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Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma.

Langevin SM, Kuhnell D, Niu L, Biesiada J, Leung YK, Deka R, Chen A, Medvedovic M, Kelsey KT, Kasper S, Zhang X.

Epigenomics. 2019 Jul;11(9):987-1002. doi: 10.2217/epi-2018-0172. Epub 2019 Jun 19.


GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

Mahi NA, Najafabadi MF, Pilarczyk M, Kouril M, Medvedovic M.

Sci Rep. 2019 May 20;9(1):7580. doi: 10.1038/s41598-019-43935-8.


Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries.

Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK.

Cell Chem Biol. 2019 May 16;26(5):765-777.e3. doi: 10.1016/j.chembiol.2019.02.018. Epub 2019 Apr 4.


ChIAPoP: a new tool for ChIA-PET data analysis.

Huang W, Medvedovic M, Zhang J, Niu L.

Nucleic Acids Res. 2019 Apr 23;47(7):e37. doi: 10.1093/nar/gkz062.


Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum.

Langevin SM, Kuhnell D, Orr-Asman MA, Biesiada J, Zhang X, Medvedovic M, Thomas HE.

RNA Biol. 2019 Jan;16(1):5-12. doi: 10.1080/15476286.2018.1564465. Epub 2019 Jan 13.


The N6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and Hypertrophy.

Dorn LE, Lasman L, Chen J, Xu X, Hund TJ, Medvedovic M, Hanna JH, van Berlo JH, Accornero F.

Circulation. 2019 Jan 22;139(4):533-545. doi: 10.1161/CIRCULATIONAHA.118.036146.


An Organoid-Based Preclinical Model of Human Gastric Cancer.

Steele NG, Chakrabarti J, Wang J, Biesiada J, Holokai L, Chang J, Nowacki LM, Hawkins J, Mahe M, Sundaram N, Shroyer N, Medvedovic M, Helmrath M, Ahmad S, Zavros Y.

Cell Mol Gastroenterol Hepatol. 2019;7(1):161-184. doi: 10.1016/j.jcmgh.2018.09.008. Epub 2018 Sep 20.


NBCe1 Na+-HCO3- cotransporter ablation causes reduced apoptosis following cardiac ischemia-reperfusion injury in vivo.

Vairamani K, Prasad V, Wang Y, Huang W, Chen Y, Medvedovic M, Lorenz JN, Shull GE.

World J Cardiol. 2018 Sep 26;10(9):97-109. doi: 10.4330/wjc.v10.i9.97.


Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.

Stathias V, Koleti A, Vidović D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC.

Sci Data. 2018 Jun 19;5:180117. doi: 10.1038/sdata.2018.117.


Interleukin-22 levels are increased in gastrointestinal graft-versus-host disease in children.

Lounder DT, Khandelwal P, Gloude NJ, Dandoy CE, Jodele S, Medvedovic M, Denson LA, Lane A, Lake K, Litts B, Wilkey A, Davies SM.

Haematologica. 2018 Oct;103(10):e480-e482. doi: 10.3324/haematol.2017.174771. Epub 2018 May 17. No abstract available.


Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma.

Haque SU, Niu L, Kuhnell D, Hendershot J, Biesiada J, Niu W, Hagan MC, Kelsey KT, Casper KA, Wise-Draper TM, Medvedovic M, Langevin SM.

Head Neck. 2018 Jul;40(7):1555-1564. doi: 10.1002/hed.25136. Epub 2018 Mar 25.


Chromium disrupts chromatin organization and CTCF access to its cognate sites in promoters of differentially expressed genes.

VonHandorf A, Sánchez-Martín FJ, Biesiada J, Zhang H, Zhang X, Medvedovic M, Puga A.

Epigenetics. 2018;13(4):363-375. doi: 10.1080/15592294.2018.1454243. Epub 2018 May 3.


Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort.

Leung YK, Ouyang B, Niu L, Xie C, Ying J, Medvedovic M, Chen A, Weihe P, Valvi D, Grandjean P, Ho SM.

Epigenetics. 2018;13(3):290-300. doi: 10.1080/15592294.2018.1445901. Epub 2018 May 16.


Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration.

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 WS, Sadayappan S, Stambrook PJ, Yu XY, Wang Y.

Nat Commun. 2018 Feb 16;9(1):700. doi: 10.1038/s41467-018-03019-z.


MicroRNA networks associated with active systemic juvenile idiopathic arthritis regulate CD163 expression and anti-inflammatory functions in macrophages through two distinct mechanisms.

Do T, Tan R, Bennett M, Medvedovic M, Grom AA, Shen N, Thornton S, Schulert GS.

J Leukoc Biol. 2018 Jan;103(1):71-85. doi: 10.1002/JLB.2A0317-107R. Epub 2017 Dec 29.


Ultra-Deep Genomic Sequencing of HCV NS5A Resistance-Associated Substitutions in HCV/HIV Coinfected Patients.

Abdel-Hameed EA, Rouster SD, Boyce CL, Zhang X, Biesiada J, Medvedovic M, Sherman KE.

Dig Dis Sci. 2018 Mar;63(3):645-652. doi: 10.1007/s10620-017-4895-1. Epub 2018 Jan 12.


The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, 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 CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A.

Cell Syst. 2018 Jan 24;6(1):13-24. doi: 10.1016/j.cels.2017.11.001. Epub 2017 Nov 29. Review.


Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data.

Koleti A, Terryn R, Stathias V, Chung C, Cooper DJ, Turner JP, Vidovic D, Forlin M, Kelley TT, D'Urso A, Allen BK, Torre D, Jagodnik KM, Wang L, Jenkins SL, 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, Schürer SC.

Nucleic Acids Res. 2018 Jan 4;46(D1):D558-D566. doi: 10.1093/nar/gkx1063.


Comprehensive microRNA-sequencing of exosomes derived from head and neck carcinoma cells in vitro reveals common secretion profiles and potential utility as salivary biomarkers.

Langevin S, Kuhnell D, Parry T, Biesiada J, Huang S, Wise-Draper T, Casper K, Zhang X, Medvedovic M, Kasper S.

Oncotarget. 2017 Jul 27;8(47):82459-82474. doi: 10.18632/oncotarget.19614. eCollection 2017 Oct 10.


GRcalculator: an online tool for calculating and mining dose-response data.

Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M.

BMC Cancer. 2017 Oct 24;17(1):698. doi: 10.1186/s12885-017-3689-3.


RNA SEQ Analysis Indicates that the AE3 Cl-/HCO3- Exchanger Contributes to Active Transport-Mediated CO2 Disposal in Heart.

Vairamani K, Wang HS, Medvedovic M, Lorenz JN, Shull GE.

Sci Rep. 2017 Aug 4;7(1):7264. doi: 10.1038/s41598-017-07585-y.


Transcriptional profiles of JIA patient blood with subsequent poor response to methotrexate.

Moncrieffe H, Bennett MF, Tsoras M, Luyrink LK, Johnson AL, Xu H, Dare J, Becker ML, Prahalad S, Rosenkranz M, O'Neil KM, Nigrovic PA, Griffin TA, Lovell DJ, Grom AA, Medvedovic M, Thompson SD.

Rheumatology (Oxford). 2017 Sep 1;56(9):1542-1551. doi: 10.1093/rheumatology/kex206.


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.

Heymann PW, Nguyen HT, Steinke JW, Turner RB, Woodfolk JA, Platts-Mills TAE, Martin L, He H, Biagini Myers J, Lindsey M, Sivaprasad U, Medvedovic M, Mahi N, Carper H, Murphy DD, Patrie J, Khurana Hershey GK.

PLoS One. 2017 May 26;12(5):e0178096. doi: 10.1371/journal.pone.0178096. eCollection 2017.


Transcriptome of the GSH-Depleted Lens Reveals Changes in Detoxification and EMT Signaling Genes, Transport Systems, and Lipid Homeostasis.

Whitson JA, Zhang X, Medvedovic M, Chen J, Wei Z, Monnier VM, Fan X.

Invest Ophthalmol Vis Sci. 2017 May 1;58(5):2666-2684. doi: 10.1167/iovs.16-21398.


CD44 variant isoform 9 emerges in response to injury and contributes to the regeneration of the gastric epithelium.

Bertaux-Skeirik N, Wunderlich M, Teal E, Chakrabarti J, Biesiada J, Mahe M, Sundaram N, Gabre J, Hawkins J, Jian G, Engevik AC, Yang L, Wang J, Goldenring JR, Qualls JE, Medvedovic M, Helmrath MA, Diwan T, Mulloy JC, Zavros Y.

J Pathol. 2017 Aug;242(4):463-475. doi: 10.1002/path.4918.


Gestational high-fat diet and bisphenol A exposure heightens mammary cancer risk.

Leung YK, Govindarajah V, Cheong A, Veevers J, Song D, Gear R, Zhu X, Ying J, Kendler A, Medvedovic M, Belcher S, Ho SM.

Endocr Relat Cancer. 2017 Jul;24(7):365-378. doi: 10.1530/ERC-17-0006. Epub 2017 May 9.


Genetic susceptibility to toxicologic lung responses among inbred mouse strains following exposure to carbon nanotubes and profiling of underlying gene networks.

Frank EA, Carreira VS, Shanmukhappa K, Medvedovic M, Prows DR, Yadav JS.

Toxicol Appl Pharmacol. 2017 Jul 15;327:59-70. doi: 10.1016/j.taap.2017.04.019. Epub 2017 Apr 19.


Correction: IL-31-Driven Skin Remodeling Involves Epidermal Cell Proliferation and Thickening That Lead to Impaired Skin-Barrier Function.

Singh B, Jegga AG, Shanmukhappa KS, Edukulla R, Khurana Hershey GK, Medvedovic M, Dillon SR, Madala SK.

PLoS One. 2017 Jan 23;12(1):e0170446. doi: 10.1371/journal.pone.0170446. eCollection 2017.


The Development of Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) During Gastric Repair Is Absent in the Aged Stomach.

Engevik AC, Feng R, Choi E, White S, Bertaux-Skeirik N, Li J, Mahe MM, Aihara E, Yang L, DiPasquale B, Oh S, Engevik KA, Giraud AS, Montrose MH, Medvedovic M, Helmrath MA, Goldenring JR, Zavros Y.

Cell Mol Gastroenterol Hepatol. 2016 May 17;2(5):605-624. eCollection 2016 Sep.


Characterization of HCV NS3 Protease Variants in HCV/HIV-Coinfected Patients by Ultra-Deep Sequence Analysis: Relationship with Hepatic Fibrosis.

Abdel-Hameed EA, Rouster SD, Zhang X, Chen J, Medvedovic M, Goodman ZD, Sherman KE.

J Acquir Immune Defic Syndr. 2017 Mar 1;74(3):353-358. doi: 10.1097/QAI.0000000000001256.


IL-31-Driven Skin Remodeling Involves Epidermal Cell Proliferation and Thickening That Lead to Impaired Skin-Barrier Function.

Singh B, Jegga AG, Shanmukhappa KS, Edukulla R, Khurana Hershey GH, Medvedovic M, Dillon SR, Madala SK.

PLoS One. 2016 Aug 24;11(8):e0161877. doi: 10.1371/journal.pone.0161877. eCollection 2016. Erratum in: PLoS One. 2017 Jan 23;12 (1):e0170446. Khurana, Gurjit H [corrected to Khurana Hershey, Gurjit H].


DNA methylome changes by estradiol benzoate and bisphenol A links early-life environmental exposures to prostate cancer risk.

Cheong A, Zhang X, Cheung YY, Tang WY, Chen J, Ye SH, Medvedovic M, Leung YK, Prins GS, Ho SM.

Epigenetics. 2016 Sep;11(9):674-689. doi: 10.1080/15592294.2016.1208891. Epub 2016 Jul 14.


Reprogramming of the Epigenome by MLL1 Links Early-Life Environmental Exposures to Prostate Cancer Risk.

Wang Q, Trevino LS, Wong RL, Medvedovic M, Chen J, Ho SM, Shen J, Foulds CE, Coarfa C, O'Malley BW, Shilatifard A, Walker CL.

Mol Endocrinol. 2016 Aug;30(8):856-71. doi: 10.1210/me.2015-1310. Epub 2016 May 24.


Loss of IκB kinase β promotes myofibroblast transformation and senescence through activation of the ROS-TGFβ autocrine loop.

Chen L, Peng Z, Meng Q, Mongan M, Wang J, Sartor M, Chen J, Niu L, Medvedovic M, Kao W, Xia Y.

Protein Cell. 2016 May;7(5):338-50. doi: 10.1007/s13238-015-0241-6. Epub 2016 Mar 5.


In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands.

Govindarajah V, Leung YK, Ying J, Gear R, Bornschein RL, Medvedovic M, Ho SM.

J Nutr Biochem. 2016 Mar;29:73-82. doi: 10.1016/j.jnutbio.2015.11.003. Epub 2015 Nov 26.


Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks.

Sun X, Medvedovic M.

IET Syst Biol. 2016 Feb;10(1):10-6. doi: 10.1049/iet-syb.2015.0034.


The genetic fingerprint of susceptibility for transplant-associated thrombotic microangiopathy.

Jodele S, Zhang K, Zou F, Laskin B, Dandoy CE, Myers KC, Lane A, Meller J, Medvedovic M, Chen J, Davies SM.

Blood. 2016 Feb 25;127(8):989-96. doi: 10.1182/blood-2015-08-663435. Epub 2015 Nov 24.


Ah Receptor Activation by Dioxin Disrupts Activin, BMP, and WNT Signals During the Early Differentiation of Mouse Embryonic Stem Cells and Inhibits Cardiomyocyte Functions.

Wang Q, Kurita H, Carreira V, Ko CI, Fan Y, Zhang X, Biesiada J, Medvedovic M, Puga A.

Toxicol Sci. 2016 Feb;149(2):346-57. doi: 10.1093/toxsci/kfv246. Epub 2015 Nov 15.


Disruption of Ah Receptor Signaling during Mouse Development Leads to Abnormal Cardiac Structure and Function in the Adult.

Carreira VS, Fan Y, Kurita H, Wang Q, Ko CI, Naticchioni M, Jiang M, Koch S, Zhang X, Biesiada J, Medvedovic M, Xia Y, Rubinstein J, Puga A.

PLoS One. 2015 Nov 10;10(11):e0142440. doi: 10.1371/journal.pone.0142440. eCollection 2015.


Bisphenol A Disrupts HNF4α-Regulated Gene Networks Linking to Prostate Preneoplasia and Immune Disruption in Noble Rats.

Lam HM, Ho SM, Chen J, Medvedovic M, Tam NN.

Endocrinology. 2016 Jan;157(1):207-19. doi: 10.1210/en.2015-1363. Epub 2015 Oct 23.


Fibrocytes Regulate Wilms Tumor 1-Positive Cell Accumulation in Severe Fibrotic Lung Disease.

Sontake V, Shanmukhappa SK, DiPasquale BA, Reddy GB, Medvedovic M, Hardie WD, White ES, Madala SK.

J Immunol. 2015 Oct 15;195(8):3978-91. doi: 10.4049/jimmunol.1500963. Epub 2015 Sep 14.


Exposure of Human Prostaspheres to Bisphenol A Epigenetically Regulates SNORD Family Noncoding RNAs via Histone Modification.

Ho SM, Cheong A, Lam HM, Hu WY, Shi GB, Zhu X, Chen J, Zhang X, Medvedovic M, Leung YK, Prins GS.

Endocrinology. 2015 Nov;156(11):3984-95. doi: 10.1210/en.2015-1067. Epub 2015 Aug 6.


Ah Receptor Signaling Controls the Expression of Cardiac Development and Homeostasis Genes.

Carreira VS, Fan Y, Wang Q, Zhang X, Kurita H, Ko CI, Naticchioni M, Jiang M, Koch S, Medvedovic M, Xia Y, Rubinstein J, Puga A.

Toxicol Sci. 2015 Oct;147(2):425-35. doi: 10.1093/toxsci/kfv138. Epub 2015 Jul 2.


Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate.

Wong RL, Wang Q, Treviño LS, Bosland MC, Chen J, Medvedovic M, Prins GS, Kannan K, Ho SM, Walker CL.

Epigenetics. 2015;10(2):127-34. doi: 10.1080/15592294.2015.1009768.


Sex- and tissue-specific methylome changes in brains of mice perinatally exposed to lead.

Sánchez-Martín FJ, Lindquist DM, Landero-Figueroa J, Zhang X, Chen J, Cecil KM, Medvedovic M, Puga A.

Neurotoxicology. 2015 Jan;46:92-100. doi: 10.1016/j.neuro.2014.12.004. Epub 2014 Dec 18.


Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale.

Buhule OD, Minster RL, Hawley NL, Medvedovic M, Sun G, Viali S, Deka R, McGarvey ST, Weeks DE.

Front Genet. 2014 Oct 13;5:354. doi: 10.3389/fgene.2014.00354. eCollection 2014.


Targeting GPR30 with G-1: a new therapeutic target for castration-resistant prostate cancer.

Lam HM, Ouyang B, Chen J, Ying J, Wang J, Wu CL, Jia L, Medvedovic M, Vessella RL, Ho SM.

Endocr Relat Cancer. 2014;21(6):903-14. doi: 10.1530/ERC-14-0402. Epub 2014 Oct 6.


SPDEF inhibits prostate carcinogenesis by disrupting a positive feedback loop in regulation of the Foxm1 oncogene.

Cheng XH, Black M, Ustiyan V, Le T, Fulford L, Sridharan A, Medvedovic M, Kalinichenko VV, Whitsett JA, Kalin TV.

PLoS Genet. 2014 Sep 25;10(9):e1004656. doi: 10.1371/journal.pgen.1004656. eCollection 2014 Sep.


SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis.

Sivaprasad U, Kinker KG, Ericksen MB, Lindsey M, Gibson AM, Bass SA, Hershey NS, Deng J, Medvedovic M, Khurana Hershey GK.

J Invest Dermatol. 2015 Jan;135(1):160-169. doi: 10.1038/jid.2014.353. Epub 2014 Aug 11.


Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis uncovers broad changes in chromatin structure resulting from hexavalent chromium exposure.

Ovesen JL, Fan Y, Zhang X, Chen J, Medvedovic M, Xia Y, Puga A.

PLoS One. 2014 May 16;9(5):e97849. doi: 10.1371/journal.pone.0097849. eCollection 2014.

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