Today is Friday, Nov. 16, 2018

Department of

Environmental Health

Photo of  Mario Medvedovic, PhD

Mario Medvedovic, PhD

Professor and Director, Division of Biostatistics and Bioinformatics

  • Master's Degree: University of Zagreb
  • Master's Degree: Bowling Green State University
  • Doctoral Degree: University of Cincinnati

Research/Clinical Interests

Bioinformatics. Omics data analysis. RNA-seq and scRNA-seq management, processing, statistical and systems biology analysis. Mining of public domain omics datasets and signatures. Pharmacogenomics and Toxicogenomics.

Contact Information
  • Kettering Laboratory
  • Room 110
  • 160 Panzeca Way
  • Cincinnati, Ohio 45267
  • Office 513-558-8564
  • Email

Peer Reviewed Publications

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Abdel-Hameed, E. A.; Rouster, S. D.; Boyce, C. L.; Zhang, X.; Biesiada, J.; Medvedovic, M.; Sherman, K. E. 2018. Ultra-Deep Genomic Sequencing of HCV NS5A Resistance-Associated Substitutions in HCV/HIV Coinfected Patients Dig Dis Sci, 63 3 , 645-652

Do, T.; Tan, R.; Bennett, M.; Medvedovic, M.; Grom, A. A.; Shen, N.; Thornton, S.; Schulert, G. S. 2018. MicroRNA networks associated with active systemic juvenile idiopathic arthritis regulate CD163 expression and anti-inflammatory functions in macrophages through two distinct mechanisms J Leukoc Biol, 103 1 , 71-85

Haque, S. U.; Niu, L.; Kuhnell, D.; Hendershot, J.; Biesiada, J.; Niu, W.; Hagan, M. C.; Kelsey, K. T.; Casper, K. A.; Wise-Draper, T. M.; Medvedovic, M.; Langevin, S. M. 2018. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma Head Neck, 194 1 , 79-89

Huang, W.; Feng, Y.; Liang, J.; Yu, H.; Wang, C.; Wang, B.; Wang, M.; Jiang, L.; Meng, W.; Cai, W.; Medvedovic, M.; Chen, J.; Paul, C.; Davidson, W. S.; Sadayappan, S.; Stambrook, P. J.; Yu, X. Y.; Wang, Y. 2018. Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration Nat Commun, 9 1 , 700

Keenan, A. B.; Jenkins, S. L.; Jagodnik, K. M.; Koplev, S.; He, E.; Torre, D.; Wang, Z.; Dohlman, A. B.; Silverstein, M. C.; Lachmann, A.; Kuleshov, M. V.; Ma'ayan, A.; Stathias, V.; Terryn, R.; Cooper, D.; Forlin, M.; Koleti, A.; Vidovic, D.; Chung, C.; Schurer, S. C.; Vasiliauskas, J.; Pilarczyk, M.; Shamsaei, B.; Fazel, M.; Ren, Y.; Niu, W.; Clark, N. A.; White, S.; Mahi, N.; Zhang, L.; Kouril, M.; Reichard, J. F.; Sivaganesan, S.; Medvedovic, M.; Meller, J.; Koch, R. J.; Birtwistle, M. R.; Iyengar, R.; Sobie, E. A.; Azeloglu, E. U.; Kaye, J.; Osterloh, J.; Haston, K.; Kalra, J.; Finkbiener, S.; Li, J.; Milani, P.; Adam, M.; Escalante-Chong, R.; Sachs, K.; Lenail, A.; Ramamoorthy, D.; Fraenkel, E.; Daigle, G.; Hussain, U.; Coye, A.; Rothstein, J.; Sareen, D.; Ornelas, L.; Banuelos, M.; Mandefro, B.; Ho, R.; Svendsen, C. N.; Lim, R. G.; Stocksdale, J.; Casale, M. S.; Thompson, T. G.; Wu, J.; Thompson, L. M.; Dardov, V.; Venkatraman, V.; Matlock, A.; Van Eyk, J. E.; Jaffe, J. D.; Papanastasiou, M.; Subramanian, A.; Golub, T. R.; Erickson, S. D.; Fallahi-Sichani, M.; Hafner, M.; Gray, N. S.; Lin, J. R.; Mills, C. E.; Muhlich, J. L.; Niepel, M.; Shamu, C. E.; Williams, E. H.; W 2018. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations Cell Syst, 6 1 , 13-24

Koleti, A.; Terryn, R.; Stathias, V.; Chung, C.; Cooper, D. J.; Turner, J. P.; Vidovic, D.; Forlin, M.; Kelley, T. T.; D'Urso, A.; Allen, B. K.; Torre, D.; Jagodnik, K. M.; Wang, L.; Jenkins, S. L.; Mader, C.; Niu, W.; Fazel, M.; Mahi, N.; Pilarczyk, M.; Clark, N.; Shamsaei, B.; Meller, J.; Vasiliauskas, J.; Reichard, J.; Medvedovic, M.; Ma'ayan, A.; Pillai, A.; Schurer, S. C. 2018. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data Nucleic Acids Res, 46 D1 , D558-D566

Leung, Y. K.; Ouyang, B.; Niu, L.; Xie, C.; Ying, J.; Medvedovic, M.; Chen, A.; Weihe, P.; Valvi, D.; Grandjean, P.; Ho, S. M. 2018. Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort Epigenetics, 24 7 , 1-32

VonHandorf, A.; Sanchez-Martin, F. J.; Biesiada, J.; Zhang, H.; Zhang, X.; Medvedovic, M.; Puga, A. 2018. Chromium disrupts chromatin organization and CTCF access to its cognate sites in promoters of differentially expressed genes Epigenetics, 7 157 , 1-32

Abdel-Hameed, E. A.; Rouster, S. D.; Zhang, X.; Chen, J.; Medvedovic, M.; Goodman, Z. D.; Sherman, K. E. 2017. Characterization of HCV NS3 Protease Variants in HCV/HIV-Coinfected Patients by Ultra-Deep Sequence Analysis: Relationship with Hepatic Fibrosis J Acquir Immune Defic Syndr, 74 3 , 353-358

Bertaux-Skeirik, N.; Wunderlich, M.; Teal, E.; Chakrabarti, J.; Biesiada, J.; Mahe, M.; Sundaram, N.; Gabre, J.; Hawkins, J.; Jian, G.; Engevik, A. C.; Yang, L.; Wang, J.; Goldenring, J. R.; Qualls, J. E.; Medvedovic, M.; Helmrath, M. A.; Diwan, T.; Mulloy, J. C.; Zavros, Y. 2017. CD44 variant isoform 9 emerges in response to injury and contributes to the regeneration of the gastric epithelium J Pathol, 242 4 , 463-475

Clark, N. A.; Hafner, M.; Kouril, M.; Williams, E. H.; Muhlich, J. L.; Pilarczyk, M.; Niepel, M.; Sorger, P. K.; Medvedovic, M. 2017. GRcalculator: an online tool for calculating and mining dose-response data BMC Cancer, 17 1 , 698

Frank, E. A.; Carreira, V. S.; Shanmukhappa, K.; Medvedovic, M.; Prows, D. R.; Yadav, J. S. 2017. Genetic susceptibility to toxicologic lung responses among inbred mouse strains following exposure to carbon nanotubes and profiling of underlying gene networks Toxicol Appl Pharmacol, 327 9 , 59-70

Heymann, P. W.; Nguyen, H. T.; Steinke, J. W.; Turner, R. B.; Woodfolk, J. A.; Platts-Mills, T. A. E.; Martin, L.; He, H.; Biagini Myers, J.; Lindsey, M.; Sivaprasad, U.; Medvedovic, M.; Mahi, N.; Carper, H.; Murphy, D. D.; Patrie, J.; Khurana Hershey, G. K. 2017. Rhinovirus infection results in stronger and more persistent genomic dysregulation: Evidence for altered innate immune response in asthmatics at baseline, early in infection, and during convalescence PLoS One, 12 5 , e0178096

Langevin, S.; Kuhnell, D.; Parry, T.; Biesiada, J.; Huang, S.; Wise-Draper, T.; Casper, K.; Zhang, X.; Medvedovic, M.; Kasper, S. 2017. Comprehensive microRNA-sequencing of exosomes derived from head and neck carcinoma cells in vitro reveals common secretion profiles and potential utility as salivary biomarkers Oncotarget, 8 47 , 82459-82474

Leung, Y. K.; Govindarajah, V.; Cheong, A.; Veevers, J.; Song, D.; Gear, R.; Zhu, X.; Ying, J.; Kendler, A.; Medvedovic, M.; Belcher, S.; Ho, S. M. 2017. Gestational high-fat diet and bisphenol A exposure heightens mammary cancer risk Endocr Relat Cancer, 24 7 , 365-378

Moncrieffe, H.; Bennett, M. F.; Tsoras, M.; Luyrink, L. K.; Johnson, A. L.; Xu, H.; Dare, J.; Becker, M. L.; Prahalad, S.; Rosenkranz, M.; O'Neil, K. M.; Nigrovic, P. A.; Griffin, T. A.; Lovell, D. J.; Grom, A. A.; Medvedovic, M.; Thompson, S. D. 2017. Transcriptional profiles of JIA patient blood with subsequent poor response to methotrexate Rheumatology (Oxford), 56 9 , 1542-1551

Singh, B.; Jegga, A. G.; Shanmukhappa, K. S.; Edukulla, R.; Khurana Hershey, G. K.; Medvedovic, M.; Dillon, S. R.; Madala, S. K. 2017. Correction: IL-31-Driven Skin Remodeling Involves Epidermal Cell Proliferation and Thickening That Lead to Impaired Skin-Barrier Function PLoS One, 12 1 , e0170446

Vairamani, K.; Wang, H. S.; Medvedovic, M.; Lorenz, J. N.; Shull, G. E. 2017. RNA SEQ Analysis Indicates that the AE3 Cl(-)/HCO3(-) Exchanger Contributes to Active Transport-Mediated CO2 Disposal in Heart Sci Rep, 7 1 , 7264

Whitson, J. A.; Zhang, X.; Medvedovic, M.; Chen, J.; Wei, Z.; Monnier, V. M.; Fan, X. 2017. Transcriptome of the GSH-Depleted Lens Reveals Changes in Detoxification and EMT Signaling Genes, Transport Systems, and Lipid Homeostasis Invest Ophthalmol Vis Sci, 58 5 , 2666-2684

Chen, L.; Peng, Z.; Meng, Q.; Mongan, M.; Wang, J.; Sartor, M.; Chen, J.; Niu, L.; Medvedovic, M.; Kao, W.; Xia, Y. 2016. Loss of IkappaB kinase beta promotes myofibroblast transformation and senescence through activation of the ROS-TGFbeta autocrine loop Protein Cell, 7 5 , 338-50

Cheong, A.; Zhang, X.; Cheung, Y. Y.; Tang, W. Y.; Chen, J.; Ye, S. H.; Medvedovic, M.; Leung, Y. K.; Prins, G. S.; Ho, S. M. 2016. DNA methylome changes by estradiol benzoate and bisphenol A links early-life environmental exposures to prostate cancer risk Epigenetics, 11 9 , 674-689

Engevik, A. C.; Feng, R.; Choi, E.; White, S.; Bertaux-Skeirik, N.; Li, J.; Mahe, M. M.; Aihara, E.; Yang, L.; DiPasquale, B.; Oh, S.; Engevik, K. A.; Giraud, A. S.; Montrose, M. H.; Medvedovic, M.; Helmrath, M. A.; Goldenring, J. R.; Zavros, Y. 2016. The Development of Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) During Gastric Repair Is Absent in the Aged Stomach Cell Mol Gastroenterol Hepatol, 2 5 , 605-624

Govindarajah, V.; Leung, Y. K.; Ying, J.; Gear, R.; Bornschein, R. L.; Medvedovic, M.; Ho, S. M. 2016. In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands J Nutr Biochem, 29 6 , 73-82

Jodele, S.; Zhang, K.; Zou, F.; Laskin, B.; Dandoy, C. E.; Myers, K. C.; Lane, A.; Meller, J.; Medvedovic, M.; Chen, J.; Davies, S. M. 2016. The genetic fingerprint of susceptibility for transplant-associated thrombotic microangiopathy Blood, 127 8 , 989-96

Lam, H. M.; Ho, S. M.; Chen, J.; Medvedovic, M.; Tam, N. N. 2016. Bisphenol A Disrupts HNF4alpha-Regulated Gene Networks Linking to Prostate Preneoplasia and Immune Disruption in Noble Rats Endocrinology, 157 1 , 207-19

Singh, B.; Jegga, A. G.; Shanmukhappa, K. S.; Edukulla, R.; Khurana Hershey, G. H.; Medvedovic, M.; Dillon, S. R.; Madala, S. K. 2016. IL-31-Driven Skin Remodeling Involves Epidermal Cell Proliferation and Thickening That Lead to Impaired Skin-Barrier Function PLoS One, 11 8 , e0161877

Sun, X.; Medvedovic, M. 2016. Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks IET Syst Biol, 10 1 , 10-6

Wang, Q.; Kurita, H.; Carreira, V.; Ko, C. I.; Fan, Y.; Zhang, X.; Biesiada, J.; Medvedovic, M.; Puga, A. 2016. Ah Receptor Activation by Dioxin Disrupts Activin, BMP, and WNT Signals During the Early Differentiation of Mouse Embryonic Stem Cells and Inhibits Cardiomyocyte Functions Toxicol Sci, 149 2 , 346-57

Wang, Q.; Trevino, L. S.; Wong, R. L.; Medvedovic, M.; Chen, J.; Ho, S. M.; Shen, J.; Foulds, C. E.; Coarfa, C.; O'Malley, B. W.; Shilatifard, A.; Walker, C. L. 2016. Reprogramming of the Epigenome by MLL1 Links Early-Life Environmental Exposures to Prostate Cancer Risk Mol Endocrinol, 30 8 , 856-71

Carreira, V. S.; Fan, Y.; Kurita, H.; Wang, Q.; Ko, C. I.; Naticchioni, M.; Jiang, M.; Koch, S.; Zhang, X.; Biesiada, J.; Medvedovic, M.; Xia, Y.; Rubinstein, J.; Puga, A. 2015. Disruption of Ah Receptor Signaling during Mouse Development Leads to Abnormal Cardiac Structure and Function in the Adult PLoS One, 10 11 , e0142440

Carreira, V. S.; Fan, Y.; Wang, Q.; Zhang, X.; Kurita, H.; Ko, C. I.; Naticchioni, M.; Jiang, M.; Koch, S.; Medvedovic, M.; Xia, Y.; Rubinstein, J.; Puga, A. 2015. Ah Receptor Signaling Controls the Expression of Cardiac Development and Homeostasis Genes Toxicol Sci, 147 2 , 425-35

Ho, S. M.; Cheong, A.; Lam, H. M.; Hu, W. Y.; Shi, G. B.; Zhu, X.; Chen, J.; Zhang, X.; Medvedovic, M.; Leung, Y. K.; Prins, G. S. 2015. Exposure of Human Prostaspheres to Bisphenol A Epigenetically Regulates SNORD Family Noncoding RNAs via Histone Modification Endocrinology, 156 11 , 3984-95

Sanchez-Martin, F. J.; Lindquist, D. M.; Landero-Figueroa, J.; Zhang, X.; Chen, J.; Cecil, K. M.; Medvedovic, M.; Puga, A. 2015. Sex- and tissue-specific methylome changes in brains of mice perinatally exposed to lead Neurotoxicology, 46 1 , 92-100

Sivaprasad, U.; Kinker, K. G.; Ericksen, M. B.; Lindsey, M.; Gibson, A. M.; Bass, S. A.; Hershey, N. S.; Deng, J.; Medvedovic, M.; Khurana Hershey, G. K. 2015. SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis J Invest Dermatol, 135 1 , 160-169

Sontake, V.; Shanmukhappa, S. K.; DiPasquale, B. A.; Reddy, G. B.; Medvedovic, M.; Hardie, W. D.; White, E. S.; Madala, S. K. 2015. Fibrocytes Regulate Wilms Tumor 1-Positive Cell Accumulation in Severe Fibrotic Lung Disease J Immunol, 195 8 , 3978-91

Wong, R. L.; Wang, Q.; Trevino, L. S.; Bosland, M. C.; Chen, J.; Medvedovic, M.; Prins, G. S.; Kannan, K.; Ho, S. M.; Walker, C. L. 2015. Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate Epigenetics, 10 2 , 127-34

Buhule, O. D.; Minster, R. L.; Hawley, N. L.; Medvedovic, M.; Sun, G.; Viali, S.; Deka, R.; McGarvey, S. T.; Weeks, D. E. 2014. Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale Front Genet, 5 1 , 354

Cheng, X. H.; Black, M.; Ustiyan, V.; Le, T.; Fulford, L.; Sridharan, A.; Medvedovic, M.; Kalinichenko, V. V.; Whitsett, J. A.; Kalin, T. V. 2014. SPDEF inhibits prostate carcinogenesis by disrupting a positive feedback loop in regulation of the Foxm1 oncogene PLoS Genet, 10 9 , e1004656

Kinker, K. G.; Gibson, A. M.; Bass, S. A.; Day, B. P.; Deng, J.; Medvedovic, M.; Figueroa, J. A.; Hershey, G. K.; Chen, W. 2014. Overexpression of dimethylarginine dimethylaminohydrolase 1 attenuates airway inflammation in a mouse model of asthma PLoS One, 9 1 , e85148

Lam, H. M.; Ouyang, B.; Chen, J.; Ying, J.; Wang, J.; Wu, C. L.; Jia, L.; Medvedovic, M.; Vessella, R. L.; Ho, S. M. 2014. Targeting GPR30 with G-1: a new therapeutic target for castration-resistant prostate cancer Endocr Relat Cancer, 21 6 , 903-14

Madala, S. K.; Edukulla, R.; Phatak, M.; Schmidt, S.; Davidson, C.; Acciani, T. H.; Korfhagen, T. R.; Medvedovic, M.; Lecras, T. D.; Wagner, K.; Hardie, W. D. 2014. Dual targeting of MEK and PI3K pathways attenuates established and progressive pulmonary fibrosis PLoS One, 9 1 , e86536

Meng, Q.; Jin, C.; Chen, Y.; Chen, J.; Medvedovic, M.; Xia, Y. 2014. Expression of signaling components in embryonic eyelid epithelium PLoS One, 9 2 , e87038

Ovesen, J. L.; Fan, Y.; Zhang, X.; Chen, J.; Medvedovic, M.; Xia, Y.; Puga, A. 2014. Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis uncovers broad changes in chromatin structure resulting from hexavalent chromium exposure PLoS One, 9 5 , e97849

Ovesen, J. L.; Fan, Y.; Chen, J.; Medvedovic, M.; Xia, Y.; Puga, A. 2014. Long-term exposure to low-concentrations of Cr(VI) induce DNA damage and disrupt the transcriptional response to benzo[a]pyrene Toxicology, 316 5489 , 14-24

Bastola, P.; Stratton, Y.; Kellner, E.; Mikhaylova, O.; Yi, Y.; Sartor, M. A.; Medvedovic, M.; Biesiada, J.; Meller, J.; Czyzyk-Krzeska, M. F. 2013. Folliculin contributes to VHL tumor suppressing activity in renal cancer through regulation of autophagy PLoS One, 8 7 , e70030

Chen, J.; Hu, Z.; Phatak, M.; Reichard, J.; Freudenberg, J. M.; Sivaganesan, S.; Medvedovic, M. 2013. Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules PLoS Comput Biol, 9 9 , e1003198

Jin, C.; Chen, J.; Meng, Q.; Carreira, V.; Tam, N. N.; Geh, E.; Karyala, S.; Ho, S. M.; Zhou, X.; Medvedovic, M.; Xia, Y. 2013. Deciphering gene expression program of MAP3K1 in mouse eyelid morphogenesis Dev Biol, 374 1 , 96-107

Kim, J. Y.; Valencia, T.; Abu-Baker, S.; Linares, J.; Lee, S. J.; Yajima, T.; Chen, J.; Eroshkin, A.; Castilla, E. A.; Brill, L. M.; Medvedovic, M.; Leitges, M.; Moscat, J.; Diaz-Meco, M. T. 2013. c-Myc phosphorylation by PKCzeta represses prostate tumorigenesis Proc Natl Acad Sci U S A, 110 16 , 6418-23

Ma, L.; Tao, Y.; Duran, A.; Llado, V.; Galvez, A.; Barger, J. F.; Castilla, E. A.; Chen, J.; Yajima, T.; Porollo, A.; Medvedovic, M.; Brill, L. M.; Plas, D. R.; Riedl, S. J.; Leitges, M.; Diaz-Meco, M. T.; Richardson, A. D.; Moscat, J. 2013. Control of nutrient stress-induced metabolic reprogramming by PKCzeta in tumorigenesis Cell, 152 3 , 599-611

Shioda, T.; Rosenthal, N. F.; Coser, K. R.; Suto, M.; Phatak, M.; Medvedovic, M.; Carey, V. J.; Isselbacher, K. J. 2013. Expressomal approach for comprehensive analysis and visualization of ligand sensitivities of xenoestrogen responsive genes Proc Natl Acad Sci U S A, 110 41 , 16508-13

Wang, Q.; Chen, J.; Ko, C. I.; Fan, Y.; Carreira, V.; Chen, Y.; Xia, Y.; Medvedovic, M.; Puga, A. 2013. Disruption of aryl hydrocarbon receptor homeostatic levels during embryonic stem cell differentiation alters expression of homeobox transcription factors that control cardiomyogenesis Environ Health Perspect, 121 11-12 , 1334-43

Kim, D. H.; Sartor, M. A.; Bain, J. R.; Sandoval, D.; Stevens, R. D.; Medvedovic, M.; Newgard, C. B.; Woods, S. C.; Seeley, R. J. 2012. Rapid and weight-independent improvement of glucose tolerance induced by a peptide designed to elicit apoptosis in adipose tissue endothelium Diabetes, 61 9 , 2299-310

Leikauf, G. D.; Pope-Varsalona, H.; Concel, V. J.; Liu, P.; Bein, K.; Berndt, A.; Martin, T. M.; Ganguly, K.; Jang, A. S.; Brant, K. A.; Dopico, R. A., Jr.; Upadhyay, S.; Di, Y. P.; Li, Q.; Hu, Z.; Vuga, L. J.; Medvedovic, M.; Kaminski, N.; You, M.; Alexander, D. C.; McDunn, J. E.; Prows, D. R.; Knoell, D. L.; Fabisiak, J. P. 2012. Integrative assessment of chlorine-induced acute lung injury in mice Am J Respir Cell Mol Biol, 47 2 , 234-44

Wang, X.; Zhu, H.; Zhang, X.; Liu, Y.; Chen, J.; Medvedovic, M.; Li, H.; Weiss, M. J.; Ren, X.; Fan, G. C. 2012. Loss of the miR-144/451 cluster impairs ischaemic preconditioning-mediated cardioprotection by targeting Rac-1 Cardiovasc Res, 94 2 , 379-90

Fabisiak, J. P.; Medvedovic, M.; Alexander, D. C.; McDunn, J. E.; Concel, V. J.; Bein, K.; Jang, A. S.; Berndt, A.; Vuga, L. J.; Brant, K. A.; Pope-Varsalona, H.; Dopico, R. A., Jr.; Ganguly, K.; Upadhyay, S.; Li, Q.; Hu, Z.; Kaminski, N.; Leikauf, G. D. 2011. Integrative metabolome and transcriptome profiling reveals discordant energetic stress between mouse strains with differential sensitivity to acrolein-induced acute lung injury Mol Nutr Food Res, 55 9 , 1423-34

Freudenberg, J. M.; Sivaganesan, S.; Phatak, M.; Shinde, K.; Medvedovic, M. 2011. Generalized random set framework for functional enrichment analysis using primary genomics datasets Bioinformatics, 27 1 , 70-7

Howard, T. D.; Ho, S. M.; Zhang, L.; Chen, J.; Cui, W.; Slager, R.; Gray, S.; Hawkins, G. A.; Medvedovic, M.; Wagner, J. D. 2011. Epigenetic changes with dietary soy in cynomolgus monkeys PLoS One, 6 10 , e26791

Joshi, V. K.; Freudenberg, J. M.; Hu, Z.; Medvedovic, M. 2011. WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results Source Code Biol Med, 6 8 , 3

Knauf, J. A.; Sartor, M. A.; Medvedovic, M.; Lundsmith, E.; Ryder, M.; Salzano, M.; Nikiforov, Y. E.; Giordano, T. J.; Ghossein, R. A.; Fagin, J. A. 2011. Progression of BRAF-induced thyroid cancer is associated with epithelial-mesenchymal transition requiring concomitant MAP kinase and TGFbeta signaling Oncogene, 30 28 , 3153-62

Leikauf, G. D.; Concel, V. J.; Liu, P.; Bein, K.; Berndt, A.; Ganguly, K.; Jang, A. S.; Brant, K. A.; Dietsch, M.; Pope-Varsalona, H.; Dopico, R. A., Jr.; Di, Y. P.; Li, Q.; Vuga, L. J.; Medvedovic, M.; Kaminski, N.; You, M.; Prows, D. R. 2011. Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1 Am J Respir Crit Care Med, 183 11 , 1499-509

SenthamaraiKannan, P.; Sartor, M. A.; O'Connor, K. T.; Neumann, J. C.; Klyza, J. P., Jr.; Succop, P. A.; Wagner, B. D.; Karyala, S.; Medvedovic, M.; Menon, A. G. 2011. Identification of maternally regulated fetal gene networks in the placenta with a novel embryo transfer system in mice Physiol Genomics, 43 7 , 317-24

Wilhide, M. E.; Tranter, M.; Ren, X.; Chen, J.; Sartor, M. A.; Medvedovic, M.; Jones, W. K. 2011. Identification of a NF-kappaB cardioprotective gene program: NF-kappaB regulation of Hsp70.1 contributes to cardioprotection after permanent coronary occlusion J Mol Cell Cardiol, 51 1 , 82-9

Freudenberg, J. M.; Sivaganesan, S.; Wagner, M.; Medvedovic, M. 2010. A semi-parametric Bayesian model for unsupervised differential co-expression analysis BMC Bioinformatics, 11 1 , 234

Leikauf, G. D.; Pope-Varsalona, H.; Concel, V. J.; Liu, P.; Bein, K.; Brant, K. A.; Dopico, R. A.; Di, Y. P.; Jang, A. S.; Dietsch, M.; Medvedovic, M.; Li, Q.; Vuga, L. J.; Kaminski, N.; You, M.; Prows, D. R. 2010. Functional genomics of chlorine-induced acute lung injury in mice Proc Am Thorac Soc, 7 4 , 294-6

Shinde, K.; Phatak, M.; Johannes, F. M.; Chen, J.; Li, Q.; Vineet, J. K.; Hu, Z.; Ghosh, K.; Meller, J.; Medvedovic, M. 2010. Genomics Portals: integrative web-platform for mining genomics data BMC Genomics, 11 7 , 27

Stark, J. M.; Barmada, M. M.; Winterberg, A. V.; Majumber, N.; Gibbons, W. J., Jr.; Stark, M. A.; Sartor, M. A.; Medvedovic, M.; Kolls, J.; Bein, K.; Mailaparambil, B.; Krueger, M.; Heinzmann, A.; Leikauf, G. D.; Prows, D. R. 2010. Genomewide association analysis of respiratory syncytial virus infection in mice J Virol, 84 5 , 2257-69

Tam, N. N.; Szeto, C. Y.; Freudenberg, J. M.; Fullenkamp, A. N.; Medvedovic, M.; Ho, S. M. 2010. Research resource: estrogen-driven prolactin-mediated gene-expression networks in hormone-induced prostatic intraepithelial neoplasia Mol Endocrinol, 24 11 , 2207-17

Tranter, M.; Ren, X.; Forde, T.; Wilhide, M. E.; Chen, J.; Sartor, M. A.; Medvedovic, M.; Jones, W. K. 2010. NF-kappaB driven cardioprotective gene programs; Hsp70.3 and cardioprotection after late ischemic preconditioning J Mol Cell Cardiol, 49 4 , 664-72

Wang, X.; Zhang, X.; Ren, X. P.; Chen, J.; Liu, H.; Yang, J.; Medvedovic, M.; Hu, Z.; Fan, G. C. 2010. MicroRNA-494 targeting both proapoptotic and antiapoptotic proteins protects against ischemia/reperfusion-induced cardiac injury Circulation, 122 13 , 1308-18

Bein, K.; Wesselkamper, S. C.; Liu, X.; Dietsch, M.; Majumder, N.; Concel, V. J.; Medvedovic, M.; Sartor, M. A.; Henning, L. N.; Venditto, C.; Borchers, M. T.; Barchowsky, A.; Weaver, T. E.; Tichelaar, J. W.; Prows, D. R.; Korfhagen, T. R.; Hardie, W. D.; Bachurski, C. J.; Leikauf, G. D. 2009. Surfactant-associated protein B is critical to survival in nickel-induced injury in mice Am J Respir Cell Mol Biol, 41 2 , 226-36

Borchers, M. T.; Wesselkamper, S. C.; Deshmukh, H.; Beckman, E.; Medvedovic, M.; Sartor, M.; Leikauf, G. D.; H. E. I. Health Review Committee 2009. The role of T cells in the regulation of acrolein-induced pulmonary inflammation and epithelial-cell pathology Res Rep Health Eff Inst, 30 146 , 5-29

Freudenberg, J. M.; Joshi, V. K.; Hu, Z.; Medvedovic, M. 2009. CLEAN: CLustering Enrichment ANalysis BMC Bioinformatics, 10 9 , 234

Gandhi, M. S.; Stringer, J. R.; Nikiforova, M. N.; Medvedovic, M.; Nikiforov, Y. E. 2009. Gene position within chromosome territories correlates with their involvement in distinct rearrangement types in thyroid cancer cells Genes Chromosomes Cancer, 48 3 , 222-8

Genter, M. B.; Warner, B. M.; Medvedovic, M.; Sartor, M. A. 2009. Comparison of rat olfactory mucosal responses to carcinogenic and non-carcinogenic chloracetanilides Food Chem Toxicol, 47 6 , 1051-7

Medvedovic, M.; Gear, R.; Freudenberg, J. M.; Schneider, J.; Bornschein, R.; Yan, M.; Mistry, M. J.; Hendrix, H.; Karyala, S.; Halbleib, D.; Heffelfinger, S.; Clegg, D. J.; Anderson, M. W. 2009. Influence of fatty acid diets on gene expression in rat mammary epithelial cells Physiol Genomics, 38 1 , 80-8

Medvedovic, M.; Halbleib, D.; Miller, M. L.; LaDow, K.; Sartor, M. A.; Tomlinson, C. R. 2009. Gene expression profiling of blood to predict the onset of leukemia Blood Cells Mol Dis, 42 1 , 64-70

Sartor, M. A.; Leikauf, G. D.; Medvedovic, M. 2009. LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data Bioinformatics, 25 2 , 211-7

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.; Puga, A. 2009. Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs Environ Health Perspect, 117 7 , 1139-46

Zhang, X.; Leav, I.; Revelo, M. P.; Deka, R.; Medvedovic, M.; Jiang, Z.; Ho, S. M. 2009. Deletion hotspots in AMACR promoter CpG island are cis-regulatory elements controlling the gene expression in the colon PLoS Genet, 5 1 , e1000334

Bakshi, S.; Zhang, X.; Godoy-Tundidor, S.; Cheng, R. Y.; Sartor, M. A.; Medvedovic, M.; Ho, S. M. 2008. 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 6 , 769-76

Borchers, M. T.; Wesselkamper, S. C.; Eppert, B. L.; Motz, G. T.; Sartor, M. A.; Tomlinson, C. R.; Medvedovic, M.; Tichelaar, J. W. 2008. Nonredundant functions of alphabeta and gammadelta T cells in acrolein-induced pulmonary pathology Toxicol Sci, 105 1 , 188-99

Tam, N. N.; Szeto, C. Y.; Sartor, M. A.; Medvedovic, M.; Ho, S. M. 2008. Gene expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17beta-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats Neoplasia, 10 1 , 20-40

Tang, W. Y.; Newbold, R.; Mardilovich, K.; Jefferson, W.; Cheng, R. Y.; Medvedovic, M.; Ho, S. M. 2008. Persistent hypomethylation in the promoter of nucleosomal binding protein 1 (Nsbp1) correlates with overexpression of Nsbp1 in mouse uteri neonatally exposed to diethylstilbestrol or genistein Endocrinology, 149 12 , 5922-31

Ganguly, K.; Stoeger, T.; Wesselkamper, S. C.; Reinhard, C.; Sartor, M. A.; Medvedovic, M.; Tomlinson, C. R.; Bolle, I.; Mason, J. M.; Leikauf, G. D.; Schulz, H. 2007. Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure Physiol Genomics, 31 3 , 410-21

Hardie, W. D.; Korfhagen, T. R.; Sartor, M. A.; Prestridge, A.; Medvedovic, M.; Le Cras, T. D.; Ikegami, M.; Wesselkamper, S. C.; Davidson, C.; Dietsch, M.; Nichols, W.; Whitsett, J. A.; Leikauf, G. D. 2007. Genomic profile of matrix and vasculature remodeling in TGF-alpha induced pulmonary fibrosis Am J Respir Cell Mol Biol, 37 3 , 309-21

Liu, X.; Jessen, W. J.; Sivaganesan, S.; Aronow, B. J.; Medvedovic, M. 2007. Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data BMC Bioinformatics, 8 4 , 283

Popa, I.; Zubkova, I.; Medvedovic, M.; Romantseva, T.; Mostowski, H.; Boyd, R.; Zaitseva, M. 2007. Regeneration of the adult thymus is preceded by the expansion of K5+K8+ epithelial cell progenitors and by increased expression of Trp63, cMyc and Tcf3 transcription factors in the thymic stroma Int Immunol, 19 11 , 1249-60

Erwin, C. R.; Jarboe, M. D.; Sartor, M. A.; Medvedovic, M.; Stringer, K. F.; Warner, B. W.; Bates, M. D. 2006. Developmental characteristics of adapting mouse small intestine crypt cells Gastroenterology, 130 4 , 1324-32

Gandhi, M.; Medvedovic, M.; Stringer, J. R.; Nikiforov, Y. E. 2006. Interphase chromosome folding determines spatial proximity of genes participating in carcinogenic RET/PTC rearrangements Oncogene, 25 16 , 2360-6

Icenhour, C. R.; Arnold, J.; Medvedovic, M.; Cushion, M. T. 2006. Competitive coexistence of two Pneumocystis species Infect Genet Evol, 6 3 , 177-86

Liu, X.; Sivaganesan, S.; Yeung, K. Y.; Guo, J.; Bumgarner, R. E.; Medvedovic, M. 2006. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset Bioinformatics, 22 14 , 1737-44

Medvedovic, M.; Tomlinson, C. R.; Call, M. K.; Grogg, M.; Tsonis, P. A. 2006. Gene expression and discovery during lens regeneration in mouse: regulation of epithelial to mesenchymal transition and lens differentiation Mol Vis, 12 9 , 422-40

Mesa, C., Jr.; Mirza, M.; Mitsutake, N.; Sartor, M.; Medvedovic, M.; Tomlinson, C.; Knauf, J. A.; Weber, G. F.; Fagin, J. A. 2006. Conditional activation of RET/PTC3 and BRAFV600E in thyroid cells is associated with gene expression profiles that predict a preferential role of BRAF in extracellular matrix remodeling Cancer Res, 66 13 , 6521-9

Sartor, M. A.; Zorn, A. M.; Schwanekamp, J. A.; Halbleib, D.; Karyala, S.; Howell, M. L.; Dean, G. E.; Medvedovic, M.; Tomlinson, C. R. 2006. 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 Res, 34 1 , 185-200

Sartor, M. A.; Tomlinson, C. R.; Wesselkamper, S. C.; Sivaganesan, S.; Leikauf, G. D.; Medvedovic, M. 2006. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments BMC Bioinformatics, 7 7 , 538

Schwanekamp, J. A.; Sartor, M. A.; Karyala, S.; Halbleib, D.; Medvedovic, M.; Tomlinson, C. R. 2006. Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin Biochim Biophys Acta, 1759 8-9 , 388-402

Wesselkamper, S. C.; McDowell, S. A.; Medvedovic, M.; Dalton, T. P.; Deshmukh, H. S.; Sartor, M. A.; Case, L. M.; Henning, L. N.; Borchers, M. T.; Tomlinson, C. R.; Prows, D. R.; Leikauf, G. D. 2006. The role of metallothionein in the pathogenesis of acute lung injury Am J Respir Cell Mol Biol, 34 1 , 73-82

Puxeddu, E.; Knauf, J. A.; Sartor, M. A.; Mitsutake, N.; Smith, E. P.; Medvedovic, M.; Tomlinson, C. R.; Moretti, S.; Fagin, J. A. 2005. 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

Puxeddu, E.; Zhao, G.; Stringer, J. R.; Medvedovic, M.; Moretti, S.; Fagin, J. A. 2005. 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, 570 1 , 17-32

Stringer, J. R.; Larson, J. S.; Fischer, J. M.; Medvedovic, M.; Hersh, M. N.; Boivin, G. P.; Stringer, S. L. 2005. Modeling variation in tumors in vivo Proc Natl Acad Sci U S A, 102 7 , 2408-13

Wesselkamper, S. C.; Case, L. M.; Henning, L. N.; Borchers, M. T.; Tichelaar, J. W.; Mason, J. M.; Dragin, N.; Medvedovic, M.; Sartor, M. A.; Tomlinson, C. R.; Leikauf, G. D. 2005. Gene expression changes during the development of acute lung injury: role of transforming growth factor beta Am J Respir Crit Care Med, 172 11 , 1399-411

Bahassi el, M.; Karyala, S.; Tomlinson, C. R.; Sartor, M. A.; Medvedovic, M.; Hennigan, R. F. 2004. Critical regulation of genes for tumor cell migration by AP-1 Clin Exp Metastasis, 21 4 , 293-304

Guo, J.; Sartor, M.; Karyala, S.; Medvedovic, M.; Kann, S.; Puga, A.; Ryan, P.; Tomlinson, C. R. 2004. Expression of genes in the TGF-beta signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice Toxicol Appl Pharmacol, 194 1 , 79-89

Karyala, S.; Guo, J.; Sartor, M.; Medvedovic, M.; Kann, S.; Puga, A.; Ryan, P.; Tomlinson, C. R. 2004. Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice Cardiovasc Toxicol, 4 1 , 47-73

Medvedovic, M.; Yeung, K. Y.; Bumgarner, R. E. 2004. Bayesian mixture model based clustering of replicated microarray data Bioinformatics, 20 8 , 1222-32

Puga, A.; Sartor, M. A.; Huang, M. Y.; Kerzee, J. K.; Wei, Y. D.; Tomlinson, C. R.; Baxter, C. S.; Medvedovic, M. 2004. Gene expression profiles of mouse aorta and cultured vascular smooth muscle cells differ widely, yet show common responses to dioxin exposure Cardiovasc Toxicol, 4 4 , 385-404

Sartor, M.; Schwanekamp, J.; Halbleib, D.; Mohamed, I.; Karyala, S.; Medvedovic, M.; Tomlinson, C. R. 2004. Microarray results improve significantly as hybridization approaches equilibrium Biotechniques, 36 5 , 790-6

Sonntag, D. M.; de Boer, J.; Medvedovic, M.; Baxter, C. S.; LeMasters, G.; Talaska, G. 2004. Mutational biases associated with potential iron-binding DNA motifs in rodent lacI and human p53 mutational databases Mutat Res, 550 1-2 , 73-88

Vineis, P.; Schulte, P. A.; Carreon, T.; Bailer, A. J.; Medvedovic, M. 2004. Issues of design and analysis in studies of gene-environment interactions IARC Sci Publ, 7 157 , 417-35

Yeung, K. Y.; Medvedovic, M.; Bumgarner, R. E. 2004. From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol, 5 7 , R48

Zhang, J.; Moseley, A.; Jegga, A. G.; Gupta, A.; Witte, D. P.; Sartor, M.; Medvedovic, M.; Williams, S. S.; Ley-Ebert, C.; Coolen, L. M.; Egnaczyk, G.; Genter, M. B.; Lehman, M.; Lingrel, J.; Maggio, J.; Parysek, L.; Walsh, R.; Xu, M.; Aronow, B. J. 2004. Neural system-enriched gene expression: relationship to biological pathways and neurological diseases Physiol Genomics, 18 2 , 167-83

Tsuneoka, Y.; Dalton, T. P.; Miller, M. L.; Clay, C. D.; Shertzer, H. G.; Talaska, G.; Medvedovic, M.; Nebert, D. W. 2003. 4-aminobiphenyl-induced liver and urinary bladder DNA adduct formation in Cyp1a2(-/-) and Cyp1a2(+/+) mice J Natl Cancer Inst, 95 16 , 1227-37

Yeung, K. Y.; Medvedovic, M.; Bumgarner, R. E. 2003. Clustering gene-expression data with repeated measurements Genome Biol, 4 5 , R34

Knauf, J. A.; Ward, L. S.; Nikiforov, Y. E.; Nikiforova, M.; Puxeddu, E.; Medvedovic, M.; Liron, T.; Mochly-Rosen, D.; Fagin, J. A. 2002. Isozyme-specific abnormalities of PKC in thyroid cancer: evidence for post-transcriptional changes in PKC epsilon J Clin Endocrinol Metab, 87 5 , 2150-9

Medvedovic, M.; Sivaganesan, S. 2002. Bayesian infinite mixture model based clustering of gene expression profiles Bioinformatics, 18 9 , 1194-206

King, N. M.; Oakley, G. G.; Medvedovic, M.; Dixon, K. 2001. XPA protein alters the specificity of ultraviolet light-induced mutagenesis in vitro Environ Mol Mutagen, 37 4 , 329-39

Li, Y.; Carty, M. P.; Oakley, G. G.; Seidman, M. M.; Medvedovic, M.; Dixon, K. 2001. Expression of ATM in ataxia telangiectasia fibroblasts rescues defects in DNA double-strand break repair in nuclear extracts Environ Mol Mutagen, 37 2 , 128-40

Levin, L. S.; Rice, C. H.; Lemasters, G. K.; Lockey, J. E.; Medvedovic, M. 2000. What is the potential measurement error in occupational exposure studies? J Air Waste Manag Assoc, 50 6 , 941-7

Nikiforova, M. N.; Stringer, J. R.; Blough, R.; Medvedovic, M.; Fagin, J. A.; Nikiforov, Y. E. 2000. Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells Science, 290 5489 , 138-41

Puga, A.; Maier, A.; Medvedovic, M. 2000. The transcriptional signature of dioxin in human hepatoma HepG2 cells Biochem Pharmacol, 60 8 , 1129-42

Bhattacharya, A.; Warren, J.; Teuschler, J.; Dimov, M.; Medvedovic, M.; Lemasters, G. 1999. Development and evaluation of a microprocessor-based ergonomic dosimeter for evaluating carpentry tasks Appl Ergon, 30 6 , 543-53

Liu, S.; Medvedovic, M.; Dixon, K. 1999. Mutational specificity in a shuttle vector replicating in chromium(VI)-treated mammalian cells Environ Mol Mutagen, 33 4 , 313-9

McKay, R. T.; Levin, L. S.; Lockey, J. E.; Lemasters, G. K.; Medvedovic, M.; Papes, D. M.; Simpson, S. R.; Rice, C. H. 1999. Weight change and lung function: implications for workplace surveillance studies J Occup Environ Med, 41 7 , 596-604

Bhattacharya, A.; Smelser, D. T.; Berger, O.; Shukla, R.; Medvedovic, M. 1998. 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 1 , 57-64

Lockey, J. E.; Levin, L. S.; Lemasters, G. K.; McKay, R. T.; Rice, C. H.; Hansen, K. R.; Papes, D. M.; Simpson, S.; Medvedovic, M. 1998. Longitudinal estimates of pulmonary function in refractory ceramic fiber manufacturing workers Am J Respir Crit Care Med, 157 4 Pt 1 , 1226-33

Ward, L. S.; Brenta, G.; Medvedovic, M.; Fagin, J. A. 1998. Studies of allelic loss in thyroid tumors reveal major differences in chromosomal instability between papillary and follicular carcinomas J Clin Endocrinol Metab, 83 2 , 525-30

Smith, L. B.; Bhattacharya, A.; Lemasters, G.; Succop, P.; Puhala, E., 2nd; Medvedovic, M.; Joyce, J. 1997. Effect of chronic low-level exposure to jet fuel on postural balance of US Air Force personnel J Occup Environ Med, 39 7 , 623-32