Mario Medvedovic

Mario Medvedovic

Professor and Director, Division of Biostatistics and Bioinformatics

Kettering Lab Complex

110

COM EH Bio Medvedovic Lab - 0056

Kettering Laboratory
Room 110
Cincinnati, Ohio 45267

Professional Summary

Dr. Medvedovic is developing statistical and machine learning methods, computational tools and bioinformatics infrastructure for learning from omics data, and applying them in interdisciplinary biomedical research. His group has developed comprehensive protocols for data management, processing, statistical and systems biology analysis of RNA-seq data and several other NGS assays. They have also amassed a vast library of public domain omics datasets and signatues, and developed user-friendly tools their analysis (http://ilincs.org). As a leader of the Bioinformatics Core in the Center for Environmental Genetics for last 10 years, Dr. Medvedovic has been assisting investigators in converting their omics data into meaningful information through the use of appropriate data-management and computational/statistical methodologies. Dr. Medvedovic is also one of the principal investigators (MPI: Medvedovic, Ma’ayan, Schurer) of the multi-institutional (University of Cincinnati, Mt Sinai, University of Miami) U54 BD2K-LINCS Data Coordination and Integration Center. Data science research component of this project is focused on developing methods for leveraging LINCS perturbation data in identifying drivers of disease processes, and revealing mechanism of action of drugs and other chemical perturbagens based on their transcriptional signatures.​ 
 

Education

Master's Degree, University of Zagreb 1992 (Applied Math and Computer Science)

Master's Degree, Bowling Green State University 1994 (Applied Statistics)

Doctoral Degree, University of Cincinnati 1998 (Biostatistics)

Research Support

Grant: #R01 HG003749 Investigators:Medvedovic, Mario 07-01-2006 -12-31-2011 National Human Genome Research Institute Bayesian Mixture Modeling of Functional Genomics Data Role:PI $1,381,417.00 Closed Level:Federal

Grant: #SRS 001746 Investigators:Medvedovic, Mario 07-01-2005 -06-30-2007 Ohio Cancer Research Associates Global Gene Expression Profiles for the Very Early Prediction of Breast Cancer Role:PI $52,500.00 Closed Level:Private Non-Profit

Grant: #5-R21-HG-002849-02-A0-S0-E0 Investigators:Medvedovic, Mario 09-30-2003 -06-30-2006 National Human Genome Research Institute Computational Tools for Bayesian Mixture Modeling of Functional Genomic Data Role:PI $301,613.00 Closed Level:Federal

Grant: #1-R03-LM-008248-02-A0-S0-E0 Investigators:Medvedovic, Mario 04-01-2004 -03-31-2007 National Library of Medicine Joint Modeling of Genomic and Functional Genomic Data Role:PI $153,500.00 Closed Level:Federal

Grant: #U01 ES015675 / 0006165 Investigators:Borchers, Michael; Medvedovic, Mario; Tichelaar, Jay 07-01-2007 -05-31-2011 National Institute of Environmental Health Sciences Functional Genomics of Chemical-Induced Acute Lung Injury Role:Collaborator $111,619.00 Closed Level:Federal

Grant: #R21 ES013827 Investigators:Medvedovic, Mario 02-01-2006 -08-31-2007 National Institute of Environmental Health Sciences Role of Fetal TCDD-Activated AHR in Adult Heart Disease Role:PI $74,286.00 Closed Level:Federal

Grant: #004 / U01ES016003 Investigators:Medvedovic, Mario 07-01-2007 -05-31-2011 National Institute of Environmental Health Sciences Genomics and Proteomic Biomarkers of Biological Responses to Exposure Role:PI $105,268.00 Closed Level:Federal

Grant: #CHMC 104355 / DK078392 Investigators:Liu, Xiangdong; Medvedovic, Mario 08-01-2007 -05-31-2012 National Inst of Diabetes and Digestive and Kidney Disease Digestive Health Center: Bench to Bedside Research in Pediatric Digestive Disease Role:PI $20,447.00 Closed Level:Federal

Grant: #P30 ES006096-16A1 Investigators:Caruso, Joseph; Deka, Ranjan; Embi, Peter; Greis, Kenneth; Ho, Shuk Mei; Lemasters, Grace; Medvedovic, Mario; Meller, Jaroslaw; Nebert, Daniel; Pinney, Susan; Puga, Alvaro; Rohs, Amy; Woo, Daniel 04-01-2008 -03-31-2013 National Institute of Environmental Health Sciences Environmental Genetics Role:Collaborator $8,028,782.00 Active Level:Federal

Grant: #R21 LM009662 Investigators:Medvedovic, Mario 09-30-2008 -09-29-2011 National Library of Medicine Integrative Probabilistic Models for Identifying Transcriptional Modules Role:PI $373,500.00 Closed Level:Federal

Grant: #R56 ES006273 Investigators:Medvedovic, Mario; Puga, Alvaro 09-01-2009 -08-31-2011 National Institute of Environmental Health Sciences Molecular Mechanisms of Dioxin Action Role:Collaborator $453,870.00 Closed Level:Federal

Grant: #28751 / 98013852 / RC2 ES018789 Investigators:Ho, Shuk Mei; Medvedovic, Mario 09-24-2009 -08-31-2011 National Institute of Environmental Health Sciences Developmental Reprogramming of Prostate Carcinogenesis by BPA Role:Collaborator $729,951.00 Closed Level:Federal

Grant: #E4753 / RC2ES018758 Investigators:Ho, Shuk Mei; Medvedovic, Mario 09-21-2009 -06-30-2011 National Institute of Environmental Health Sciences Developmental Exposure to Low-Dose Bisphenol A and Human Prostate Cancer Role:Collaborator $466,390.00 Closed Level:Federal

Grant: #U01 ES019480 Investigators:Belcher, Scott; Ben-Jonathan, Nira; Ho, Shuk Mei; Levin, Linda; Medvedovic, Mario; Miller, Marian; Stambrook, Peter; Tso, Patrick P.W. 09-22-2010 -05-31-2015 National Institute of Environmental Health Sciences Susceptible Window of High Fat Diet/Bisphenol A Programming of Breast Cancer Risk Role:Collaborator $1,790,100.00 Active Level:Federal

Grant: #R01 ES006273 Investigators:Medvedovic, Mario; Puga, Alvaro 04-01-2011 -01-31-2016 National Institute of Environmental Health Sciences Molecular Mechanisms of Dioxin Action Role:Collaborator $1,275,591.00 Active Level:Federal

Grant: #R21 ES020048 Investigators:Medvedovic, Mario; Puga, Alvaro 06-09-2011 -05-31-2013 National Institute of Environmental Health Sciences Epigenetics of Lead Toxicity in Mouse Brain Role:Collaborator $440,475.00 Active Level:Federal

Grant: #R21 CA156042 Investigators:Ho, Shuk Mei; Levin, Linda; Medvedovic, Mario; Tam, Neville Ngai Chung 08-01-2011 -07-31-2014 National Cancer Institute Gene Methylation Targets for Prostate Cancer Prevention by Early Soy Exposure Role:Collaborator $375,623.00 Active Level:Federal

Grant: #U01HL111638 Investigators:Medvedovic, Mario; Reichard, John; Sivaganesan, Siva 09-24-2011 -06-30-2014 National Heart, Lung and Blood Institute Integrative Statistical Methods and Tools for Analysis of Perturbation Signatures Role:PI $1,111,422.00 Active Level:Federal

Grant: #U01ES020988 Investigators:Ho, Shuk Mei; Kendler, Ady; Leung, Yuet Kin; Medvedovic, Mario 09-19-2011 -05-31-2015 National Institute of Environmental Health Sciences Chronic Exposure to Bisphenol A and Uterine Cancer Risk Markers Role:Collaborator $524,179.00 Active Level:Federal

Grant: #130426 \ 2P01AR048929-06 Investigators:Medvedovic, Mario 09-01-2011 -08-30-2016 National Institute of Arthritis, Musculoskeletal and Skin Disease Gene Expression in Pediatric Arthritis Role:PI $245,245.00 Active Level:Federal

Grant: #2012-02586-01-00 \ R01ES022071 Investigators:Ho, Shuk Mei; Leung, Yuet Kin; Medvedovic, Mario 08-23-2012 -04-30-2017 National Institute of Environmental Health Sciences Effects of Arsenic on Human Prostate Stem Cells and Prostate Cancer Risk Role:Collaborator $154,665.00 Active Level:Federal

Grant: #11212355057091/ R01ES021477 Investigators:Ho, Shuk Mei; Leung, Yuet Kin; Medvedovic, Mario 02-01-2013 -10-31-2013 National Institute of Environmental Health Sciences Glucose Metabolism in Adults Prenatally Exposed to Diabetogenic Pollutants Role:Collaborator $32,671.00 Active Level:Federal

Grant: #R01 HL119190 Investigators:Cushion, Melanie; Medvedovic, Mario; Porollo, Alexey 05-22-2013 -02-28-2018 National Heart, Lung and Blood Institute Directed Culturing of Pneumocystis Using Metatranscriptomics Role:Collaborator $404,514.00 Active Level:Federal

Grant: #P30ES006096 Investigators:Caruso, Joseph; Chen, Aimin; Deka, Ranjan; Greis, Kenneth; Haynes, Erin; Ho, Shuk Mei; Lemasters, Grace; Leung, Yuet Kin; Medvedovic, Mario; Meller, Jaroslaw; Meloncon, Lisa; Pinney, Susan; Porollo, Alexey; Puga, Alvaro; Thomas, Michael; Woo, Daniel; Yadav, Jagjit; Yancey, Elissa 04-01-2013 -03-31-2018 National Institute of Environmental Health Sciences Environmental Genetics Role:Leader of Bioinformatics Core $1,743,768.00 Active

Grant: #W81XWH-14-1-0347 / CA130028 Investigators:Czyzyk-Krzeska, Maria; Medvedovic, Mario; Meller, Jaroslaw 09-30-2014 -09-29-2016 Department of the Army Medical Research Acquisition Activity CA130028-Effects of Tobacco Smoke (TS) on growth of clear cell renal cell carcinoma (ccRCC) Role:Collaborator $474,562.00 Awarded Level:Federal

Grant: #0255-7855-4609 / U54 HL127624 Investigators:Medvedovic, Mario; Meller, Jaroslaw; Sivaganesan, Siva 09-29-2014 -04-30-2019 National Heart, Lung and Blood Institute Data Coordination and Integration Center for LINCS-BD2K Role:PI $609,822.00 Active Level:Federal

Grant: #R56 HL128493 Investigators:Chen, Aimin; Deka, Ranjan; Langevin, Scott; Leung, Yuet Kin; Medvedovic, Mario 09-19-2016 -08-31-2017 National Heart, Lung and Blood Institute Integrated GWAS and EWAS of Cardiometabolic Traits in an Island Population Role:Collaborator $677,923.00 Active Level:Federal

Grant: #211-2017-M-94370 Investigators:Medvedovic, Mario 06-06-2017 -10-14-2018 Centers for Disease Control and Prevention Building Toxlcogenomics Database for Occupational Health Risk Assessment of Engineered Nanomaterials Role:PI $24,304.00 Active Level:Federal

Grant: #R21DE027227 Investigators:Kasper, Susan; Langevin, Scott; Medvedovic, Mario; Wise-Draper, Trisha; Zhang, Xiang 09-01-2017 -08-31-2019 National Institute of Dental and Craniofacial Research Exosomal miRNA as Salivary Biomarkers for HPV+ Head and Neck Carcinoma Role:Collaborator $239,250.00 Awarded Level:Federal

Grant: #ES010807 Investigators:Biesiada, Jacek; Medvedovic, Mario; Niu, Liang; Puga, Alvaro; Xia, Ying 09-30-2017 -06-30-2022 National Institute of Environmental Health Sciences Molecular Mechanisms of Complex Mixture Toxicity Role:Collaborator $445,504.00 Awarded Level:Federal

Grant: #LAM0133PB07-18 Investigators:Medvedovic, Mario; Yu, Jane 09-01-2018 -08-31-2019 Lymphangioleiomyomatosis Foundation (LAM) Single-Cell-RNA Sequencing for Identifying Differential Responses to Sirolimus Therapy in LAM Role:Collaborator $10,000.00 Active Level:Private Non-Profit

Grant: #R61DA048439 Investigators:Blackard, Jason; Brown, Jennifer; Lyons, Michael; Medvedovic, Mario; Sherman, Kenneth 03-01-2019 -12-31-2021 National Institutes of Health Omics analysis of HIV during synthetic opioid exposure Role:Collaborator $573,135.00 Awarded Level:Federal

Grant: #R01HD098106 Investigators:Medvedovic, Mario; Puga, Alvaro; Xia, Ying 04-09-2019 -03-31-2024 National Institute of Child Health and Human Development Gene-environment interactions in epithelial morphogenesis Role:Collaborator $463,850.00 Awarded Level:Federal

Grant: #75D30118P01991 NIOSH/CDC Investigators:Medvedovic, Mario 09-01-2018 -12-31-2020 Centers for Disease Control and Prevention Building Toxlcogenomics Database for Occupational Health Risk Assessment of Engineered Nanomaterials Role:PI $48,123.00 Awarded Level:Federal

Grant: #0255-C015-4609 / U54HL127624 Investigators:Medvedovic, Mario; Meller, Jaroslaw; Sivaganesan, Siva 07-01-2019 -06-30-2020 National Institute of Allergy and Infectious Diseases Data Coordination and Integration Center for LINCS-BD2K Role:PI $551,515.00 Active Level:Federal

Publications

Peer Reviewed Publications

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.; 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.; 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Huang, Weichun; Medvedovic, Mario; Zhang, Jingwen; Niu, Liang (2019. )ChIAPoP: a new tool for ChIA-PET data analysis.Nucleic acids research, ,

Dorn, Lisa E; Lasman, Lior; Chen, Jing; Xu, Xianyao; Hund, Thomas J; Medvedovic, Mario; Hanna, Jacob H; van Berlo, Jop H; Accornero, Federica (2019. )The N6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and Hypertrophy.Circulation, ,139 (4 ),533-545

Steele, Nina G; Chakrabarti, Jayati; Wang, Jiang; Biesiada, Jacek; Holokai, Loryn; Chang, Julie; Nowacki, Lauren M; Hawkins, Jennifer; Mahe, Maxime; Sundaram, Nambirajan; Shroyer, Noah; Medvedovic, Mario; Helmrath, Michael; Ahmad, Syed; Zavros, Yana (2019. )An Organoid-Based Preclinical Model of Human Gastric Cancer.Cellular and molecular gastroenterology and hepatology, ,7 (1 ),161-184

Langevin, Scott M; Kuhnell, Damaris; Orr-Asman, Melissa A; Biesiada, Jacek; Zhang, Xiang; Medvedovic, Mario; Thomas, Hala Elnakat (2019. )Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum.RNA biology, ,16 (1 ),5-12

Lounder, Dana T; Khandelwal, Pooja; Gloude, Nicholas J; Dandoy, Christopher E; Jodele, Sonata; Medvedovic, Mario; Denson, Lee A; Lane, Adam; Lake, Kelly; Litts, Bridget; Wilkey, Alyss; Davies, Stella M (2018. )Interleukin-22 levels are increased in gastrointestinal graft-versus-host disease in children.Haematologica, ,103 (10 ),e480-e482

Vairamani, Kanimozhi; Prasad, Vikram; Wang, Yigang; Huang, Wei; Chen, Yinhua; Medvedovic, Mario; Lorenz, John N; Shull, Gary E (2018. )NBCe1 Na+-HCO3- cotransporter ablation causes reduced apoptosis following cardiac ischemia-reperfusion injury in vivo.World journal of cardiology, ,10 (9 ),97-109

Haque, Sulsal-Ul; Niu, Liang; Kuhnell, Damaris; Hendershot, Jacob; Biesiada, Jacek; Niu, Wen; Hagan, Matthew C; Kelsey, Karl T; Casper, Keith A; Wise-Draper, Trisha M; Medvedovic, Mario; Langevin, Scott M (2018. )Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma.Head & neck, ,40 (7 ),1555-1564

Stathias, Vasileios; Koleti, Amar; Vidovi?, Dušica; Cooper, Daniel J; Jagodnik, Kathleen M; Terryn, Raymond; Forlin, Michele; Chung, Caty; Torre, Denis; Ayad, Nagi; Medvedovic, Mario; Ma'ayan, Avi; Pillai, Ajay; Schürer, Stephan C (2018. )Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.Scientific data, ,5 ,180117

Abdel-Hameed, Enass A; Rouster, Susan D; Boyce, Ceejay L; Zhang, Xiang; Biesiada, Jacek; Medvedovic, Mario; Sherman, Kenneth E (2018. )Ultra-Deep Genomic Sequencing of HCV NS5A Resistance-Associated Substitutions in HCV/HIV Coinfected Patients.Digestive diseases and sciences, ,63 (3 ),645-652

Huang, Wei; Feng, Yuliang; Liang, Jialiang; Yu, Hao; Wang, Cheng; Wang, Boyu; Wang, Mingyang; Jiang, Lin; Meng, Wei; Cai, Wenfeng; Medvedovic, Mario; Chen, Jenny; Paul, Christian; Davidson, W Sean; Sadayappan, Sakthivel; Stambrook, Peter J; Yu, Xi-Yong; Wang, Yigang (2018. )Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration.Nature communications, ,9 (1 ),700

Keenan, Alexandra B; Jenkins, Sherry L; Jagodnik, Kathleen M; Koplev, Simon; He, Edward; Torre, Denis; Wang, Zichen; Dohlman, Anders B; Silverstein, Moshe C; Lachmann, Alexander; Kuleshov, Maxim V; Ma'ayan, Avi; Stathias, Vasileios; Terryn, Raymond; Cooper, Daniel; Forlin, Michele; Koleti, Amar; Vidovic, Dusica; Chung, Caty; Schürer, Stephan C; Vasiliauskas, Jouzas; Pilarczyk, Marcin; Shamsaei, Behrouz; Fazel, Mehdi; Ren, Yan; Niu, Wen; Clark, Nicholas A; White, Shana; Mahi, Naim; Zhang, Lixia; Kouril, Michal; Reichard, John F; Sivaganesan, Siva; Medvedovic, Mario; Meller, Jaroslaw; Koch, Rick J; Birtwistle, Marc R; Iyengar, Ravi; Sobie, Eric A; Azeloglu, Evren U; Kaye, Julia; Osterloh, Jeannette; Haston, Kelly; Kalra, Jaslin; Finkbiener, Steve; Li, Jonathan; Milani, Pamela; Adam, Miriam; Escalante-Chong, Renan; Sachs, Karen; Lenail, Alex; Ramamoorthy, Divya; Fraenkel, Ernest; Daigle, Gavin; Hussain, Uzma; Coye, Alyssa; Rothstein, Jeffrey; Sareen, Dhruv; Ornelas, Loren; Banuelos, Maria; Mandefro, Berhan; Ho, Ritchie; Svendsen, Clive N; Lim, Ryan G; Stocksdale, Jennifer; Casale, Malcolm S; Thompson, Terri G; Wu, Jie; Thompson, Leslie M; Dardov, Victoria; Venkatraman, Vidya; Matlock, Andrea; Van Eyk, Jennifer E; Jaffe, Jacob D; Papanastasiou, Malvina; Subramanian, Aravind; Golub, Todd R; Erickson, Sean D; Fallahi-Sichani, Mohammad; Hafner, Marc; Gray, Nathanael S; Lin, Jia-Ren; Mills, Caitlin E; Muhlich, Jeremy L; Niepel, Mario; Shamu, Caroline E; Williams, Elizabeth H; Wrobel, David; Sorger, Peter K; Heiser, Laura M; Gray, Joe W; Korkola, James E; Mills, Gordon B; LaBarge, Mark; Feiler, Heidi S; Dane, Mark A; Bucher, Elmar; Nederlof, Michel; Sudar, Damir; Gross, Sean; Kilburn, David F; Smith, Rebecca; Devlin, Kaylyn; Margolis, Ron; Derr, Leslie; Lee, Albert; Pillai, Ajay (2018. )The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.Cell systems, ,6 (1 ),13-24

Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel J; Turner, John P; Vidovic, Dušica; Forlin, Michele; Kelley, Tanya T; D'Urso, Alessandro; Allen, Bryce K; Torre, Denis; Jagodnik, Kathleen M; Wang, Lily; Jenkins, Sherry L; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma'ayan, Avi; Pillai, Ajay; Schürer, Stephan 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 research, ,46 (D1 ),D558-D566

VonHandorf, Andrew; Sánchez-Martín, Francisco Javier; Biesiada, Jacek; Zhang, Hongxia; Zhang, Xiang; Medvedovic, Mario; Puga, Alvaro (2018. )Chromium disrupts chromatin organization and CTCF access to its cognate sites in promoters of differentially expressed genes.Epigenetics, ,13 (4 ),363-375

Leung, Yuet-Kin; Ouyang, Bin; Niu, Liang; Xie, Changchun; Ying, Jun; Medvedovic, Mario; Chen, Aimin; Weihe, Pal; Valvi, Damaskini; Grandjean, Philippe; Ho, Shuk-Mei (2018. )Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort.Epigenetics, ,13 (3 ),290-300

Do, Thuy; Tan, Rachel; Bennett, Mark; Medvedovic, Mario; Grom, Alexei A; Shen, Nan; Thornton, Sherry; Schulert, Grant S (2018. )MicroRNA networks associated with active systemic juvenile idiopathic arthritis regulate CD163 expression and anti-inflammatory functions in macrophages through two distinct mechanisms.Journal of leukocyte biology, ,103 (1 ),71-85

Clark, Nicholas A; Hafner, Marc; Kouril, Michal; Williams, Elizabeth H; Muhlich, Jeremy L; Pilarczyk, Marcin; Niepel, Mario; Sorger, Peter K; Medvedovic, Mario (2017. )GRcalculator: an online tool for calculating and mining dose-response data.BMC cancer, ,17 (1 ),698

Moncrieffe, Halima; Bennett, Mark F; Tsoras, Monica; Luyrink, Lorie K; Johnson, Anne L; Xu, Huan; Dare, Jason; Becker, Mara L; Prahalad, Sampath; Rosenkranz, Margalit; O'Neil, Kathleen M; Nigrovic, Peter A; Griffin, Thomas A; Lovell, Daniel J; Grom, Alexei A; Medvedovic, Mario; Thompson, Susan D (2017. )Transcriptional profiles of JIA patient blood with subsequent poor response to methotrexate.Rheumatology (Oxford, England), ,56 (9 ),1542-1551

Vairamani, Kanimozhi; Wang, Hong-Sheng; Medvedovic, Mario; Lorenz, John N; Shull, Gary E (2017. )RNA SEQ Analysis Indicates that the AE3 Cl-/HCO3- Exchanger Contributes to Active Transport-Mediated CO2 Disposal in Heart.Scientific reports, ,7 (1 ),7264

Bertaux-Skeirik, Nina; Wunderlich, Mark; Teal, Emma; Chakrabarti, Jayati; Biesiada, Jacek; Mahe, Maxime; Sundaram, Nambirajan; Gabre, Joel; Hawkins, Jennifer; Jian, Gao; Engevik, Amy C; Yang, Li; Wang, Jiang; Goldenring, James R; Qualls, Joseph E; Medvedovic, Mario; Helmrath, Michael A; Diwan, Tayyab; Mulloy, James C; Zavros, Yana (2017. )CD44 variant isoform 9 emerges in response to injury and contributes to the regeneration of the gastric epithelium.The Journal of pathology, ,242 (4 ),463-475

Langevin, Scott; Kuhnell, Damaris; Parry, Tess; Biesiada, Jacek; Huang, Shouxiong; Wise-Draper, Trisha; Casper, Keith; Zhang, Xiang; Medvedovic, Mario; Kasper, Susan (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

Frank, Evan A; Carreira, Vinicius S; Shanmukhappa, Kumar; Medvedovic, Mario; Prows, Daniel R; Yadav, Jagjit S (2017. )Genetic susceptibility to toxicologic lung responses among inbred mouse strains following exposure to carbon nanotubes and profiling of underlying gene networks.Toxicology and applied pharmacology, ,327 ,59-70

Leung, Yuet-Kin; Govindarajah, Vinothini; Cheong, Ana; Veevers, Jennifer; Song, Dan; Gear, Robin; Zhu, Xuegong; Ying, Jun; Kendler, Ady; Medvedovic, Mario; Belcher, Scott; Ho, Shuk-Mei (2017. )Gestational high-fat diet and bisphenol A exposure heightens mammary cancer risk.Endocrine-related cancer, ,24 (7 ),365-378

Heymann, Peter W; Nguyen, Huyen-Tran; Steinke, John W; Turner, Ronald B; Woodfolk, Judith A; Platts-Mills, Thomas A E; Martin, Lisa; He, Hua; Biagini Myers, Jocelyn; Lindsey, Mark; Sivaprasad, Umasundari; Medvedovic, Mario; Mahi, Naim; Carper, Holliday; Murphy, Deborah D; Patrie, James; Khurana Hershey, Gurjit 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

Whitson, Jeremy A; Zhang, Xiang; Medvedovic, Mario; Chen, Jenny; Wei, Zongbo; Monnier, Vincent M; Fan, Xingjun (2017. )Transcriptome of the GSH-Depleted Lens Reveals Changes in Detoxification and EMT Signaling Genes, Transport Systems, and Lipid Homeostasis.Investigative ophthalmology & visual science, ,58 (5 ),2666-2684

Abdel-Hameed, Enass A; Rouster, Susan D; Zhang, Xiang; Chen, Jing; Medvedovic, Mario; Goodman, Zachary D; Sherman, Kenneth E (2017. )Characterization of HCV NS3 Protease Variants in HCV/HIV-Coinfected Patients by Ultra-Deep Sequence Analysis: Relationship with Hepatic Fibrosis.Journal of acquired immune deficiency syndromes (1999), ,74 (3 ),353-358

Singh, Brijendra; Jegga, Anil G; Shanmukhappa, Kumar S; Edukulla, Ramakrishna; Khurana Hershey, Gurjit Kaur; Medvedovic, Mario; Dillon, Stacey R; Madala, Satish 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

Cheong, Ana; Zhang, Xiang; Cheung, Yuk-Yin; Tang, Wan-Yee; Chen, Jing; Ye, Shu-Hua; Medvedovic, Mario; Leung, Yuet-Kin; Prins, Gail S; Ho, Shuk-Mei (2016. )DNA methylome changes by estradiol benzoate and bisphenol A links early-life environmental exposures to prostate cancer risk.Epigenetics, ,11 (9 ),674-689

Singh, Brijendra; Jegga, Anil G; Shanmukhappa, Kumar S; Edukulla, Ramakrishna; Khurana Hershey, Gurjit H; Medvedovic, Mario; Dillon, Stacey R; Madala, Satish 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

Wang, Quan; Trevino, Lindsey S; Wong, Rebecca Lee Yean; Medvedovic, Mario; Chen, Jing; Ho, Shuk-Mei; Shen, Jianjun; Foulds, Charles E; Coarfa, Cristian; O'Malley, Bert W; Shilatifard, Ali; Walker, Cheryl L (2016. )Reprogramming of the Epigenome by MLL1 Links Early-Life Environmental Exposures to Prostate Cancer Risk.Molecular endocrinology (Baltimore, Md.), ,30 (8 ),856-71

Engevik, Amy C; Feng, Rui; Choi, Eunyoung; White, Shana; Bertaux-Skeirik, Nina; Li, Jing; Mahe, Maxime M; Aihara, Eitaro; Yang, Li; DiPasquale, Betsy; Oh, Sunghee; Engevik, Kristen A; Giraud, Andrew S; Montrose, Marshall H; Medvedovic, Mario; Helmrath, Michael A; Goldenring, James R; Zavros, Yana (2016. )The Development of Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) During Gastric Repair Is Absent in the Aged Stomach.Cellular and molecular gastroenterology and hepatology, ,2 (5 ),605-624

Chen, Liang; Peng, Zhimin; Meng, Qinghang; Mongan, Maureen; Wang, Jingcai; Sartor, Maureen; Chen, Jing; Niu, Liang; Medvedovic, Mario; Kao, Winston; Xia, Ying (2016. )Loss of I?B kinase ? promotes myofibroblast transformation and senescence through activation of the ROS-TGF? autocrine loop.Protein & cell, ,7 (5 ),338-50

Govindarajah, Vinothini; Leung, Yuet-Kin; Ying, Jun; Gear, Robin; Bornschein, Robert L; Medvedovic, Mario; Ho, Shuk-Mei (2016. )In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands.The Journal of nutritional biochemistry, ,29 ,73-82

Jodele, Sonata; Zhang, Kejian; Zou, Fanggeng; Laskin, Benjamin; Dandoy, Christopher E; Myers, Kasiani C; Lane, Adam; Meller, Jaroslav; Medvedovic, Mario; Chen, Jenny; Davies, Stella M (2016. )The genetic fingerprint of susceptibility for transplant-associated thrombotic microangiopathy.Blood, ,127 (8 ),989-96

Sun, Xiaodian; Medvedovic, Mario (2016. )Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks.IET systems biology, ,10 (1 ),10-6

Wang, Qin; Kurita, Hisaka; Carreira, Vinicius; Ko, Chia-I; Fan, Yunxia; Zhang, Xiang; Biesiada, Jacek; Medvedovic, Mario; Puga, Alvaro (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.Toxicological sciences : an official journal of the Society of Toxicology, ,149 (2 ),346-57

Lam, Hung-Ming; Ho, Shuk-Mei; Chen, Jing; Medvedovic, Mario; Tam, Neville Ngai Chung (2016. )Bisphenol A Disrupts HNF4?-Regulated Gene Networks Linking to Prostate Preneoplasia and Immune Disruption in Noble Rats.Endocrinology, ,157 (1 ),207-19

Carreira, Vinicius S; Fan, Yunxia; Kurita, Hisaka; Wang, Qin; Ko, Chia-I; Naticchioni, Mindi; Jiang, Min; Koch, Sheryl; Zhang, Xiang; Biesiada, Jacek; Medvedovic, Mario; Xia, Ying; Rubinstein, Jack; Puga, Alvaro (2015. )Disruption of Ah Receptor Signaling during Mouse Development Leads to Abnormal Cardiac Structure and Function in the Adult.PloS one, ,10 (11 ),e0142440

Ho, Shuk-Mei; Cheong, Ana; Lam, Hung-Ming; Hu, Wen-Yang; Shi, Guang-Bin; Zhu, Xuegong; Chen, Jing; Zhang, Xiang; Medvedovic, Mario; Leung, Yuet-Kin; Prins, Gail S (2015. )Exposure of Human Prostaspheres to Bisphenol A Epigenetically Regulates SNORD Family Noncoding RNAs via Histone Modification.Endocrinology, ,156 (11 ),3984-95

Sontake, Vishwaraj; Shanmukhappa, Shiva K; DiPasquale, Betsy A; Reddy, Geereddy B; Medvedovic, Mario; Hardie, William D; White, Eric S; Madala, Satish K (2015. )Fibrocytes Regulate Wilms Tumor 1-Positive Cell Accumulation in Severe Fibrotic Lung Disease.Journal of immunology (Baltimore, Md. : 1950), ,195 (8 ),3978-91

Carreira, Vinicius S; Fan, Yunxia; Wang, Qing; Zhang, Xiang; Kurita, Hisaka; Ko, Chia-I; Naticchioni, Mindi; Jiang, Min; Koch, Sheryl; Medvedovic, Mario; Xia, Ying; Rubinstein, Jack; Puga, Alvaro (2015. )Ah Receptor Signaling Controls the Expression of Cardiac Development and Homeostasis Genes.Toxicological sciences : an official journal of the Society of Toxicology, ,147 (2 ),425-35

Wong, Rebecca Lee Yean; Wang, Quan; Treviño, Lindsey S; Bosland, Maarten C; Chen, Jing; Medvedovic, Mario; Prins, Gail S; Kannan, Kurunthachalam; Ho, Shuk-Mei; Walker, Cheryl Lyn (2015. )Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate.Epigenetics, ,10 (2 ),127-34

Sivaprasad, Umasundari; Kinker, Kayla G; Ericksen, Mark B; Lindsey, Mark; Gibson, Aaron M; Bass, Stacey A; Hershey, Nicolas S; Deng, Jingyuan; Medvedovic, Mario; Khurana Hershey, Gurjit K (2015. )SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis.The Journal of investigative dermatology, ,135 (1 ),160-169

Sánchez-Martín, Francisco Javier; Lindquist, Diana M; Landero-Figueroa, Julio; Zhang, Xiang; Chen, Jing; Cecil, Kim M; Medvedovic, Mario; Puga, Alvaro (2015. )Sex- and tissue-specific methylome changes in brains of mice perinatally exposed to lead.Neurotoxicology, ,46 ,92-100

Buhule, Olive D; Minster, Ryan L; Hawley, Nicola L; Medvedovic, Mario; Sun, Guangyun; Viali, Satupaitea; Deka, Ranjan; McGarvey, Stephen T; Weeks, Daniel E (2014. )Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale.Frontiers in genetics, ,5 ,354

Cheng, Xin-Hua; Black, Markaisa; Ustiyan, Vladimir; Le, Tien; Fulford, Logan; Sridharan, Anusha; Medvedovic, Mario; Kalinichenko, Vladimir V; Whitsett, Jeffrey A; Kalin, Tanya V (2014. )SPDEF inhibits prostate carcinogenesis by disrupting a positive feedback loop in regulation of the Foxm1 oncogene.PLoS genetics, ,10 (9 ),e1004656

Ovesen, Jerald L; Fan, Yunxia; Zhang, Xiang; Chen, Jing; Medvedovic, Mario; Xia, Ying; Puga, Alvaro (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, Jerald L; Fan, Yunxia; Chen, Jing; Medvedovic, Mario; Xia, Ying; Puga, Alvaro (2014. )Long-term exposure to low-concentrations of Cr(VI) induce DNA damage and disrupt the transcriptional response to benzo[a]pyrene.Toxicology, ,316 ,14-24

Meng, Qinghang; Jin, Chang; Chen, Yinglei; Chen, Jing; Medvedovic, Mario; Xia, Ying (2014. )Expression of signaling components in embryonic eyelid epithelium.PloS one, ,9 (2 ),e87038

Madala, Satish K; Edukulla, Ramakrishna; Phatak, Mukta; Schmidt, Stephanie; Davidson, Cynthia; Acciani, Thomas H; Korfhagen, Thomas R; Medvedovic, Mario; Lecras, Timothy D; Wagner, Kimberly; Hardie, William D (2014. )Dual targeting of MEK and PI3K pathways attenuates established and progressive pulmonary fibrosis.PloS one, ,9 (1 ),e86536

Kinker, Kayla G; Gibson, Aaron M; Bass, Stacey A; Day, Brandy P; Deng, Jingyuan; Medvedovic, Mario; Figueroa, Julio A Landero; Hershey, Gurjit K Khurana; Chen, Weiguo (2014. )Overexpression of dimethylarginine dimethylaminohydrolase 1 attenuates airway inflammation in a mouse model of asthma.PloS one, ,9 (1 ),e85148

Lam, Hung-Ming; Ouyang, Bin; Chen, Jing; Ying, Jun; Wang, Jiang; Wu, Chin-Lee; Jia, Li; Medvedovic, Mario; Vessella, Robert L; Ho, Shuk-Mei (2014. )Targeting GPR30 with G-1: a new therapeutic target for castration-resistant prostate cancer.Endocrine-related cancer, ,21 (6 ),903-14

Wang, Qin; Chen, Jing; Ko, Chia-I; Fan, Yunxia; Carreira, Vinicius; Chen, Yinglei; Xia, Ying; Medvedovic, Mario; Puga, Alvaro Disruption of aryl hydrocarbon receptor homeostatic levels during embryonic stem cell differentiation alters expression of homeobox transcription factors that control cardiomyogenesis.Environmental health perspectives, ,121 (11-12 ),1334-43

Shioda, Toshi; Rosenthal, Noël F; Coser, Kathryn R; Suto, Mizuki; Phatak, Mukta; Medvedovic, Mario; Carey, Vincent J; Isselbacher, Kurt J (2013. )Expressomal approach for comprehensive analysis and visualization of ligand sensitivities of xenoestrogen responsive genes.Proceedings of the National Academy of Sciences of the United States of America, ,110 (41 ),16508-13

Bastola, Prabhat; Stratton, Yiwen; Kellner, Emily; Mikhaylova, Olga; Yi, Ying; Sartor, Maureen A; Medvedovic, Mario; Biesiada, Jacek; Meller, Jarek; Czyzyk-Krzeska, Maria F (2013. )Folliculin contributes to VHL tumor suppressing activity in renal cancer through regulation of autophagy.PloS one, ,8 (7 ),e70030

Kim, Ji Young; Valencia, Tania; Abu-Baker, Shadi; Linares, Juan; Lee, Sang Jun; Yajima, Tomoko; Chen, Jing; Eroshkin, Alexey; Castilla, Elias A; Brill, Laurence M; Medvedovic, Mario; Leitges, Michael; Moscat, Jorge; Diaz-Meco, Maria T (2013. )c-Myc phosphorylation by PKC? represses prostate tumorigenesis.Proceedings of the National Academy of Sciences of the United States of America, ,110 (16 ),6418-23

Jin, Chang; Chen, Jing; Meng, Qinghang; Carreira, Vinicius; Tam, Neville N C; Geh, Esmond; Karyala, Saikumar; Ho, Shuk-Mei; Zhou, Xiangtian; Medvedovic, Mario; Xia, Ying (2013. )Deciphering gene expression program of MAP3K1 in mouse eyelid morphogenesis.Developmental biology, ,374 (1 ),96-107

Ma, Li; Tao, Yongzhen; Duran, Angeles; Llado, Victoria; Galvez, Anita; Barger, Jennifer F; Castilla, Elias A; Chen, Jing; Yajima, Tomoko; Porollo, Aleksey; Medvedovic, Mario; Brill, Laurence M; Plas, David R; Riedl, Stefan J; Leitges, Michael; Diaz-Meco, Maria T; Richardson, Adam D; Moscat, Jorge (2013. )Control of nutrient stress-induced metabolic reprogramming by PKC? in tumorigenesis.Cell, ,152 (3 ),599-611

Chen, Jing; Hu, Zhen; Phatak, Mukta; Reichard, John; Freudenberg, Johannes M; Sivaganesan, Siva; Medvedovic, Mario (2013. )Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules.PLoS computational biology, ,9 (9 ),e1003198

Kim, Dong-Hoon; Sartor, Maureen A; Bain, James R; Sandoval, Darleen; Stevens, Robert D; Medvedovic, Mario; Newgard, Christopher B; Woods, Stephen C; Seeley, Randy 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, George D; Pope-Varsalona, Hannah; Concel, Vincent J; Liu, Pengyuan; Bein, Kiflai; Berndt, Annerose; Martin, Timothy M; Ganguly, Koustav; Jang, An Soo; Brant, Kelly A; Dopico, Richard A; Upadhyay, Swapna; Di, Y P Peter; Li, Qian; Hu, Zhen; Vuga, Louis J; Medvedovic, Mario; Kaminski, Naftali; You, Ming; Alexander, Danny C; McDunn, Jonathan E; Prows, Daniel R; Knoell, Daren L; Fabisiak, James P (2012. )Integrative assessment of chlorine-induced acute lung injury in mice.American journal of respiratory cell and molecular biology, ,47 (2 ),234-44

Wang, Xiaohong; Zhu, Hongyan; Zhang, Xiaowei; Liu, Yong; Chen, Jing; Medvedovic, Mario; Li, Hongliang; Weiss, Mitchell J; Ren, Xiaoping; Fan, Guo-Chang (2012. )Loss of the miR-144/451 cluster impairs ischaemic preconditioning-mediated cardioprotection by targeting Rac-1.Cardiovascular research, ,94 (2 ),379-90

Fabisiak, James P; Medvedovic, Mario; Alexander, Danny C; McDunn, Jonathan E; Concel, Vincent J; Bein, Kiflai; Jang, An Soo; Berndt, Annerose; Vuga, Louis J; Brant, Kelly A; Pope-Varsalona, Hannah; Dopico, Richard A; Ganguly, Koustav; Upadhyay, Swapna; Li, Qian; Hu, Zhen; Kaminski, Naftali; Leikauf, George D (2011. )Integrative metabolome and transcriptome profiling reveals discordant energetic stress between mouse strains with differential sensitivity to acrolein-induced acute lung injury.Molecular nutrition & food research, ,55 (9 ),1423-34

Wilhide, Michael E; Tranter, Michael; Ren, Xiaoping; Chen, Jing; Sartor, Maureen A; Medvedovic, Mario; Jones, W Keith (2011. )Identification of a NF-?B cardioprotective gene program: NF-?B regulation of Hsp70.1 contributes to cardioprotection after permanent coronary occlusion.Journal of molecular and cellular cardiology, ,51 (1 ),82-9

Leikauf, George D; Concel, Vincent J; Liu, Pengyuan; Bein, Kiflai; Berndt, Annerose; Ganguly, Koustav; Jang, An Soo; Brant, Kelly A; Dietsch, Maggie; Pope-Varsalona, Hannah; Dopico, Richard A; Di, Y P Peter; Li, Qian; Vuga, Louis J; Medvedovic, Mario; Kaminski, Naftali; You, Ming; Prows, Daniel R (2011. )Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1.American journal of respiratory and critical care medicine, ,183 (11 ),1499-509

SenthamaraiKannan, Paranthaman; Sartor, Maureen A; O'Connor, Kyle T; Neumann, Jonathan C; Klyza, James P; Succop, Paul A; Wagner, Brad D; Karyala, Saikumar; Medvedovic, Mario; Menon, Anil G (2011. )Identification of maternally regulated fetal gene networks in the placenta with a novel embryo transfer system in mice.Physiological genomics, ,43 (7 ),317-24

Joshi, Vineet K; Freudenberg, Johannes M; Hu, Zhen; Medvedovic, Mario (2011. )WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results.Source code for biology and medicine, ,6 ,3

Freudenberg, Johannes M; Sivaganesan, Siva; Phatak, Mukta; Shinde, Kaustubh; Medvedovic, Mario (2011. )Generalized random set framework for functional enrichment analysis using primary genomics datasets.Bioinformatics (Oxford, England), ,27 (1 ),70-7

Howard, Timothy D; Ho, Shuk-Mei; Zhang, Li; Chen, Jing; Cui, Wei; Slager, Rebecca; Gray, Stanton; Hawkins, Gregory A; Medvedovic, Mario; Wagner, Janice D (2011. )Epigenetic changes with dietary soy in cynomolgus monkeys.PloS one, ,6 (10 ),e26791

Tam, Neville N C; Szeto, Carol Y Y; Freudenberg, Johannes M; Fullenkamp, Amy N; Medvedovic, Mario; Ho, Shuk-Mei (2010. )Research resource: estrogen-driven prolactin-mediated gene-expression networks in hormone-induced prostatic intraepithelial neoplasia.Molecular endocrinology (Baltimore, Md.), ,24 (11 ),2207-17

Tranter, Michael; Ren, Xiaoping; Forde, Tiffany; Wilhide, Michael E; Chen, Jing; Sartor, Maureen A; Medvedovic, Mario; Jones, W Keith (2010. )NF-kappaB driven cardioprotective gene programs; Hsp70.3 and cardioprotection after late ischemic preconditioning.Journal of molecular and cellular cardiology, ,49 (4 ),664-72

Wang, Xiaohong; Zhang, Xiaowei; Ren, Xiao-Ping; Chen, Jing; Liu, Hongzhu; Yang, Junqi; Medvedovic, Mario; Hu, Zhuowei; Fan, Guo-Chang (2010. )MicroRNA-494 targeting both proapoptotic and antiapoptotic proteins protects against ischemia/reperfusion-induced cardiac injury.Circulation, ,122 (13 ),1308-18

Leikauf, George D; Pope-Varsalona, Hannah; Concel, Vincent J; Liu, Pengyuan; Bein, Kiflai; Brant, Kelly A; Dopico, Richard A; Di, Y Peter; Jang, An-Soo; Dietsch, Maggie; Medvedovic, Mario; Li, Qian; Vuga, Louis J; Kaminski, Naftali; You, Ming; Prows, Daniel R (2010. )Functional genomics of chlorine-induced acute lung injury in mice.Proceedings of the American Thoracic Society, ,7 (4 ),294-6

Freudenberg, Johannes M; Sivaganesan, Siva; Wagner, Michael; Medvedovic, Mario (2010. )A semi-parametric Bayesian model for unsupervised differential co-expression analysis.BMC bioinformatics, ,11 ,234

Stark, James M; Barmada, M Michael; Winterberg, Abby V; Majumber, Nilanjana; Gibbons, William J; Stark, Marilyn A; Sartor, Maureen A; Medvedovic, Mario; Kolls, Jay; Bein, Kiflai; Mailaparambil, Beena; Krueger, Marcus; Heinzmann, Andrea; Leikauf, George D; Prows, Daniel R (2010. )Genomewide association analysis of respiratory syncytial virus infection in mice.Journal of virology, ,84 (5 ),2257-69

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario (2010. )Genomics Portals: integrative web-platform for mining genomics data.BMC genomics, ,11 ,27

Borchers, Michael T; Wesselkamper, Scott C; Deshmukh, Hitesh; Beckman, Erin; Medvedovic, Mario; Sartor, Maureen; Leikauf, George D (2009. )The role of T cells in the regulation of acrolein-induced pulmonary inflammation and epithelial-cell pathology. Research report (Health Effects Institute), ,(146 ),5-29

Bein, Kiflai; Wesselkamper, Scott C; Liu, Xiangdong; Dietsch, Maggie; Majumder, Nilanjana; Concel, Vincent J; Medvedovic, Mario; Sartor, Maureen A; Henning, Lisa N; Venditto, Carmen; Borchers, Michael T; Barchowsky, Aaron; Weaver, Timothy E; Tichelaar, Jay W; Prows, Daniel R; Korfhagen, Thomas R; Hardie, William D; Bachurski, Cindy J; Leikauf, George D (2009. )Surfactant-associated protein B is critical to survival in nickel-induced injury in mice.American journal of respiratory cell and molecular biology, ,41 (2 ),226-36

Freudenberg, Johannes M; Joshi, Vineet K; Hu, Zhen; Medvedovic, Mario (2009. )CLEAN: CLustering Enrichment ANalysis.BMC bioinformatics, ,10 ,234

Sartor, Maureen A; Schnekenburger, Michael; Marlowe, Jennifer L; Reichard, John F; Wang, Ying; Fan, Yunxia; Ma, Ci; Karyala, Saikumar; Halbleib, Danielle; Liu, Xiangdong; Medvedovic, Mario; Puga, Alvaro (2009. )Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs.Environmental health perspectives, ,117 (7 ),1139-46

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.Physiological genomics, ,38 (1 ),80-8

Gandhi, Manoj S; Stringer, James R; Nikiforova, Marina N; Medvedovic, Mario; Nikiforov, Yuri 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

Sartor, Maureen A; Leikauf, George D; Medvedovic, Mario (2009. )LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data.Bioinformatics (Oxford, England), ,25 (2 ),211-7

Medvedovic, Mario; Halbleib, Danielle; Miller, Marian L; LaDow, Kathy; Sartor, Maureen A; Tomlinson, Craig R Gene expression profiling of blood to predict the onset of leukemia.Blood cells, molecules & diseases, ,42 (1 ),64-70

Zhang, Xiang; Leav, Irwin; Revelo, Monica P; Deka, Ranjan; Medvedovic, Mario; Jiang, Zhong; Ho, Shuk-Mei (2009. )Deletion hotspots in AMACR promoter CpG island are cis-regulatory elements controlling the gene expression in the colon.PLoS genetics, ,5 (1 ),e1000334

Tang, Wan-Yee; Newbold, Retha; Mardilovich, Katerina; Jefferson, Wendy; Cheng, Robert Y S; Medvedovic, Mario; Ho, Shuk-Mei (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

Borchers, Michael T; Wesselkamper, Scott C; Eppert, Bryan L; Motz, Gregory T; Sartor, Maureen A; Tomlinson, Craig R; Medvedovic, Mario; Tichelaar, Jay W (2008. )Nonredundant functions of alphabeta and gammadelta T cells in acrolein-induced pulmonary pathology.Toxicological sciences : an official journal of the Society of Toxicology, ,105 (1 ),188-99

Bakshi, Shlomo; Zhang, Xiang; Godoy-Tundidor, Sonia; Cheng, Robert Yuk Sing; Sartor, Maureen A; Medvedovic, Mario; Ho, Shuk-Mei (2008. )Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor.Environmental health perspectives, ,116 (6 ),769-76

Tam, Neville N C; Szeto, Carol Ying-Ying; Sartor, Maureen A; Medvedovic, Mario; Ho, Shuk-Mei (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 (New York, N.Y.), ,10 (1 ),20-40

Ganguly, Koustav; Stoeger, Tobias; Wesselkamper, Scott C; Reinhard, Claudia; Sartor, Maureen A; Medvedovic, Mario; Tomlinson, Craig R; Bolle, Ines; Mason, John M; Leikauf, George D; Schulz, Holger (2007. )Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure.Physiological genomics, ,31 (3 ),410-21

Popa, Ileana; Zubkova, Iryna; Medvedovic, Mario; Romantseva, Tatiana; Mostowski, Howard; Boyd, Richard; Zaitseva, Marina (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.International immunology, ,19 (11 ),1249-60

Hardie, William D; Korfhagen, Thomas R; Sartor, Maureen A; Prestridge, Adrienne; Medvedovic, Mario; Le Cras, Timothy D; Ikegami, Machiko; Wesselkamper, Scott C; Davidson, Cynthia; Dietsch, Maggie; Nichols, William; Whitsett, Jeffrey A; Leikauf, George D (2007. )Genomic profile of matrix and vasculature remodeling in TGF-alpha induced pulmonary fibrosis.American journal of respiratory cell and molecular biology, ,37 (3 ),309-21

Liu, Xiangdong; Jessen, Walter J; Sivaganesan, Siva; Aronow, Bruce J; Medvedovic, Mario (2007. )Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.BMC bioinformatics, ,8 ,283

Sartor, Maureen A; Tomlinson, Craig R; Wesselkamper, Scott C; Sivaganesan, Siva; Leikauf, George D; Medvedovic, Mario (2006. )Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments.BMC bioinformatics, ,7 ,538

Schwanekamp, Jennifer A; Sartor, Maureen A; Karyala, Saikumar; Halbleib, Danielle; Medvedovic, Mario; Tomlinson, Craig R Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin.Biochimica et biophysica acta, ,1759 (8-9 ),388-402

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

Mesa, Cleo; Mirza, Mana; Mitsutake, Norisato; Sartor, Maureen; Medvedovic, Mario; Tomlinson, Craig; Knauf, Jeffrey A; Weber, Georg F; Fagin, James 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 research, ,66 (13 ),6521-9

Medvedovic, Mario; Tomlinson, Craig R; Call, Mindy K; Grogg, Matthew; Tsonis, Panagiotis A (2006. )Gene expression and discovery during lens regeneration in mouse: regulation of epithelial to mesenchymal transition and lens differentiation. Molecular vision, ,12 ,422-40

Icenhour, Crystal R; Arnold, Jonathan; Medvedovic, Mario; Cushion, Melanie T (2006. )Competitive coexistence of two Pneumocystis species.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, ,6 (3 ),177-86

Erwin, Christopher R; Jarboe, Marcus D; Sartor, Maureen A; Medvedovic, Mario; Stringer, Keith F; Warner, Brad W; Bates, Michael D (2006. )Developmental characteristics of adapting mouse small intestine crypt cells.Gastroenterology, ,130 (4 ),1324-32

Sartor, Maureen A; Zorn, Aaron M; Schwanekamp, Jennifer A; Halbleib, Danielle; Karyala, Saikumar; Howell, Michael L; Dean, Gary E; Medvedovic, Mario; Tomlinson, Craig 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 research, ,34 (1 ),185-200

Wesselkamper, Scott C; McDowell, Susan A; Medvedovic, Mario; Dalton, Timothy P; Deshmukh, Hitesh S; Sartor, Maureen A; Case, Lisa M; Henning, Lisa N; Borchers, Michael T; Tomlinson, Craig R; Prows, Daniel R; Leikauf, George D (2006. )The role of metallothionein in the pathogenesis of acute lung injury.American journal of respiratory cell and molecular biology, ,34 (1 ),73-82

Wesselkamper, Scott C; Case, Lisa M; Henning, Lisa N; Borchers, Michael T; Tichelaar, Jay W; Mason, John M; Dragin, Nadine; Medvedovic, Mario; Sartor, Maureen A; Tomlinson, Craig R; Leikauf, George D (2005. )Gene expression changes during the development of acute lung injury: role of transforming growth factor beta.American journal of respiratory and critical care medicine, ,172 (11 ),1399-411

Puxeddu, Efisio; Zhao, Guisheng; Stringer, James R; Medvedovic, Mario; Moretti, Sonia; Fagin, James 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.Mutation research, ,570 (1 ),17-32

Stringer, James R; Larson, Jon S; Fischer, Jared M; Medvedovic, Mario; Hersh, Megan N; Boivin, Gregory P; Stringer, Saundra L (2005. )Modeling variation in tumors in vivo.Proceedings of the National Academy of Sciences of the United States of America, ,102 (7 ),2408-13

Zhang, Jianhua; Moseley, Amy; Jegga, Anil G; Gupta, Ashima; Witte, David P; Sartor, Maureen; Medvedovic, Mario; Williams, Sarah S; Ley-Ebert, Cathy; Coolen, Lique M; Egnaczyk, Gregory; Genter, Mary Beth; Lehman, Michael; Lingrel, Jerry; Maggio, John; Parysek, Linda; Walsh, Ryan; Xu, Ming; Aronow, Bruce J (2004. )Neural system-enriched gene expression: relationship to biological pathways and neurological diseases.Physiological genomics, ,18 (2 ),167-83

Sonntag, David M; de Boer, Johan; Medvedovic, Mario; Baxter, C Stuart; LeMasters, Grace; Talaska, Glenn (2004. )Mutational biases associated with potential iron-binding DNA motifs in rodent lacI and human p53 mutational databases.Mutation research, ,550 (1-2 ),73-88

Sartor, Maureen; Schwanekamp, Jennifer; Halbleib, Danielle; Mohamed, Ismail; Karyala, Saikumar; Medvedovic, Mario; Tomlinson, Craig R (2004. )Microarray results improve significantly as hybridization approaches equilibrium.BioTechniques, ,36 (5 ),790-6

Puga, Alvaro; Sartor, Maureen A; Huang, Ming-Ya; Kerzee, J Kevin; Wei, Yu-Dan; Tomlinson, Craig R; Baxter, C Stuart; Medvedovic, Mario (2004. )Gene expression profiles of mouse aorta and cultured vascular smooth muscle cells differ widely, yet show common responses to dioxin exposure. Cardiovascular toxicology, ,4 (4 ),385-404

Karyala, Saikumar; Guo, Junhai; Sartor, Maureen; Medvedovic, Mario; Kann, Simone; Puga, Alvaro; Ryan, Patrick; Tomlinson, Craig 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. Cardiovascular toxicology, ,4 (1 ),47-73

Bahassi, El Mustapha; Karyala, Saikumar; Tomlinson, Craig R; Sartor, Maureen A; Medvedovic, Mario; Hennigan, Robert F (2004. )Critical regulation of genes for tumor cell migration by AP-1. Clinical & experimental metastasis, ,21 (4 ),293-304

Yeung, Ka Yee; Medvedovic, Mario; Bumgarner, Roger E (2004. )From co-expression to co-regulation: how many microarray experiments do we need?.Genome biology, ,5 (7 ),R48

Vineis, Paolo; Schulte, Paul A; Carreón, Tania; Bailer, A John; Medvedovic, Mario (2004. )Issues of design and analysis in studies of gene-environment interactions. IARC scientific publications, ,(157 ),417-35

Guo, Junhai; Sartor, Maureen; Karyala, Saikumar; Medvedovic, Mario; Kann, Simone; Puga, Alvaro; Ryan, Patrick; Tomlinson, Craig 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. Toxicology and applied pharmacology, ,194 (1 ),79-89

Tsuneoka, Yutaka; Dalton, Timothy P; Miller, Marian L; Clay, Corey D; Shertzer, Howard G; Talaska, Glenn; Medvedovic, Mario; Nebert, Daniel W (2003. )4-aminobiphenyl-induced liver and urinary bladder DNA adduct formation in Cyp1a2(-/-) and Cyp1a2(+/+) mice. Journal of the National Cancer Institute, ,95 (16 ),1227-37

Yeung, Ka Yee; Medvedovic, Mario; Bumgarner, Roger E (2003. )Clustering gene-expression data with repeated measurements. Genome biology, ,4 (5 ),R34

Medvedovic, Mario; Sivaganesan, Siva (2002. )Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics (Oxford, England), ,18 (9 ),1194-206

Knauf, Jeffrey A; Ward, Laura S; Nikiforov, Yuri E; Nikiforova, Marina; Puxeddu, Efisio; Medvedovic, Mario; Liron, Tamar; Mochly-Rosen, Daria; Fagin, James A (2002. )Isozyme-specific abnormalities of PKC in thyroid cancer: evidence for post-transcriptional changes in PKC epsilon.The Journal of clinical endocrinology and metabolism, ,87 (5 ),2150-9

King, N M; Oakley, G G; Medvedovic, M; Dixon, K (2001. )XPA protein alters the specificity of ultraviolet light-induced mutagenesis in vitro. Environmental and molecular mutagenesis, ,37 (4 ),329-39

Smith, L B; Bhattacharya, A; Lemasters, G; Succop, P; Puhala, E; Medvedovic, M; Joyce, J (1997. )Effect of chronic low-level exposure to jet fuel on postural balance of US Air Force personnel. Journal of occupational and environmental medicine, ,39 (7 ),623-32

Research and Practice 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

Academic - Kettering Laboratory
Room 110
Cincinnati  Ohio, 45267
Phone: 513-558-8564
mario.medvedovic@uc.edu