Publications

CSBL Publications

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.