby, W Cook, A Cox, EK Lee, Computational experience with parallel mixed integer programming in a Distributed Environment. Annals of Operations Research -- Parallel Optimization 90: 19-43, 1999.

EK Lee, J Mitchell, Computational experience of an interior-poin t SQP algorithm in a parallel branch-and-bound framework. High Performance Optimization Techniques, Franks, Roos, Terlaky, Zhang (Eds), Kluwer Academic Publishers, 329-347, 1997.

M Junger, EK Lee, P Mutzel, T Odenthal, A polyhedral approach to the multi-layer crossing minimization problem. Graph Drawing, Lecture Notes in Computer Science, Springer-Verlag, LNCS Vol. 1353: 13-24 1997.

EK Lee, J Mitchell, Computational experience of an interior-point algorithm in a parallel branch-and-cut framework. Proceedings for SIAM Conference on Parallel Processing for Scientific Computing, 1-9, 1997.

RJ Gallagher, EK Lee, D Patterson, Constrained Discriminant Analysis via 0/1 Mixed Integer Programming. Annals of Operations Research, Special Issue on Non-Traditional Approaches to Statistical Classification and Regression, 74, 65-88, 1997.

EK Lee, J Mitchell, Computational experience in nonlinear mixed integer programming. The Operations Research Proceedings, Springer, 95-100, 1996.

EK Lee, On facets of knapsack equality polytopes, Journal of Optimization Theory and Applications 94(1): 223-239, 1994.

RE Bixby, EK Lee, Solving a truck dispatching scheduling probl em using branch-and-cut, Operations Research 46(3): 355-367, 1994.

M McCabe, EK Lee, P Vertino, Multi-factorial prediction of aberrant CpG island methylation in cancer. AACR Special Conference Cancer Epigenetics (Boston, MA), A73, 2008.

M McCabe, EK Lee, P Vertino, Predicting methylation-prone CpG islands in human cancer. Proc. Amer. Assn. Cancer Res. 48:Abs 2839, 2007.

M McCabe, EK Lee, P Vertino, Multi-Factorial prediction of aberrant CpG island methylation in Cancer, The Sixth Georgia Tech - Oak Ridge International Conference on Bioinformatics -- In silico Biology: Gene Discovery and Systems Genomics, 35, 2007.

EK Lee, KD Cha, JO Deasy, Robust Optimization to Accommodate Effects of Systematic Treatment Uncertainties. Medical Physics 34(6):2523-2524, 2007.

EK Lee, KD Cha, JO Deasy, Robust optimization to accommodate effects of systematic treatment uncertainties. In Proceedings for International Conference on The Use of Computers in Radiation Therapy. 6256:1-5, 2007.

EK Lee, KD Cha, T Bortfeld, JO Deasy, 4D image-guided treatment planning optimization for managing organ motion in radiotherapy planning. Proceedings for International Conference on The Use of Computers in Radiation Therapy. 6205:1-5, 2007.

EK Lee, Large-scale pattern recognition and classification approaches for disease diagnosis, Biomedical Engineering Systems Biology and Bioinformatics, 2006.

EK Lee, M Zaider, Incorporating biological metabolite information within treatment of prostate carcinoma and analysis of dose escalation effect. International Journal of Radiation Oncology Biology Physics 66(3) Supplement 1, S572-S573 2006.

EK Lee, KD Cha, T Bortfeld, JO Deasy, 4D Image-guided Treatment Planning Optimization for Managing Respiratory Effect in Radiotherapy Planning. Medical Physics 33(6) 2191-2192, 2006

EK Lee, D Lewis, KD Cha, Efficient IMRT Delivery --- Fast Generation of Integer-Valued Beam Profiles. Medical Physics 33(6) 2096, 2006.

P Mehta, L Simpson, EK Lee, T Lyle, W Book, Endothelin-Receptor Antagonists Improve Exercise Tolerance and Oxygen Saturations in Adults with the Eisenmenger Syndrome. American Heart Association Scientific Sessions 3190, Nov 2005.

EK Lee, T Easton, K Gupta, Novel Evolutionary Models and Applications to the Sequence Alignment Problem. The Fifth Georgia Tech - Oak Ridge International Conference on Bioinformatics -- Computational Genomics and Evolutionary Biology, 63, Nov 2005.

EK Lee, FA Feltus, JF Costello, C Plass, PM Vertino, Large-Scale Genomic Pattern Recognition and Classification of Aberrantly Hypermethylated CpG Island Loci in Human Cancer. The Fifth Georgia Tech - Oak Ridge International Conference on Bioinformatics -- Computational Genomics and Evolutionary Biology, 62, Nov 2005.

FA Feltus, EK Lee, JF Costello, C Plass, PM Vertino, DNA Patterns Associated With CpG Island Methylation State. The Fifth Georgia Tech - Oak Ridge International Conference on Bioinformatics -- Computational Genomics and Evolutionary Biology, 50, Nov 2005.

EK Lee, K Cha, T Bortfeld, JO Deasy, Multistage Treatment Planning Optimization for Managing Organ Motion in Radiotherapy Planning. International Journal of Radiation Oncology Biology Physics 63 (Supplement 1: Proceedings of the 47th Annual ASTRO Meeting): S209-S210, 2005.

EK Lee, K Cha, T Bortfeld, JO Deasy, Multistage Treatment Planning Optimization for Managing Organ Motion in Radiotherapy Planning. Medical Physics 32(6) 1925, 2005.

EK Lee, T Bortfeld, JO Deasy, Robust Optimization Including Effects of Systematic Treatment Errors. Medical Physics 32(6) 1978, 2005.

EK Lee, D Lewis, Fast Integer-Valued Smoothing of Beam Profiles in Intensity Modulated Radiation Therapy. Medical Physics 32(6) 1974, 2005.

EK Lee, M Zaider, Incorporating Biological Metabolite Information Within Treatment of Prostate Carcinoma. International Journal of Radiation Oncology, Biology and Physics 60(1) S370-371, ASTRO 2004.

EK Lee, KD Cha, J Shi, Automated Data Collection and Integration for Cancer Treatment Design and Clinic al Quality Evaluation Investigation. Joint BECON/BISTIC 2004 Symposium Biomedical Informatics for Clinical Decision Support: A Vision for the 21st Century, NIH Bethesda, p23 Jun 2004.

EK Lee, Optimization Techniques and Their Suitability and Robustness for IMRT Planning, invited presentation at 46th American Association of Physicists in Medicine Annual Meeting Pittsburgh 2004. Medical Physics 31(6) 1762, 2004.

EK Lee, Handling Multiple Clinical Objectives in Intensity Modulated Radiation Therapy Treatment Planning, abstract selected for oral presentation at 46th American Association of Physicists in Medicine Annual Meeting Pittsburgh 2004. Medical Physics 31(6) 1777, 2004.

J Deasy, EK Lee, M Langer, T Bortfeld, Y Zhang, H Liu, R Mohan, R Ahuja, J Dempsey, A Pollack, J Rosenman, A Eisbruch, R Rardin, J Purdy, C Zakarian, J Alaly, An IMRT Treatment Planning Research Collaboratory, abstract selected for oral presentation at 46th American Association of Physicists in Medicine Annual Meeting Pittsburgh 2004. Medical Physics 31(6) 1775, 2004.

M Koshy, JC Landry , JD Lawson, N Esiashivilli, CA Staley, JY Ting, R Howell, S Ghavidel, EK Lee, LW Davis, Potential For Toxicity Reduction Using Intensity Modulated Radiation Therapy (IMRT) For Retroperitoneal Sarcoma, accepted for presentation at ASTRO Utah 2003. International Journal of Radiation Oncology, Biology, Physics 57(2 Suppl):S448-9, ASTRO 2003.

EK Lee, T Fox, I Crocker, Beam Geometry and Intensity Map Optimization in IMRT via Computational Optimization, abstract selected for oral presentation at AAPM San Diego July 2003. Medical Physics 30(6) 1385-1386, 2003.

EK Lee, JO Deasy, I El Naqa, I Kawrakow, M Vicic, Integrating a Monte Carlo Based Optimization Module Into CERR for Designing IMRT Plans, abstract selected for presentation at AAPM San Diego July 2003. Medical Physics 30(6) 1324, 2003.

M Koshy, JC Landry, JD Lawson, N Esiashivilli, CA Staley, JY Ting, R Howell, S Ghavidel, EK Lee, LW Davis, Intensity modulated radiation therapy (IMRT) for retroperitoneal sarcoma: A case for dose escalation and organ at risk (OAR) toxicity reduction. American Radium Society Houston, Texas. Cancer Journal Scientific American 2003.

EK Lee, R Wagman, M Zaider, Treatment planning with automated planning volume definition for HDR brachytherapy -- Application to intraluminal treatment of the bile duct. International Conference on Translational Research and Pre-Clinical Strategies in Clinical Radio-Oncology'' ICTR 2003 Advances In Translational Radiation Oncology: From Molecular Signalling to Cancer Cure, March 2003.

EK Lee, M Zaider, Intra-Operative Dynamic Dose Optimization in Permanent Prostate Implants. International Conference on Translational Research and Pre-Clinical Strategies in Clinical Radio-Oncology'' ICTR 2003 Advances In Translational Radiation Oncology: From Molecular Signalling to Cancer Cure, March 2003.

FA Feltus, JF Costello, C Plass, EK Lee, PM Vertino, Identifying sequence patterns associated with aberrant CpG island methylation. Proceedings of American Association of Cancer Research LB:3. 2002.

EK Lee, M Zaider, Intra-Operative Dynamic Dose Optimization for Prostate Permanent Implants. 44th American Association of Physicists in Medicine Annual Meeting. Medical Physics 29(6) 1228, 2002.

EK Lee, T Fox, I Crocker, Mixed Integer Programming Techniques Applied to IMRT Treatment Planning Optimization. 44th American Association of Physicists in Medicine Annual Meeting. Medical Physics 29(6) 1259, 2002.

JO Deasy, EK Lee, I Kawrakow, C Zakarian, A Prototype Monte Carlo-Based IMRT Treatment Planning Research System. 44th American Association of Physicists in Medicine Annual Meeting. Medical Physics 29(6) 1254, 2002.

EK Lee, K Godette, C Anderson, J Keller, Effect of Race and Radiation Treatment Modalities on Biochemical Failure in Prostate Cancer Cases. 44th American Association of Physicists in Medicine Annual Meeting. Medical Physics 29(6) Supplement, 2002.

EK Lee, AY Fung, M Zaider, Automated planning volume contouring in soft-tissue sarcoma adjuvant brachytherapy treatment. International Journal of Radiation Oncology, Biology, Physics, 51:3 (ASTRO 2001): 391.

EK Lee, T Fox, I Crocker, Computational Optimization for Brain Tumor Radiosurgery Treatment Planning. 43rd American Association of Physicists in Medicine Annual Meeting. Medical Physics 28(6) 1304, 2001.

EK Lee, An Innovative Computerized Treatment Planning System for Permanent Prostate Implants. The American Association for the Advancement of Science 2001 Annual Meeting & Science Innovation Exposition, A41, February 2001. (Invited presentation with media briefings.)

EK Lee, M Zaider, Intra-Operative Iterative Treatment-Plan Optimization for Prostate Permanent Implants. 2nd International Innovative Solutions for Prostate Cancer Care meeting, 32-33, 2001.

M Zaider, EK Lee, MRS-guided Dose-Escalation Treatment Planning Optimization for Permanent Prostate Implants. 2nd International Innovative Solutions for Prostate Cancer Care meeting, 36, 2001.

M Zaider, EK Lee, K Zakian, HA Amols, M Zelefsky, J Dyke, J Koutcher, Intensity-modulated conformal treatment planning for prostate implants using biological imaging. International Journal of Radiation Oncology, Biology and Physics 45(3):351, ASTRO 1999.

EK Lee, M Zaider, M Zelefsky, On the definition of effective planning volume in permanent prostate implants. International Journal of Radiation Oncology, Biology and Physics 45(3):261-262,ASTRO 1999.

D Silvern, EK Lee, RJ Gallagher, LG Stabile, RD Ennis, CR Moorthy, M Zaider, Treatment Planning for Permanent Prostate Implants: Genetic Algorithm versus Integer Programming. Medical & Biological Engineering & Computing, vol.35, Supplement Part 2, 1997.