Laboratory for Computational Systems Biology
Mario, Medvedovic Mario Medvedovic
Associate Professor
MARIO.MEDVEDOVIC@UC.EDU
558-8564
332 Kettering

NIH Bios

Research Description

Dr. Medvedovic is developing new statistical and computational procedures for the analysis of complex genomics data, and applying these methods in collaborative boimedical research efforts. His recent work is focused on the development and application of unsupervised statistical learning approaches based on the Bayesian infinite mixture model. The focus of his collaborative research is in molecular studies of breast and prostate cancers.
 

Education

University of Zagreb, Zagreb, Croatia B.S. 1992 Applied Math/Computer Science
Bowling Green State Univ., Ohio M.S. 1994 Applied Statistics
University of Cincinnati, Cincinnati, OH Ph.D. 1998 Biostatistics

Professional Experience

2007 Associate Professor, Department of Environmental Health, University of Cincinnati
2004-2007 (Secondary app) Assistant Professor, Division of Biomedical Informatics, Cincinnati Children’s Hospital Research Foundation
2004-2007 Assistant Professor, Department of Environmental Health, University of Cincinnati
2001 Associate Director for Bioinformatics, Center for Biostatistical Services, University of Cincinnati.
2001 Member of the Center for Genome Information, University of Cincinnati.
2000- 2004 Research Assistant Professor, Department of Environmental Health, University of Cincinnati.
1999–2000 Senior Research Associate, Department of Environmental Health, University of Cincinnati.
1994–1998 Graduate Research Assistant, Department of Environmental Health, University of Cincinnati.
1996–1996 Adjunct Instructor, College of Evening and Continuing Education, University of Cincinnati Adjunct Instructor, University College, University of Cincinnati
1992-1994 Graduate Teaching Assistant, Department of Mathematics and Statistics, Bowling Green State University.

Publications

Most Recent

  • Freudenberg JM, Sivaganesan S, Wagner M, Medvedovic M. Semi-parametric Bayesian model for unsupervised differential co-expression analysis identifies novel molecular subtypes. BMC Bioinformatics, Accepted 2010.

  • Shinde K, Phatak M, Freudenberg JM, Chen J, Li Q, Joshi VK, Hu Z, Ghosh K, Meller J, Medvedovic M. Genomics Portals: Integrative Web-Platform for Mining Genomics Data. BMC Genomics. 2010 Jan 13;11(1):27. [Epub ahead of print].

  • Stark JM, Barmada MM, Winterberg AV, Majumber N, Gibbons WJ Jr, Stark MA, Sartor MA, Medvedovic M, Kolls J, Bein K, Mailaparambil B, Krueger M, Heinzmann A, Leikauf GD, Prows DR. Genomewide association analysis of respiratory syncytial virus infection in mice.  J Virol. 2009 Dec 16. [Epub ahead of print].

  • Freudenberg MJ, Joshi KV, Hu Z, Medvedovic M, CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics 10:234, 2009.

  • Medvedovic M, Gear R, Freudenberg JM, Schneider J, Bornschein R, Yan M, Mistry MJ, Hendrix H, Karyala S, Halbleib D, Heffelfinger S, Clegg DJ, Anderson MW. Influence of Fatty Acid Diets on Gene Expression in Rat Mammary Epithelial Cells. Physiologic Genomics 10: 80-88, 2009.

  • Genter MB, Warner BM, Medvedovic M, Sartor, MA. Comparison of rat olfactory mucosal responses to carcinogenic and non-carcinogenic chloracetanilides. Food and Chemical Toxicology. 47: 1051-1057, 2009.
  • Medvedovic M, Halbleib D, Miller ML, LaDow K, Sartor MA, and Tomlinson CR, Gene expression profiling of blood to predict the onset of leukemia. Blood Cells Mol Dis. 42: 64-70, 2009.

  • Gandhi MS, Stringer JR, Nikiforova MN, Medvedovic M, and Nikiforov YE. Gene position within chromosome territories correlates with their involvement in distinct rearrangement types in thyroid cancer cells. Genes Chromosomes.Cancer 48: 222-228, 2009.

  • Zhang X, Leav I, Revelo MP, Deka R, Medvedovic M, Jiang Z, and Ho SM. Deletion Hotspots in AMACR Promoter CpG Island Are cis-Regulatory Elements Controlling the Gene Expression in the Colon. PLoS Genet 5: e1000334, 2009.

  • Bien K, Wesselkamper SC, Liu X, Dietsch M, Majumder N, Concel VJ, Medvedovic M, Sartor M, Henning LN, Venditto C, Borchers MT, Barchowsky A, Weaver TE, Tichelaar JW, Prows DR, Korfhagen TR, Hardie WD, Bachurski CJ, and Leikauf GD. Surfactant Associated Protein B is Critical to Survival in Nickel-induced Injury in Mice. Am.J Respir.Cell Mol Biol, 2009.

  • Sartor, M.A., Schnekenburger, M., Marlowe, J.L., Reichard, J.F., Wang, Y., Fan, Y., Ma, C., Karyala, S., Halbleib, D., Liu, X., Medvedovic, M., and Puga, A. The aryl hydrocarbon receptor regulatory network controls multiple morphogenetic 117:1139–1146, 2009.and developmental programs.  Environ Health Perspect. 117:1139–1146, 2009.

  • Neville N.C. Tam, Carol Ying-Ying Szeto, Maureen Sartor, Mario Medvedovic, Shuk-Mei Ho. Gene-expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17b-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats. Neoplasia. 2008 10: 20-40.

  • Bakshi S, Zhang X, Godoy-Tundidor S, Cheng RY, Sartor MA, Medvedovic M, and Ho SM, Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor. Environ.Health Perspect. 116: 769-776, 2008.

  • Borchers MT, Wesselkamper SC, Eppert BL, Motz GT, Sartor MA, Tomlinson CR, Medvedovic M, and Tichelaar JW, Nonredundant functions of alphabeta and gammadelta T cells in acrolein-induced pulmonary pathology. Toxicol.Sci 105: 188-199, 2008.

  • Tang,WY, Newbold, R, Mardilovich, K, Jefferson, W, Cheng, R, Szeto, C,  Medvedovic, M, Shuk-Mei Ho. Identification of nucleosomal binding protein 1 (Nsbp1) as a gene susceptible to diethylstilbestrol- or genistein-induced developmental reprogramming via DNA methylation in the mouse uterus. Endocrinology. 2008 Jul 31. [Epub ahead of print].

  • Sartor MA, Leikauf GD, and Medvedovic M. LRpath: A logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics, 2008.

2007

  • Schwanekamp JA, Sartor MA, Karyala S, Halbleib D, Medvedovic M, Tomlinson CR. Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin. Biochim Biophys Acta. 2007.

  • Cao B, Medvedovic M, Meller J. Prediction of Transmembrane Domains and Pore-facing Residues in Beta-barrel Membrane Proteins. Applications of Statistical and Machine Learning Methods in Bioinformatics. Editors: Jaroslaw Meller and Wielsav Novak. Peter Lang GmbH, Berlin. 2007.

  • Hardie WD, Korfhagen TR, Sartor MA,  Prestridge A, Medvedovic M, Le Cras TD, Ikegami M,  Tomlinson CR, Nichols W, Wesselkamper SC,  Whitsett JA, Leikauf GD. Genomic Signature of Matrix and Vasculature Remodeling in TGFa-induced Pulmonary Fibrosis. Am J Respir Cell Mol Biol. 2007 May 11; [Epub ahead of print]

  • Liu X, Jessen W, Sivaganesan S, Aronow B, Medvedovic M. Bayesian hierarchical models for learning transcriptional modules from expression and location data. BMC Bioinformatics. 2007 Aug 3;8:283.

  • Ganguly K, Stoeger T, Wesselkamper SC, Reinhard C, Sartor MA, Medvedovic M, Tomlinson CR, Bolle I, Mason JM, Leikauf GD,  Schulz H. Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure. Physiol Genomics. 2007 Nov 14;31(3):410-421.

  • Popa I, Zubkova I, Medvedovic M, Romantseva T, Mostowski H, Zaitseva M. Transcription factors that control proliferation of epithelial cell progenitors are up-regulated in the stroma of the regenerating adult thymus: results of the microarray study. Int Immunol. 2007 Nov;19(11):1249-60.

2006

  • Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, and Medvedovic M, Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics 7: 538, 2006. (Support Page)

  • Liu X, Sivaganesan S, Yeung K.Y., Bumgarner RE, and Medvedovic M. Bayesian context-specific infinite mixture model for clustering of gene expression profiles across diverse microarray datasets. Bioinformatics 22:1737-44. 2006. (Support Page)(preprint)

  • Medvedovic M, Tomlinson CR, Call MK, Grogg M, Tsonis PA. Gene Expression and Discovery during Lens Regeneration in Mouse: Regulation of EMT and Lens Differentiation. Mol Vis. 12:422-40. 2006

  • Sartor MA, Zorn AM, Schwanekamp J, Halbleib D, Karyala S, Howell ML, Dean GE, Medvedovic M, Tomlinson CR. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Research 34(1):185-200. 2006.

  • Medvedovic, M., Wiest, J.S. DNA Microarrays and Computational Analysis of DNA Microarray Data in Cancer Research. In Molecular Carcinogenesis, Warshawsky and Landolph, CRC Press, 2006 (preprint)

  • Erwin CR, Jarboe MD, Sartor MA, Medvedovic M, Warner BW, Bates MD. Developmental Characteristics of Adapting Small Intestine Crypt Cells. Gastroenterology 130(4):1324-32. 2006.

  • Mesa CJr., Mirza M, Mitsutake N, Sartor MA, Medvedovic M, Tomlinson CR, Knauf JA, Weber G, Fagin JA. Conditional activation of the RET/PTC3 and B-RAFV600E oncoproteins in thyroid cells is associated with unique patterns of gene expression that predict distinct functional properties and a preferential role of BRAF in extracellular matrix remodeling. Cancer Research, 66(13):6521-9. 2006.

  • Wesselkamper SC, McDowell SA, Medvedovic M, Dalton TP, Deshmukh HS, Sartor MA, Case LM, Henning LN, Borchers MT, Tomlinson CR, Prows DR, Leikauf GD. The Role of Metallothionein in the Pathogenesis of Acute Lung Injury. Am J Respir Cell Mol Biol. 34(1):73-82. 2006.

  • Gandhi M., Medvedovic M., Stringer J.R., Nikiforov, Y. Interphase chromosome folding determines spatial proximity of genes participating in carcinogenic ret/ptc rearrangements. Oncogene. 25(16):2360-6. 2006.
  • Crystal R Icenhour, Jonathan Arnold, Mario Medvedovic, and Melanie T Cushion. Competitive Coexistence of Two Pneumocystis Species. Infection, Genetics and Evolution 6(3):177-86. 2006.

2005

  • Stringer JR, Larson JS, Fischer JM, Medvedovic M, Hersh MN, Boivin GP, Stringer SL. Modeling variation in tumors in vivo.  Proc Natl Acad Sci U S A. 2005 Feb 3; [Epub ahead of print].

  • Puxeddu E, Zhao G, Stringer JR, Medvedovic M, Moretti S, Fagin JA. Characterization of novel non-clonal intrachromosomal rearrangements between the H4 and PTEN genes (H4/PTEN) in human thyroid cell lines and papillary thyroid cancer specimens. Mutat Res. 15: 17-32. 2005

  • Puxeddu E, Knauf JA, Sartor MA, Mitsutake N, Smith EP, Medvedovic M, Tomlinson CR, Moretti S, Fagin JA. RET/PTC-induced gene expression in thyroid PCCL3 cells reveals early activation of genes involved in regulation of the immune response Endocr Relat Cancer. 12(2):319-34. 2005

  • Wesselkamper SC, Case LM, Henning LN, Borchers MT, Tichelaar JW, Mason JM, Dragin N, Medvedovic M, Sartor MA, Tomlinson CR, Leikauf GD. Gene Expression Changes During the Development of Acute Lung Injury: Role of TGF-{beta}. Am J Respir Cell Mol Biol. 172(11):1399-411. 2005

     

2004

  • Medvedovic M., Guo, J., Bayesian Model-Averaging in Unsupervised Learning From Microarray Data. BIOKDD 2004. (PDF)

  • Bahassi, E.M., Karyla, S., Tomlinson, C.R., Sartor, M.A., Medvedovic, M., Hennigan, R.F. Inhibition of AP-1 Function Differentially Affects Tumor Cell Proliferation and Migration. Clinical and Experimental Metastasis, (In Press) 2004.

  • Puga, A., Sartor, M.A., Huang, M-Y, Kerzee, K.J., Wei, Y-D, Tomlinson, C.R., Baxter, C.S., Medvedovic, M. Gene expression profiles of mouse aourta and cultured vascular smooth muscle cells are widely different, yet show common responses to dioxin exposure. Cardiovascular Toxicology 4(4):385-404.2004.  (Abstract)

  • Leikauf GD, Hardie WD, Wesselkamper SC, Bachurski CJ, Medvedovic M, Sartor MA, Tomlinson CR, McDowell SA, Henning LM, Case LM, Tichelaar JW, Prows DR, Korfhagen TR: Resolving Gene-Environment Interactions in Complex Traits: Acute Lung Injury. Am J Respir Cell Mol Biol. (In Press)

  • Whitsett JA, Bachurski CJ, Barnes KC, Bunn PA, Jr., Case LM, Cook DN, Crooks D, Duncan MW, Dwyer-Nield L, Elston RC, Fessler MB, Franklin WA, Friedman N, Garcia JG, Geraci MW, Glasgow C, Glasser SW, Hardie WD, Henning LM, Johnson GL, Kawkitinarong K, Keith RL, Korfhagen TR, Leikauf GD, Liggett SB, Malcolm KC, Malkinson AM, Mariani TJ, McDowell SA, McGraw DW, Medvedovic M, Moss J, Nogee LM, Nonas S, Pacheco-Rodriguez G, Palmer LJ, Peters DG, Prows DR, Redline S, Regev A, Sartor MA, Schwartz DA, Silverman EK, Steagall WK, Stearman RS, Taveira-DaSilva A, Tichelaar JW, Tomlinson CR, Tsukada K, Weaver TE, Wert SE, Wesselkamper SC, Worthen GS, Xu Y, Zerbe L, Zhang Y, Zhang Y, Choi AM, and Kaminski N, Functional genomics of lung disease. Am.J.Respir.Cell Mol.Biol. 31: S1-S81, 2004.

  • Yeung KY, Medvedovic M, and Bumgarner RE, From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol. 5: R48, 2004.

  • Zhang J., Moseley A., Jegga A.G., Gupta A., Witte D.P., Sartor M., Medvedovic M., Williams S.S., Ley-Ebert C., Coolen L., Egnaczyk G., Genter M.B., Lehman M., Lingrel J., Maggio J., Parysek L., Walsh R., Xu M., Aronow B.J. Neural system-enriched gene expression, relationship to biological pathways and neurological diseases. Physiologic Genomics 18: 167-183, 2004.

  • Sonntag, D.M., de Boer, J., Medvedovic, M., Baxter, S.C., LeMasters, G., Dourson, M., Talaska, G. Mutational biases associated with potential iron-binding DNA motifs in rodent lacI and human p53 mutational databases. Mutat.Res. 550: 73-88, 2004.

  • Sartor, M.A., Schwanekamp, J., Halbleib, D., Mohamed, I., Karyala, S., Medvedovic, M. and Tomlinson, C.R. Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques 36: 790-796, 2004.(Abstract)

  • Medvedovic, M., Yeung, K.Y., Bumgarner, R.E. Bayesian Mixtures for Clustering Replicated Microarray Data. Bioinformatics. 20: 1222-1232, 2004.(PDF)

  • Vineis,P., Schulte,P.A., Carreón,T., Bailer,J.A.,Medvedovic,M. Design and Analysis Issues in Studies of Gene-Environment Interactions. IARC Scientific Publications, 57: 417-453. 2004.

  • Karyala, S., Guo, J., Sartor, M., Medvedovic, M., Kann, S., Puga, A., Ryan, P., and Tomlinson, C.R.. Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice. Cardiovascular Toxicology, 4: 47-74. 2004.(Abstract)

  • Guo, J., Sartor, M., Karyala, S., Medvedovic, M., Puga, A., Ryan, P., Tomlinson, C.R. Expression of genes in the TGF-β signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice. Toxicology and Applied Pharmacology 194: 79-89. 2004.(Abstract)

2003 and before

  • Yutaka Tsuneoka, Timothy P. Dalton, Marian L. Miller, Corey D. Clay, Howard G. Shertzer, Glenn Talaska, Mario Medvedovic, Daniel W. Nebert. Liver and Urinary Bladder DNA Adduct Formation Induced by 4-Aminobiphenyl in Cyp1a2(-/-) and Cyp1a2(+/+) Mice. J. Natl. Cancer Inst. 95(16):1227-37. 2003.

  • Yeung, K.Y., Medvedovic,M. Bumgarner, R.E. Clustering Gene Expression Data With Repeated Measurements. Genome Biology 4(5): R34. 2003

  • Medvedovic M., Sivaganesan S. Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics 18: 1194-1206, 2002. (PDF)

  • Knauf J.A., Ward L.S., Nikiforov Y., Nikiforova M, Puxeddu E., Medvedovic M., Nui W., Liron T., Mochly-Rosen D., Fagin J.A.. Isozyme-specific abnormalities of protein kinase c in thyroid cancer: Evidence for epigenetic changes in pkc epsilon. The Journal of Clinical Endocrinology & Metabolism 87: 2150-2159, 2002.

  • King N.M., Oakley G., Medvedovic M., Dixon K. The XPA Protein Alters the Specificity of Ultraviolet Light-Induced Mutagenesis in Vitro. Environmental and Molecular Mutagenesis. Environmental and Molecular Mutagenesis, 37:329-39, 2001.

  • Medvedovic M., Succop P., Dixon K., Shukla R. Clustering mutational spectra via classification likelihood and Markov Chain Monte Carlo Algorithm. Journal of Agricultural, Biological and Environmental Statistics, 6: 19-37. 2001.(PDF)

  • Li Y., Carty, M.P., Oakley, G.G., Seidman, M.M., Medvedovic M., Dixon, K. Expression of ATM in Ataxia Telangiectasia Fibroblasts Rescues Defects in DNA Double-Strand Break Repair in Nuclear Extracts. Environmental and Molecular Mutagenesis, 37: 128-140. 2001.

  • Puga A., Maier A., Medvedovic M. The transcriptional signature of dioxin in human hepatoma HepG2 cells. Biochemical Pharmacology, 60: 1129-1142. 2000. (Abstract)

  • Nikiforova M., Stringer J.R., Blough R., Medvedovic M., Fagin J.A., Nikiforov Y.A. Proximity of Chromosomal Loci That Participate in Radiation-Induced Translocations in Human Cells. Science, 290: 138-141. 2000.

  • Medvedovic M. Clustering Multinomial Observations via Classification Likelihood and MCMC Algorithms. Proceedings of the Joint Statistical Meeting 2000: Statistical Computing Section. , 48-51. 2000. (PDF)

  • Levin, S.L., Rice, C.H., Lemasters, G.K., Lockey, J., Medvedovic, M. What is the Potential Measurement Error in Occupational Exposure Studies. Journal of the Air & Waste Management Association. 50: 941-947, 2000.

  • Bhattacharya, A., Teuschler, W.J., Dimov, M., Medvedovic, M., Lemasters G. Development and Evaluation of a Microprocessor Based Ergonomic Dosimeter for Evaluating Carpentry Tasks. Applied Ergonomics, 30: 543-553, 1999.

  • Liu, S., Medvedovic, M., Dixon, K. Mutational Specificity in a Shuttle Vector Replicating in Chromium(VI)-treated Mammalian Cells. Environmental And Molecular Mutagenesis, 33: (4) 313-319, 1999.

  • McKay, T.R., Levin, L., Lockey, J., Lemasters, G., Medvedovic, M., Papes, D., Simpson, S., Rice, H.C. Weight Change and Lung Function: Implications for Epidemiological and Workplace Surveillance Studies. Journal of Occupational and Environmental Medicine, 41: (7) 596-604, 1999.

  • Bhattacharya, A,, Smelser, T.D., Berger, O., Shukla, R., Medvedovic, M. The Effect of Succimer Therapy in Lead Intoxication Using Postural Balance as a Measure: A Case Study in a Nine Year Old Child. Neurotoxicology 19: 57-64, 1998.

  • Ward, S.L., Brenta, G., Medvedovic, M., Fagin, A.J.. Studies of Allelic Loss in Thyroid Tumors Reveal Major Differences in Chromosomal Instability Between Papillary and Follicular Carcinomas. Journal of Clinical Endocrinology and Metabolism. 83(2); 525-30, 1998.

  • Lockey, J., Levin, S.L., Lemasters, K.G., McKay, T.R., Hansen, R.K., Papes, D.M., Simpson, S., Medvedovic, M. Longitudinal Estimates of Pulmonary Function in Refractory Ceramic Fiber Manufacturing Workers. The American Journal of Respiratory & Critical Care Medicine. 157: 1226-33, 1998.