Mario Medvedovic, PHD

Kimura, Eiki; Mongan, Maureen; Xiao, Bo; Christianto, Antonius; Wang, Jingjing; Carreira, Vinicius S; Bolon, Brad; Zhang, Xiang; Burns, Katherine A; Biesiada, Jacek; Medvedovic, Mario; Puga, Alvaro; Xia, Ying 2024. MAP3K1 Regulates Female Reproductive Tract Development. Disease models & mechanisms, ,

Bhattacharya, Debanjan; Barille, Riccardo; Toukam, Donatien Kamdem; Gawali, Vaibhavkumar S; Kallay, Laura; Ahmed, Taukir; Brown, Hawley; Rezvanian, Sepideh; Karve, Aniruddha; Desai, Pankaj B; Medvedovic, Mario; Wang, Kyle; Ionascu, Dan; Harun, Nusrat; Wang, Chenran; Baschnagel, Andrew M; Kritzer, Joshua A; Cook, James M; Pomeranz Krummel, Daniel A; Sengupta, Soma 2023. GABA(A) receptor activation drives GABARAP-Nix mediated autophagy to radiation-sensitize primary and brain-metastatic lung adenocarcinoma tumors. bioRxiv : the preprint server for biology, ,

Galiveti, Chenna R; Kuhnell, Damaris; Biesiada, Jacek; Zhang, Xiang; Kelsey, Karl T; Takiar, Vinita; Tang, Alice L; Wise-Draper, Trisha M; Medvedovic, Mario; Kasper, Susan; Langevin, Scott M 2023. Small extravesicular microRNA in head and neck squamous cell carcinoma and its potential as a liquid biopsy for early detection. Head & neck, 45 1, 212-224

Kimura, Eiki; Mongan, Maureen; Xiao, Bo; Wang, Jingjing; Carreira, Vinicius S; Bolon, Brad; Zhang, Xiang; Burns, Katherine A; Biesiada, Jacek; Medvedovic, Mario; Puga, Alvaro; Xia, Ying 2023. The Role of MAP3K1 in the Development of the Female Reproductive Tract. bioRxiv : the preprint server for biology, ,

Madhuravasal Krishnan, Janani; Kong, Ling; Karns, Rebekah; Medvedovic, Mario; Sherman, Kenneth E; Blackard, Jason T 2023. The Synthetic Opioid Fentanyl Increases HIV Replication and Chemokine Co-Receptor Expression in Lymphocyte Cell Lines. Viruses, 15 4,

Verma, Rita; Aggarwal, Parul; Bischoff, Megan E; Reigle, James; Secic, Dina; Wetzel, Collin; VandenHeuvel, Katherine; Biesiada, Jacek; Ehmer, Birgit; Landero Figueroa, Julio A; Plas, David R; Medvedovic, Mario; Meller, Jarek; Czyzyk-Krzeska, Maria F 2023. Microtubule-associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells. The Journal of biological chemistry, 299 5, 104663

Crist, McKenzie; Yaniv, Benyamin; Palackdharry, Sarah; Lehn, Maria A; Medvedovic, Mario; Stone, Timothy; Gulati, Shuchi; Karivedu, Vidhya; Borchers, Michael; Fuhrman, Bethany; Crago, Audrey; Curry, Joseph; Martinez-Outschoorn, Ubaldo; Takiar, Vinita; Wise-Draper, Trisha M 2022. Metformin increases natural killer cell functions in head and neck squamous cell carcinoma through CXCL1 inhibition. Journal for immunotherapy of cancer, 10 11,

Davidson, Sarah E; Wheeler, Matthew W; Auerbach, Scott S; Sivaganesan, Siva; Medvedovic, Mario 2022. ALOHA: Aggregated local extrema splines for high-throughput dose-response analysis. Computational toxicology (Amsterdam, Netherlands), 21 ,

Evangelista, John Erol; Clarke, Daniel J B; Xie, Zhuorui; Lachmann, Alexander; Jeon, Minji; Chen, Kerwin; Jagodnik, Kathleen M; Jenkins, Sherry L; Kuleshov, Maxim V; Wojciechowicz, Megan L; Schürer, Stephan C; Medvedovic, Mario; Ma'ayan, Avi 2022. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic acids research, 50 W1, W697-W709

Ko, Chia-I; Biesiada, Jacek; Zablon, Hesbon A; Zhang, Xiang; Medvedovic, Mario; Puga, Alvaro 2022. The aryl hydrocarbon receptor directs the differentiation of murine progenitor blastomeres. Cell biology and toxicology, ,

Pilarczyk, Marcin; Fazel-Najafabadi, Mehdi; Kouril, Michal; Shamsaei, Behrouz; Vasiliauskas, Juozas; Niu, Wen; Mahi, Naim; Zhang, Lixia; Clark, Nicholas A; Ren, Yan; White, Shana; Karim, Rashid; Xu, Huan; Biesiada, Jacek; Bennett, Mark F; Davidson, Sarah E; Reichard, John F; Roberts, Kurt; Stathias, Vasileios; Koleti, Amar; Vidovic, Dusica; Clarke, Daniel J B; Schürer, Stephan C; Ma'ayan, Avi; Meller, Jarek; Medvedovic, Mario 2022. Connecting omics signatures and revealing biological mechanisms with iLINCS. Nature communications, 13 1, 4678

Pounders, Jonathan; Hill, Emily J; Hooper, Destiny; Zhang, Xiang; Biesiada, Jacek; Kuhnell, Damaris; Greenland, Hannah L; Esfandiari, Leyla; Timmerman, Emerlee; Foster, Forrest; Wang, Chenran; Walsh, Kyle B; Shatz, Rhonna; Woo, Daniel; Medvedovic, Mario; Langevin, Scott; Sawyer, Russell P 2022. MicroRNA expression within neuronal-derived small extracellular vesicles in frontotemporal degeneration. Medicine, 101 40, e30854

Sawyer, Russell P; Hill, Emily J; Yokoyama, Jennifer; Medvedovic, Mario; Ren, Yan; Zhang, Xiang; Choubey, Divaker; Shatz, Rhonna S; Miller, Bruce; Woo, Daniel 2022. Differences in peripheral immune system gene expression in frontotemporal degeneration. Medicine, 101 3, e28645

Wise-Draper, Trisha M; Gulati, Shuchi; Palackdharry, Sarah; Hinrichs, Benjamin H; Worden, Francis P; Old, Matthew O; Dunlap, Neal E; Kaczmar, John M; Patil, Yash; Riaz, Muhammed Kashif; Tang, Alice; Mark, Jonathan; Zender, Chad; Gillenwater, Ann M; Bell, Diana; Kurtzweil, Nicky; Mathews, Maria; Allen, Casey L; Mierzwa, Michelle L; Casper, Keith; Jandarov, Roman; Medvedovic, Mario; Lee, J Jack; Harun, Nusrat; Takiar, Vinita; Gillison, Maura 2022. Phase II Clinical Trial of Neoadjuvant and Adjuvant Pembrolizumab in Resectable Local-Regionally Advanced Head and Neck Squamous Cell Carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research, 28 7, 1345-1352

Zhen, Yuxuan; Ren, Yan; Medvedovic, Mario; Adams, David E; Wang, Diping; Shao, Wen-Hai 2022. Axl regulated survival/proliferation network and its therapeutic intervention in mouse models of glomerulonephritis. Arthritis research & therapy, 24 1, 284

Al Mahi, Naim; Zhang, Erik Y; Sherman, Susan; Yu, Jane J; Medvedovic, Mario 2021. Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling. International journal of molecular sciences, 22 9,

Pomeranz Krummel, Daniel A; Nasti, Tahseen H; Kaluzova, Milota; Kallay, Laura; Bhattacharya, Debanjan; Melms, Johannes C; Izar, Benjamin; Xu, Maxwell; Burnham, Andre; Ahmed, Taukir; Li, Guanguan; Lawson, David; Kowalski, Jeanne; Cao, Yichun; Switchenko, Jeffrey M; Ionascu, Dan; Cook, James M; Medvedovic, Mario; Jenkins, Andrew; Khan, Mohammad K; Sengupta, Soma 2021. Melanoma Cell Intrinsic GABAA Receptor Enhancement Potentiates Radiation and Immune Checkpoint Inhibitor Response by Promoting Direct and T Cell-Mediated Antitumor Activity. International journal of radiation oncology, biology, physics, 109 4, 1040-1053

Reigle, James; Secic, Dina; Biesiada, Jacek; Wetzel, Collin; Shamsaei, Behrouz; Chu, Johnson; Zang, Yuanwei; Zhang, Xiang; Talbot, Nicholas J; Bischoff, Megan E; Zhang, Yongzhen; Thakar, Charuhas V; Gaitonde, Krishnanath; Sidana, Abhinav; Bui, Hai; Cunningham, John T; Zhang, Qing; Schmidt, Laura S; Linehan, W Marston; Medvedovic, Mario; Plas, David R; Figueroa, Julio A Landero; Meller, Jarek; Czyzyk-Krzeska, Maria F 2021. Tobacco smoking induces metabolic reprogramming of renal cell carcinoma. The Journal of clinical investigation, 131 1,

Schulert, Grant S; Pickering, Alex V; Do, Thuy; Dhakal, Sanjeev; Fall, Ndate; Schnell, Daniel; Medvedovic, Mario; Salomonis, Nathan; Thornton, Sherry; Grom, Alexei A 2021. Monocyte and bone marrow macrophage transcriptional phenotypes in systemic juvenile idiopathic arthritis reveal TRIM8 as a mediator of IFN-? hyper-responsiveness and risk for macrophage activation syndrome. Annals of the rheumatic diseases, 80 5, 617-625

VonHandorf, Andrew; Zablon, Hesbon A; Biesiada, Jacek; Zhang, Xiang; Medvedovic, Mario; Puga, Alvaro 2021. Hexavalent chromium promotes differential binding of CTCF to its cognate sites in Euchromatin. Epigenetics, , 1-16

de Gannes, Matthew; Ko, Chia-I; Zhang, Xiang; Biesiada, Jacek; Niu, Liang; Koch, Sheryl E; Medvedovic, Mario; Rubinstein, Jack; Puga, Alvaro 2020. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicological sciences : an official journal of the Society of Toxicology, 178 2, 325-337

Jodele, Sonata; Medvedovic, Mario; Luebbering, Nathan; Chen, Jenny; Dandoy, Christopher E; Laskin, Benjamin L; Davies, Stella M 2020. Interferon-complement loop in transplant-associated thrombotic microangiopathy. Blood advances, 4 6, 1166-1177

Langevin, Scott M; Kuhnell, Damaris; Biesiada, Jacek; Zhang, Xiang; Medvedovic, Mario; Talaska, Glenn G; Burns, Katherine A; Kasper, Susan 2020. Comparability of the small RNA secretome across human biofluids concomitantly collected from healthy adults. PloS one, 15 4, e0229976

Leung, Yuet-Kin; Biesiada, Jacek; Govindarajah, Vinothini; Ying, Jun; Kendler, Ady; Medvedovic, Mario; Ho, Shuk-Mei 2020. Low-Dose Bisphenol A in a Rat Model of Endometrial Cancer: A CLARITY-BPA Study. Environmental health perspectives, 128 12, 127005

Ren, Yan; Sivaganesan, Siva; Clark, Nicholas A; Zhang, Lixia; Biesiada, Jacek; Niu, Wen; Plas, David R; Medvedovic, Mario 2020. Predicting mechanism of action of cellular perturbations with pathway activity signatures. Bioinformatics (Oxford, England), 36 18, 4781-4788

Shamsaei, Behrouz; Chojnacki, Szymon; Pilarczyk, Marcin; Najafabadi, Mehdi; Niu, Wen; Chen, Chuming; Ross, Karen; Matlock, Andrea; Muhlich, Jeremy; Chutipongtanate, Somchai; Zheng, Jie; Turner, John; Vidovi?, Dušica; Jaffe, Jake; MacCoss, Michael; Wu, Cathy; Pillai, Ajay; Ma'ayan, Avi; Schürer, Stephan; Kouril, Michal; Medvedovic, Mario; Meller, Jarek 2020. piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic acids research, 48 W1, W85-W93

Stathias, Vasileios; Turner, John; Koleti, Amar; Vidovic, Dusica; Cooper, Daniel; Fazel-Najafabadi, Mehdi; Pilarczyk, Marcin; Terryn, Raymond; Chung, Caty; Umeano, Afoma; Clarke, Daniel J B; Lachmann, Alexander; Evangelista, John Erol; Ma'ayan, Avi; Medvedovic, Mario; Schürer, Stephan C 2020. LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic acids research, 48 D1, D431-D439

Stefely, Jonathan A; Zhang, Yu; Freiberger, Elyse C; Kwiecien, Nicholas W; Thomas, Hala Elnakat; Davis, Alexander M; Lowry, Nathaniel D; Vincent, Catherine E; Shishkova, Evgenia; Clark, Nicholas A; Medvedovic, Mario; Coon, Joshua J; Pagliarini, David J; Mercer, Carol A 2020. Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy. Autophagy, 16 12, 2219-2237

Choobdar, Sarvenaz; Ahsen, Mehmet E; Crawford, Jake; Tomasoni, Mattia; Fang, Tao; Lamparter, David; Lin, Junyuan; Hescott, Benjamin; Hu, Xiaozhe; Mercer, Johnathan; Natoli, Ted; Narayan, Rajiv ; Subramanian, Aravind; Zhang, Jitao D; Stolovitzky, Gustavo; Kutalik, Zoltán; Lage, Kasper; Slonim, Donna K; Saez-Rodriguez, Julio; Cowen, Lenore J; Bergmann, Sven; Marbach, Daniel 2019. Assessment of network module identification across complex diseases. Nature methods, 16 9, 843-852

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

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

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

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

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

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

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

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

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

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

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

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, 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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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

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

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

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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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, 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

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, 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

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

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

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, 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

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

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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Medvedovic, Mario; Sivaganesan, Siva 2002. Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics (Oxford, England), 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. Environmental and molecular mutagenesis, 37 4, 329-39

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; 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

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

Mahi N.;Najafabadi M.;Pilarczyk M.;Kouril M.;Medvedovic M. 12-01-2019. GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data Scientific Reports, 9 1,

Hu Z.;Sivaganesan S.;Medvedovic M. 12-01-2010. Prior information based Bayesian Infinite Mixture Model 11th International Symposium on Artificial Intelligence and Mathematics, ISAIM 2010, ,

Nikiforova M.;Stringer J.;Blough R.;Medvedovic M.;Fagin J.;Nikiforov Y. 10-06-2000. Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells Science, 290 5489, 138-141

Meng Q.;Jin C.;Chen Y.;Chen J.;Medvedovic M. 08-26-2014. Expression of signaling components in embryonic eyelid epithelium (PLoS ONE (2014) 9, 2 (e87038) DOI PLoS ONE, 9 8,

Singh B.;Jegga A.;Shanmukhappa K.;Edukulla R.;Khurana G.;Medvedovic M.;Dillon S.;Madala S. 08-01-2016. IL-31-driven skin remodeling involves epidermal cell proliferation and thickening that lead to impai PLoS ONE, 11 8,

Niepel M.;Hafner M.;Mills C.E.;Subramanian K.;Williams E.H.;Chung M.;Gaudio B.;Barrette A.M.;Stern A.D.;Hu B.;Korkola J.E.;Shamu C.E.;Jayaraman G.;Azeloglu E.U.;Iyengar R.;Sobie E.A.;Mills G.B.;Liby T.;Jaffe J.D.;Alimova M.;Davison D.;Lu X.;Golub T.R.;Subramanian A.;Shelley B.;Svendsen C.N.;Ma'ayan A.;Medvedovic M.;Gray J.W.;Birtwistle M.R.;Heiser L.M.;Sorger P.K. 07-24-2019. A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines Cell Systems, 9 1, 35-48.e5

Langevin S.M.;Kuhnell D.;Niu L.;Biesiada J.;Leung Y.K.;Deka R.;Chen A.;Medvedovic M.;Kelsey K.T.;Kasper S.;Zhang X. 07-01-2019. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal sq Epigenomics, 11 9, 987-1002

Moret N.;Clark N.A.;Hafner M.;Wang Y.;Lounkine E.;Medvedovic M.;Wang J.;Gray N.;Jenkins J.;Sorger P.K. 05-16-2019. Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries Cell Chemical Biology, 26 5, 765-777.e3

Medvedovic M.;Succop P.;Shukla R.;Dixon K. 03-01-2001. Clustering mutational spectra via classification likelihood and markov chain monte carlo algorithms Journal of Agricultural, Biological, and Environmental Statistics, 6 1, 19-37

Jin C.;Chen J.;Meng Q.;Carreira V.;Tam N.;Geh E.;Karyala S.;Ho S.;Zhou X.;Medvedovic M.;Xia Y. 02-01-2013. Deciphering gene expression program of MAP3K1 in mouse eyelid morphogenesis Developmental Biology, 374 1, 96-107

Joshi V.;Freudenberg J.;Hu Z.;Medvedovic M. 01-17-2011. WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive Source Code for Biology and Medicine, 6 ,

Langevin S.;Kuhnell D.;Parry T.;Biesiada J.;Huang S.;Wise-Draper T.;Casper K.;Zhang X.;Medvedovic M.;Kasper S. 01-01-2017. Comprehensive microRNA-sequencing of exosomes derived from head and neck carcinoma cells in vitro re Oncotarget, 8 47, 82459-82474

Engevik A.;Feng R.;Choi E.;White S.;Bertaux-Skeirik N.;Li J.;Mahe M.;Aihara E.;Yang L.;DiPasquale B.;Oh S.;Engevik K.;Giraud A.;Montrose M.;Medvedovic M.;Helmrath M.;Goldenring J.;Zavros Y. 01-01-2016. The Development of Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) During Gastric Repair I Cellular and Molecular Gastroenterology and Hepatology, 2 5, 605-624

Buhule O.D.;Minster R.L.;Hawley N.L.;Medvedovic M.;Sun G.;Viali S.;Deka R.;McGarvey S.T.;Weeks D.E. 01-01-2014. Stratified randomization controls better for batch effects in 450K methylation analysis: A cautionar Frontiers in Genetics, 5 SEP,

Freudenberg J.;Sivaganesan S.;Phatak M.;Shinde K.;Medvedovic M. 01-01-2011. Generalized random set framework for functional enrichment analysis using primary genomics datasets Bioinformatics, 27 1, 70-77

Medvedovic M.;Wiest J. 01-01-2005. DNA microarrays and computational analysis of DNA microarray data in cancer research Molecular Carcinogenesis and the Molecular Biology of Human Cancer, , 243-262

Levin L.S.;Rice C.H.;Lemasters G.K.;Lockey J.E.;Medvedovic M. 01-01-2000. What is the potential measurement error in occupational exposure studies? Journal of the Air and Waste Management Association, 50 6, 941-947

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

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

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