I am an Associate Scientist at the University of Wisconsin Carbone Comprehensive Cancer Center (UWCCC) and the Associate Director of the UWCCC Cancer Informatics Shared Resources.

My research interests lies in data mining, artificial intelligence, machine learning, probabilistic methods, dynamical models, inductive logic programming, and statistical relational learning with applications to biological and medical data. I am particularly interested in the analysis of clinical, genomics, transcriptomics, proteomics, metagenomics, and other molecular data.


Contact

Irene M. Ong

Biostatistics and Medical Informatics
UWCCC Cancer Informatics Shared Resources
Wisconsin Institutes of Medical Research
1100 Highland Avenue
Madison, WI 53705

ong at biostat . wisc . edu


Publications

Refereed Conferences:
A.D. Swick, A.P. Stein, T.M. McCulloch, G.K. Hartig, I.M. Ong, E. Sampene, P.J. Prabakaran, C.Z. Liu, R.J. Kimple, "Defining the boundaries and expanding the utility of head and neck cancer patient derived xenografts", Oral Oncol. 2017 Jan;64:65-72.
A. Singh, E. Willems, A. Singh, I.M. Ong, and A.K. Verma, "Ultraviolet radiation-induced differential microRNA expression in the skin of hairless SKH1 mice, a widely used mouse model for dermatology research", Oncotarget, Oct 26 2016.
T.K. Sato, M. Tremaine, L.S. Parreiras, A.S. Hebert, K.S. Myers, A.J. Higbee, M. Sardi, S.J. McIlwain, I.M. Ong, R.J. Breuer, R.A. Narasimhan, M.A. McGee, Q. Dickinson, A. La Reau, D. Xie, M. Tian, J.L. Reed, Y. Zhang, J.J. Coon, C.T. Hittinger, A.P. Gasch, and R. Landick, "Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae", PLoS Genetics, 2016 Nov 9;12(11).
K.R. Katsumura, I. M. Ong, A.W. DeVilbiss, R. Sanalkumar, E.H. Bresnick, "GATA Factor-Dependent Positive-Feedback Circuit in Acute Myeloid Leukemia Cells", Cell reports, 2016; 16(9):2428-41.
S.J. McIlwain, D. Peris, M. Sardi, O.V. Moskvin, F. Zhan, K.S. Myers, N.M. Riley, A. Buzzell, L.S. Parreiras, I.M. Ong, R. Landick, J.J. Coon, A.P. Gasch, T.K. Sato, and C.T. Hittinger, "Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research", G3 (Bethesda, Md.). 2016; 6(6):1757-66.
A. Singh, E. Willems, A. Singh, B.B. Hafeez, I.M. Ong, S.L. Mehta, and A.K. Verma, "Ultraviolet radiation-induced tumor necrosis factor alpha, which is linked to the development of cutaneous SCC, modulates differential epidermal microRNAs expression", Oncotarget, 2016; 7(14):17945-56.
Y. Wu, C.K. Abbey, J. Liu, I. Ong, P. Peissig, A.A. Onitilo, J. Fan, M. Yuan, and E.S. Burnside, "Discriminatory power of common genetic variants in personalized breast cancer diagnosis", Proceedings of SPIE--the International Society for Optical Engineering, 2016; 9787.
E.L. Baar, K.A. Carbajal, I.M. Ong, D.W. Lamming, "Sex- and tissue-specific changes in mTOR signaling with age in C57BL/6J mice". Aging Cell, 2016; 15(1):155-66.
J.S. Piotrowski, S.W. Simpkins, S.C. Li, R. Deshpande, S.J. McIlwain, I.M. Ong, C.L. Myers, C. Boone, R.J. Andersen, "Chemical genomic profiling via barcode sequencing to predict compound mode of action", Methods Mol Biol., 2015;1263:299-318.
J.S. Piotrowski, H. Okada, F. Lu, S.C. Li, L. Hinchman, A. Ranjan, D. Smith, A.J. Higbee, A. Ulbrich, J.J. Coon, R. Deshpande, Y.V. Bukhman, S. McIlwain, I.M. Ong, C.L. Myers, C. Boone, R. Landick, J. Ralph, M. Kabbage, and Y. Ohya. "The plant derived, antifungal agent poacic acid targets β-1,3-glucan", Proc. Natl. Acad. Sci. U.S.A., March 24, 2015 vol. 112 no. 12 E1490-E1497, 2015.
J. Liu, Y. Wu, I.M. Ong, D. Page, P. Peissig, C. McCarty, A.A. Onitilo and E. Burnside, "Leveraging Interaction between Genetic Variants and Mammographic Findings for Personalized Breast Cancer Diagnosis", AMIA Joint Summits on Translational Science proceedings, 2015; 2015:107-11.
O.V. Moskvin, S.J. McIlwain, I.M. Ong, "CAMDA 2014: Making sense of RNA-Seq data: From low-level processing to functional analysis", Systems Biomedicine, 2 (2), 31-40, 2014.
L.S. Parreiras, R.J. Breuer, R.A. Narasimhan, A.J. Higbee, A. La Reau, M. Tremaine, L. Qin, L.B. Willis, B.D. Bice, B.L. Bonfert, R.C. Pinhancos, A.J. Balloon, N. Uppugundla, T. Liu, C. Li, D. Tanjore, I.M. Ong, H. Li, E.L. Pohlmann, J. Serate, S.T. Withers, B.A. Simmons, D.B. Hodge, M.S. Westphall, J.J. Coon, B.E. Dale, V. Balan, D.H. Keating, Y. Zhang, R. Landick, A.P. Gasch, and T.K. Sato, "Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover", PLOS ONE, September 15, 2014.
T.P. Wyche, J.S. Piotrowski, Y. Hou, D. Braun, R. Deshpande, S. McIlwain, I.M. Ong, C.L. Myers, I.A. Guzei, W.M. Westler, D.R. Andes, and T.S. Bugni, "Forazoline A: Marine-Derived Polyketide with Antifungal In Vivo Efficacy", Angewandte Chemie International Edition WILEY-VCH Verlag, 1521-3773, September, 2014.
D.H. Keating, Y. Zhang, I.M. Ong, S. McIlwain, E.H. Morales, J.A. Grass, M. Tremaine, W. Bothfeld, A. Higbee, A. Ulbrich, A.J. Balloon, M.S. Westphall, J. Aldrich, M.S. Lipton, J. Kim, O.V. Moskvin, Y.V. Bukhman, J.J. Coon, P.J. Kiley, D.M. Bates, and R. Landick, "Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification", Frontiers in Microbiology 2014 Aug 13;5:402.
R.J.F. Haft, D.H. Keating, T. Schwaegler, M.S. Schwalbach, J. Vinokur, M. Tremaine, J.M. Peters, M.V. Kotlajich, E.L. Pohlmann, I.M. Ong, J.A. Grass, P.J. Kiley, and R. Landick. "Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria", Proc. Natl. Acad. Sci. U.S.A. 2014 Jun 9;111(25):E2576-85.
Trey Sato, Tongjun Liu, Lucas Parreiras, Daniel Williams, Dana Wohlbach, Benjamin Bice, Irene Ong, Rebecca Breuer, Li Qin, Donald Busalacchi, Shweta Deshpande, Chris Daum, Audrey Gasch, and David Hodge, "Harnessing Genetic Diversity in Saccharomyces cerevisiae for Fermentation of Xylose in Hydrolysates of Alkaline Hydrogen Peroxide Pretreated Biomass", Appl Env Microbiol, 80(2) January, 2014.
K. Myers, H. Yan, I. Ong, D. Chung, K. Liang, F. Tran, S. Keles, R. Landick, and P. Kiley, "Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding", PLOS Genetics, 9(6) June, 2013.
A. Goncalves, I. Ong, J. Lewis, and V. Santos Costa, "A problog model for analyzing gene regulatory networks", Proceedings of the 22nd International Conference on Inductive Logic Programming Late Breaking Papers, Dubrovnik, Croatia, September, 2012.
S. Natarajan, I. Ong, D. Haight, D. Page, and V. Santos Costa, "Modeling Temporal Biomedical Data by SRL", Proceedings of the Statistical and Relational Learning in Bioinformatics Workshop at the European Conference on Machine Learning, Antwerp, Belgium, September, 2008.
I.M. Ong, S.E. Topper, D. Page and V. Santos Costa, "Inferring Regulatory Networks from Time Series Expression Data and Relational Data via Inductive Logic Programming", Proceedings of the Sixteenth International Conference on Inductive Logic Programming (ILP), Springer Lecture Notes in Artificial Intelligence 4455, 2007. (postscript, pdf)
J. Davis, I.M. Ong, J. Struyf, E. Burnside, D. Page and V. Santos Costa. "Change of Representation for Statistical Relational Learning" Proceedings of the 20th International Joint Conference on Artificial Intelligence (IJCAI 2007) (2007), Hyderabad, India, January 2007. (pdf)
D. Page and I.M. Ong, "Experimental Design of Time Series Data for Learning from Dynamic Bayesian Networks" Proceedings of the Pacific Symposium on Biocomputing (PSB 2006), 11:267-278 (2006), Wailea, Maui, Hawaii, January 2006. (postscript, pdf)
I.M. Ong, I. Dutra, D. Page and V. Santos Costa, "Mode Directed Path Finding", Sixteenth European Conference on Machine Learning (ECML 2005), 673-681 (2005), Porto, Portugal, 3rd - 7th October, 2005. (postscript, pdf)
J. Bockhorst and I. Ong, "FOIL-D: Efficiently Scaling FOIL for Multi-relational Data Mining of Large Databases", Fourteenth International Conference on Inductive Logic Programming (ILP 2004), 63-79 (2004), Porto, Portugal, 6th - 8th September, 2004. (postscript, pdf)
I.M. Ong, J. D. Glasner and D. Page, "Modelling Regulatory Pathways in E.coli from Time Series Expression Profiles", Bioinformatics, 18:241S-248S (2002), special issue based on the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2002), Edmonton, CA, August 2002. (postscript, pdf)

Refereed Workshops:

I.M. Ong, I. Dutra, D. Page and V. Santos Costa, "Hyperpaths: Extending PathFinding to Moded Languages", Proceedings of the Fourth Workshop on Multi-Relational Data Mining at the Eleventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (MRDM at KDD 2005) Chicago, IL, August 21, 2005.
J. Davis, V. Santos Costa, I. M. Ong, D. Page and I. Dutra, "Using Bayesian Classifiers to Combine Rules", Proceedings of the Third Workshop on Multi-Relational Data Mining at the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (MRDM at KDD 2004) Seattle, WA, August 22, 2004.