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CRISTIAN COARFA

TitleAssociate Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Cellular Biology
DivisionMolecular & Cellular Biology
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    R01DK111522     (WATERLAND, ROBERT A)Mar 1, 2017 - Feb 28, 2021
    NIH/NIDDK
    Epigenetic variation at metastable epialleles: Effects on human obesity
    Role: Co-Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Taneja G, Maity S, Jiang W, Moorthy B, Coarfa C, Ghose R. Transcriptomic profiling identifies novel mechanisms of transcriptional regulation of the cytochrome P450 (Cyp)3a11 gene. Sci Rep. 2019 Apr 30; 9(1):6663. PMID: 31040347.
      View in: PubMed
    2. Mill CP, Fiskus W, DiNardo CD, Qian Y, Raina K, Rajapakshe K, Perera D, Coarfa C, Kadia TM, Khoury JD, Saenz DT, Saenz DN, Illendula A, Takahashi K, Kornblau SM, Green MR, Futreal AP, Bushweller JH, Crews CM, Bhalla KN. RUNX1 targeted therapy for AML expressing somatic or germline mutation in RUNX1. Blood. 2019 Apr 25. PMID: 31023702.
      View in: PubMed
    3. Gunaratne PH, Pan Y, Rao AK, Lin C, Hernandez-Herrera A, Liang K, Rait AS, Venkatanarayan A, Benham AL, Rubab F, Kim SS, Rajapakshe K, Chan CK, Mangala LS, Lopez-Berestein G, Sood AK, Rowat AC, Coarfa C, Pirollo KF, Flores ER, Chang EH. Activating p53 family member TAp63: A novel therapeutic strategy for targeting p53-altered tumors. Cancer. 2019 Apr 23. PMID: 31012964.
      View in: PubMed
    4. Cheedipudi SM, Matkovich SJ, Coarfa C, Hu X, Robertson MJ, Sweet M, Taylor M, Mestroni L, Cleveland J, Willerson JT, Gurha P, Marian AJ. Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes Is Associated With Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy. Circ Res. 2019 Apr 12; 124(8):1198-1213. PMID: 30739589.
      View in: PubMed
    5. Marisetty AL, Lu L, Veo BL, Liu B, Coarfa C, Kamal MM, Kassem DH, Irshad K, Lu Y, Gumin J, Henry V, Paulucci-Holthauzen A, Rao G, Baladandayuthapani V, Lang FF, Fuller GN, Majumder S. REST-DRD2 mechanism impacts glioblastoma stem cell-mediated tumorigenesis. Neuro Oncol. 2019 04 06. PMID: 30953587.
      View in: PubMed
    6. Chen SN, Lombardi R, Karmouch J, Tsai JY, Czernuszewicz G, Taylor MRG, Mestroni L, Coarfa C, Gurha P, Marian AJ. DNA Damage Response/TP53 Pathway Is Activated and Contributes to the Pathogenesis of Dilated Cardiomyopathy Associated With LMNA (Lamin A/C) Mutations. Circ Res. 2019 Mar 15; 124(6):856-873. PMID: 30696354.
      View in: PubMed
    7. Vantaku V, Dong J, Ambati CR, Perera D, Donepudi SR, Amara CS, Putluri V, Ravi SS, Robertson MJ, Piyarathna DWB, Villanueva M, von Rundstedt FC, Karanam B, Ballester LY, Terris MK, Bollag RJ, Lerner SP, Apolo AB, Villanueva H, Lee M, Sikora AG, Lotan Y, Sreekumar A, Coarfa C, Putluri N. Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer. Clin Cancer Res. 2019 Mar 07. PMID: 30846479.
      View in: PubMed
    8. Villanueva H, Grimm SL, Dhamne S, Rajapakshe K, Visbal AP, Davis CM, Ehli EA, Hartig SM, Coarfa C, Edwards DP. Correction to: The Emerging Roles of Steroid Hormone Receptors in Ductal Carcinoma in Situ (DCIS) of the Breast. J Mammary Gland Biol Neoplasia. 2019 Mar; 24(1):109-110. PMID: 30465315.
      View in: PubMed
    9. Mahendra A, Yang X, Abnouf S, Adolacion JRT, Park D, Soomro S, Roszik J, Coarfa C, Romain G, Wanzeck K, Bridges SL, Aggarwal A, Qiu P, Agarwal SK, Mohan C, Varadarajan N. Beyond Autoantibodies: Biologic Roles of Human Autoreactive B Cells in Rheumatoid Arthritis Revealed by RNA-Sequencing. Arthritis Rheumatol. 2019 Apr; 71(4):529-541. PMID: 30407753.
      View in: PubMed
    10. Nomura M, Rainusso N, Lee YC, Dawson B, Coarfa C, Han R, Larson JL, Shuck R, Kurenbekova L, Yustein JT. Tegavivint and the ß-catenin/ALDH Axis in Chemotherapy-Resistant and Metastatic Osteosarcoma. J Natl Cancer Inst. 2019 Feb 21. PMID: 30793158.
      View in: PubMed
    11. Jiao L, Maity S, Coarfa C, Rajapakshe K, Chen L, Jin F, Putluri V, Tinker LF, Mo Q, Chen F, Sen S, Sangi-Hyghpeykar H, El-Serag HB, Putluri N. A Prospective Targeted Serum Metabolomics Study of Pancreatic Cancer in Postmenopausal Women. Cancer Prev Res (Phila). 2019 Apr; 12(4):237-246. PMID: 30723176.
      View in: PubMed
    12. Fiskus W, Cai T, DiNardo CD, Kornblau SM, Borthakur G, Kadia TM, Pemmaraju N, Bose P, Masarova L, Rajapakshe K, Perera D, Coarfa C, Mill CP, Saenz DT, Saenz DN, Sun B, Khoury JD, Shen Y, Konopleva M, Bhalla KN. Superior efficacy of cotreatment with BET protein inhibitor and BCL2 or MCL1 inhibitor against AML blast progenitor cells. Blood Cancer J. 2019 Jan 15; 9(2):4. PMID: 30647404.
      View in: PubMed
    13. Xia J, Chiu LY, Nehring RB, Bravo Núñez MA, Mei Q, Perez M, Zhai Y, Fitzgerald DM, Pribis JP, Wang Y, Hu CW, Powell RT, LaBonte SA, Jalali A, Matadamas Guzmán ML, Lentzsch AM, Szafran AT, Joshi MC, Richters M, Gibson JL, Frisch RL, Hastings PJ, Bates D, Queitsch C, Hilsenbeck SG, Coarfa C, Hu JC, Siegele DA, Scott KL, Liang H, Mancini MA, Herman C, Miller KM, Rosenberg SM. Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. Cell. 2019 Jan 10; 176(1-2):127-143.e24. PMID: 30633903.
      View in: PubMed
    14. Moye LM, Liu Y, Coarfa C, Putluri N, Rhoads JM. Plasma Urea Cycle Metabolites May Be Useful Biomarkers in Children With Eosinophilic Esophagitis. Front Pediatr. 2018; 6:423. PMID: 30687688.
      View in: PubMed
    15. Saenz DT, Fiskus W, Manshouri T, Mill CP, Qian Y, Raina K, Rajapakshe K, Coarfa C, Soldi R, Bose P, Borthakur G, Kadia TM, Khoury JD, Masarova L, Nowak AJ, Sun B, Saenz DN, Kornblau SM, Horrigan S, Sharma S, Qiu P, Crews CM, Verstovsek S, Bhalla KN. Targeting nuclear ß-catenin as therapy for post-myeloproliferative neoplasm secondary AML. Leukemia. 2019 Jun; 33(6):1373-1386. PMID: 30575820.
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    16. Chen C, Meng Q, Xia Y, Ding C, Wang L, Dai R, Cheng L, Gunaratne P, Gibbs RA, Min S, Coarfa C, Reid JG, Zhang C, Jiao C, Jiang Y, Giase G, Thomas A, Fitzgerald D, Brunetti T, Shieh A, Xia C, Wang Y, Wang Y, Badner JA, Gershon ES, White KP, Liu C. The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders. Sci Transl Med. 2018 Dec 19; 10(472). PMID: 30545964.
      View in: PubMed
    17. Zhang Y, Coarfa C, Dong X, Jiang W, Hayward-Piatkovskyi B, Gleghorn JP, Lingappan K. MicroRNA-30a as a candidate underlying sex-specific differences in neonatal hyperoxic lung injury: implications for BPD. Am J Physiol Lung Cell Mol Physiol. 2019 Jan 01; 316(1):L144-L156. PMID: 30382766.
      View in: PubMed
    18. Villanueva H, Grimm S, Dhamne S, Rajapakshe K, Visbal A, Davis CM, Ehli EA, Hartig SM, Coarfa C, Edwards DP. The Emerging Roles of Steroid Hormone Receptors in Ductal Carcinoma in Situ (DCIS) of the Breast. J Mammary Gland Biol Neoplasia. 2018 Dec; 23(4):237-248. PMID: 30338425.
      View in: PubMed
    19. Pahlavani M, Wijayatunga NN, Kalupahana NS, Ramalingam L, Gunaratne PH, Coarfa C, Rajapakshe K, Kottapalli P, Moustaid-Moussa N. Transcriptomic and microRNA analyses of gene networks regulated by eicosapentaenoic acid in brown adipose tissue of diet-induced obese mice. Biochim Biophys Acta Mol Cell Biol Lipids. 2018 12; 1863(12):1523-1531. PMID: 30261280.
      View in: PubMed
    20. Zhang M, Suarez E, Vasquez JL, Nathanson L, Peterson LE, Rajapakshe K, Basil P, Weigel NL, Coarfa C, Agoulnik IU. Inositol polyphosphate 4-phosphatase type II regulation of androgen receptor activity. Oncogene. 2019 02; 38(7):1121-1135. PMID: 30228349.
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    21. Szwarc MM, Kommagani R, Putluri V, Dubrulle J, Stossi F, Mancini MA, Coarfa C, Lanz RB, Putluri N, DeMayo FJ, Lydon JP, O'Malley BW. Steroid Receptor Coactivator-2 Controls the Pentose Phosphate Pathway through RPIA in Human Endometrial Cancer Cells. Sci Rep. 2018 Sep 03; 8(1):13134. PMID: 30177747.
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    22. Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science. 2018 09 28; 361(6409). PMID: 30139913.
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    23. Cho RJ, Alexandrov LB, den Breems NY, Atanasova VS, Farshchian M, Purdom E, Nguyen TN, Coarfa C, Rajapakshe K, Prisco M, Sahu J, Tassone P, Greenawalt EJ, Collisson EA, Wu W, Yao H, Su X, Guttmann-Gruber C, Hofbauer JP, Hashmi R, Fuentes I, Benz SC, Golovato J, Ehli EA, Davis CM, Davies GE, Covington KR, Murrell DF, Salas-Alanis JC, Palisson F, Bruckner AL, Robinson W, Has C, Bruckner-Tuderman L, Titeux M, Jonkman MF, Rashidghamat E, Lwin SM, Mellerio JE, McGrath JA, Bauer JW, Hovnanian A, Tsai KY, South AP. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa. Sci Transl Med. 2018 Aug 22; 10(455). PMID: 30135250.
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    24. Morriss GR, Rajapakshe K, Huang S, Coarfa C, Cooper TA. Mechanisms of skeletal muscle wasting in a mouse model for myotonic dystrophy type 1. Hum Mol Genet. 2018 08 15; 27(16):2789-2804. PMID: 29771332.
      View in: PubMed
    25. Jayaraman P, Parikh F, Newton JM, Hanoteau A, Rivas C, Krupar R, Rajapakshe K, Pathak R, Kanthaswamy K, MacLaren C, Huang S, Coarfa C, Spanos C, Edwards DP, Parihar R, Sikora AG. TGF-ß1 programmed myeloid-derived suppressor cells (MDSC) acquire immune-stimulating and tumor killing activity capable of rejecting established tumors in combination with radiotherapy. Oncoimmunology. 2018; 7(10):e1490853. PMID: 30288358.
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    26. Purwaha P, Gu F, Piyarathna DWB, Rajendiran T, Ravindran A, Omilian AR, Jiralerspong S, Das G, Morrison C, Ambrosone C, Coarfa C, Putluri N, Sreekumar A. Unbiased Lipidomic Profiling of Triple-Negative Breast Cancer Tissues Reveals the Association of Sphingomyelin Levels with Patient Disease-Free Survival. Metabolites. 2018 Jul 13; 8(3). PMID: 30011843.
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    27. Koh EH, Chernis N, Saha PK, Xiao L, Bader DA, Zhu B, Rajapakshe K, Hamilton MP, Liu X, Perera D, Chen X, York B, Trauner M, Coarfa C, Bajaj M, Moore DD, Deng T, McGuire SE, Hartig SM. miR-30a Remodels Subcutaneous Adipose Tissue Inflammation to Improve Insulin Sensitivity in Obesity. Diabetes. 2018 12; 67(12):2541-2553. PMID: 30002134.
      View in: PubMed
    28. Agarwal S, Milazzo G, Rajapakshe K, Bernardi R, Chen Z, Eveline B, Koster J, Perini G, Coarfa C, Shohet JM. Correction: MYCN acts as a direct co-regulator of p53 in MYCN amplified neuroblastoma. Oncotarget. 2018 Jul 06; 9(52):30024. PMID: 30042831.
      View in: PubMed
    29. Xing Z, Zhang Y, Liang K, Yan L, Xiang Y, Li C, Hu Q, Jin F, Putluri V, Putluri N, Coarfa C, Sreekumar A, Park PK, Nguyen TK, Wang S, Zhou J, Zhou Y, Marks JR, Hawke DH, Hung MC, Yang L, Han L, Ying H, Lin C. Expression of Long Noncoding RNA YIYA Promotes Glycolysis in Breast Cancer. Cancer Res. 2018 Aug 15; 78(16):4524-4532. PMID: 29967256.
      View in: PubMed
    30. DiNardo AR, Nishiguchi T, Mace EM, Rajapakshe K, Mtetwa G, Kay A, Maphalala G, Secor WE, Mejia R, Orange JS, Coarfa C, Bhalla KN, Graviss EA, Mandalakas AM, Makedonas G. Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-Specific Immune Changes. J Immunol. 2018 07 01; 201(1):124-133. PMID: 29752313.
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    31. Agarwal S, Milazzo G, Rajapakshe K, Bernardi R, Chen Z, Barberi E, Koster J, Perini G, Coarfa C, Shohet JM. MYCN acts as a direct co-regulator of p53 in MYCN amplified neuroblastoma. Oncotarget. 2018 Apr 17; 9(29):20323-20338. PMID: 29755654.
      View in: PubMed
    32. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 04 03; 23(1):194-212.e6. PMID: 29617660.
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    33. Dasgupta S, Rajapakshe K, Zhu B, Nikolai BC, Yi P, Putluri N, Choi JM, Jung SY, Coarfa C, Westbrook TF, Zhang XH, Foulds CE, Tsai SY, Tsai MJ, O'Malley BW. Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive breast cancer. Nature. 2018 04; 556(7700):249-254. PMID: 29615789.
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    34. Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajagopalan S, Colacino JA, Tsai ZT, Sartor MA, Neier K, Dolinoy DC, Pinto J, Hamanaka RB, Mutlu GM, Patisaul HB, Aylor DL, Crawford GE, Wiltshire T, Chadwick LH, Duncan CG, Garton AE, McAllister KA, Bartolomei MS, Walker CL, Tyson FL. The NIEHS TaRGET II Consortium and environmental epigenomics. Nat Biotechnol. 2018 03 06; 36(3):225-227. PMID: 29509741.
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    35. White MA, Tsouko E, Lin C, Rajapakshe K, Spencer JM, Wilkenfeld SR, Vakili SS, Pulliam TL, Awad D, Nikolos F, Katreddy RR, Kaipparettu BA, Sreekumar A, Zhang X, Cheung E, Coarfa C, Frigo DE. GLUT12 promotes prostate cancer cell growth and is regulated by androgens and CaMKK2 signaling. Endocr Relat Cancer. 2018 04; 25(4):453-469. PMID: 29431615.
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    36. Wijayatunga NN, Pahlavani M, Kalupahana NS, Kottapalli KR, Gunaratne PH, Coarfa C, Ramalingam L, Moustaid-Moussa N. An integrative transcriptomic approach to identify depot differences in genes and microRNAs in adipose tissues from high fat fed mice. Oncotarget. 2018 Feb 06; 9(10):9246-9261. PMID: 29507687.
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    37. Van Baak TE, Coarfa C, Dugué PA, Fiorito G, Laritsky E, Baker MS, Kessler NJ, Dong J, Duryea JD, Silver MJ, Saffari A, Prentice AM, Moore SE, Ghantous A, Routledge MN, Gong YY, Herceg Z, Vineis P, Severi G, Hopper JL, Southey MC, Giles GG, Milne RL, Waterland RA. Epigenetic supersimilarity of monozygotic twin pairs. Genome Biol. 2018 01 09; 19(1):2. PMID: 29310692.
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    38. Auguste G, Gurha P, Lombardi R, Coarfa C, Willerson JT, Marian AJ. Suppression of Activated FOXO Transcription Factors in the Heart Prolongs Survival in a Mouse Model of Laminopathies. Circ Res. 2018 Mar 02; 122(5):678-692. PMID: 29317431.
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    39. Kaochar S, Dong J, Torres M, Rajapakshe K, Nikolos F, Davis CM, Ehli EA, Coarfa C, Mitsiades N, Poulaki V. ICG-001 Exerts Potent Anticancer Activity Against Uveal Melanoma Cells. Invest Ophthalmol Vis Sci. 2018 01 01; 59(1):132-143. PMID: 29332125.
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    40. Mindikoglu AL, Opekun AR, Putluri N, Devaraj S, Sheikh-Hamad D, Vierling JM, Goss JA, Rana A, Sood GK, Jalal PK, Inker LA, Mohney RP, Tighiouart H, Christenson RH, Dowling TC, Weir MR, Seliger SL, Hutson WR, Howell CD, Raufman JP, Magder LS, Coarfa C. Unique metabolomic signature associated with hepatorenal dysfunction and mortality in cirrhosis. Transl Res. 2018 05; 195:25-47. PMID: 29291380.
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    41. Abbas HA, Bui NHB, Rajapakshe K, Wong J, Gunaratne P, Tsai KY, Coarfa C, Flores ER. Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes. Cancer Res. 2018 01 15; 78(2):451-462. PMID: 29180475.
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    42. Fujita J, Freire P, Coarfa C, Benham AL, Gunaratne P, Schneider MD, Dejosez M, Zwaka TP. Ronin Governs Early Heart Development by Controlling Core Gene Expression Programs. Cell Rep. 2017 Nov 07; 21(6):1562-1573. PMID: 29117561.
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    43. Sun W, Rojas Y, Wang H, Yu Y, Wang Y, Chen Z, Rajapakshe K, Xu X, Huang W, Agarwal S, Patel RH, Woodfield S, Zhao Y, Jin J, Zhang H, Major A, Hicks MJ, Shohet JM, Vasudevan SA, Coarfa C, Yang J, Nuchtern JG. EWS-FLI1 and RNA helicase A interaction inhibitor YK-4-279 inhibits growth of neuroblastoma. Oncotarget. 2017 Nov 07; 8(55):94780-94792. PMID: 29212266.
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    44. Kim H, Li F, He Q, Deng T, Xu J, Jin F, Coarfa C, Putluri N, Liu D, Songyang Z. Systematic analysis of human telomeric dysfunction using inducible telosome/shelterin CRISPR/Cas9 knockout cells. Cell Discov. 2017; 3:17034. PMID: 28955502.
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    45. York B, Li F, Lin F, Marcelo KL, Mao J, Dean A, Gonzales N, Gooden D, Maity S, Coarfa C, Putluri N, Means AR. Pharmacological inhibition of CaMKK2 with the selective antagonist STO-609 regresses NAFLD. Sci Rep. 2017 09 18; 7(1):11793. PMID: 28924233.
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    46. Vantaku V, Donepudi SR, Ambati CR, Jin F, Putluri V, Nguyen K, Rajapakshe K, Coarfa C, Battula VL, Lotan Y, Putluri N. Expression of ganglioside GD2, reprogram the lipid metabolism and EMT phenotype in bladder cancer. Oncotarget. 2017 Nov 10; 8(56):95620-95631. PMID: 29221154.
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    47. Ware MJ, Nguyen LP, Law JJ, Krzykawska-Serda M, Taylor KM, Cao HST, Anderson AO, Pulikkathara M, Newton JM, Ho JC, Hwang R, Rajapakshe K, Coarfa C, Huang S, Edwards D, Curley SA, Corr SJ. A new mild hyperthermia device to treat vascular involvement in cancer surgery. Sci Rep. 2017 09 12; 7(1):11299. PMID: 28900126.
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    48. Liu R, Lee J, Kim BS, Wang Q, Buxton SK, Balasubramanyam N, Kim JJ, Dong J, Zhang A, Li S, Gupte AA, Hamilton DJ, Martin JF, Rodney GG, Coarfa C, Wehrens XH, Yechoor VK, Moulik M. Tead1 is required for maintaining adult cardiomyocyte function, and its loss results in lethal dilated cardiomyopathy. JCI Insight. 2017 09 07; 2(17). PMID: 28878117.
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    49. Jin F, Thaiparambil J, Donepudi SR, Vantaku V, Piyarathna DWB, Maity S, Krishnapuram R, Putluri V, Gu F, Purwaha P, Bhowmik SK, Ambati CR, von Rundstedt FC, Roghmann F, Berg S, Noldus J, Rajapakshe K, Gödde D, Roth S, Störkel S, Degener S, Michailidis G, Kaipparettu BA, Karanam B, Terris MK, Kavuri SM, Lerner SP, Kheradmand F, Coarfa C, Sreekumar A, Lotan Y, El-Zein R, Putluri N. Tobacco-Specific Carcinogens Induce Hypermethylation, DNA Adducts, and DNA Damage in Bladder Cancer. Cancer Prev Res (Phila). 2017 Oct; 10(10):588-597. PMID: 28851690.
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    50. Coarfa C, Zhang Y, Maity S, Perera DN, Jiang W, Wang L, Couroucli X, Moorthy B, Lingappan K. Sexual dimorphism of the pulmonary transcriptome in neonatal hyperoxic lung injury: identification of angiogenesis as a key pathway. Am J Physiol Lung Cell Mol Physiol. 2017 Dec 01; 313(6):L991-L1005. PMID: 28818871.
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    51. Satterfield L, Shuck R, Kurenbekova L, Allen-Rhoades W, Edwards D, Huang S, Rajapakshe K, Coarfa C, Donehower LA, Yustein JT. miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. Int J Cancer. 2017 11 15; 141(10):2062-2075. PMID: 28748534.
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    52. Johnson SAS, Lin JJ, Walkey CJ, Leathers MP, Coarfa C, Johnson DL. Elevated TATA-binding protein expression drives vascular endothelial growth factor expression in colon cancer. Oncotarget. 2017 Jul 25; 8(30):48832-48845. PMID: 28415573.
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    53. Roberts JM, Martin RS, Piyarathna DB, MacKrell JG, Rocha GV, Dodge JA, Coarfa C, Krishnan V, Rowley DR, Weigel NL. Vitamin D receptor activation reduces VCaP xenograft tumor growth and counteracts ERG activity despite induction of TMPRSS2:ERG. Oncotarget. 2017 Jul 04; 8(27):44447-44464. PMID: 28591703.
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    54. Wangler MF, Chao YH, Bayat V, Giagtzoglou N, Shinde AB, Putluri N, Coarfa C, Donti T, Graham BH, Faust JE, McNew JA, Moser A, Sardiello M, Baes M, Bellen HJ. Peroxisomal biogenesis is genetically and biochemically linked to carbohydrate metabolism in Drosophila and mouse. PLoS Genet. 2017 Jun; 13(6):e1006825. PMID: 28640802.
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    55. White MA, Lin C, Rajapakshe K, Dong J, Shi Y, Tsouko E, Mukhopadhyay R, Jasso D, Dawood W, Coarfa C, Frigo DE. Glutamine Transporters Are Targets of Multiple Oncogenic Signaling Pathways in Prostate Cancer. Mol Cancer Res. 2017 08; 15(8):1017-1028. PMID: 28507054.
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    56. Piyarathna DWB, Rajendiran TM, Putluri V, Vantaku V, Soni T, von Rundstedt FC, Donepudi SR, Jin F, Maity S, Ambati CR, Dong J, Gödde D, Roth S, Störkel S, Degener S, Michailidis G, Lerner SP, Pennathur S, Lotan Y, Coarfa C, Sreekumar A, Putluri N. Distinct Lipidomic Landscapes Associated with Clinical Stages of Urothelial Cancer of the Bladder. Eur Urol Focus. 2018 12; 4(6):907-915. PMID: 28753886.
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    57. Geng C, Kaochar S, Li M, Rajapakshe K, Fiskus W, Dong J, Foley C, Dong B, Zhang L, Kwon OJ, Shah SS, Bolaki M, Xin L, Ittmann M, O'Malley BW, Coarfa C, Mitsiades N. SPOP regulates prostate epithelial cell proliferation and promotes ubiquitination and turnover of c-MYC oncoprotein. Oncogene. 2017 08 17; 36(33):4767-4777. PMID: 28414305.
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    58. Lingappan K, Maity S, Jiang W, Wang L, Couroucli X, Veith A, Zhou G, Coarfa C, Moorthy B. Role of Cytochrome P450 (CYP)1A in Hyperoxic Lung Injury: Analysis of the Transcriptome and Proteome. Sci Rep. 2017 04 04; 7(1):642. PMID: 28377578.
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    59. Marisetty AL, Singh SK, Nguyen TN, Coarfa C, Liu B, Majumder S. REST represses miR-124 and miR-203 to regulate distinct oncogenic properties of glioblastoma stem cells. Neuro Oncol. 2017 04 01; 19(4):514-523. PMID: 28040710.
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    60. Bhardwaj A, Singh H, Rajapakshe K, Tachibana K, Ganesan N, Pan Y, Gunaratne PH, Coarfa C, Bedrosian I. Regulation of miRNA-29c and its downstream pathways in preneoplastic progression of triple-negative breast cancer. Oncotarget. 2017 Mar 21; 8(12):19645-19660. PMID: 28160548.
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    61. Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH. Correction: miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2017 Mar 07; 8(10):17406. PMID: 28403581.
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    62. Saenz DT, Fiskus W, Qian Y, Manshouri T, Rajapakshe K, Raina K, Coleman KG, Crew AP, Shen A, Mill CP, Sun B, Qiu P, Kadia TM, Pemmaraju N, DiNardo C, Kim MS, Nowak AJ, Coarfa C, Crews CM, Verstovsek S, Bhalla KN. Novel BET protein proteolysis-targeting chimera exerts superior lethal activity than bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm secondary (s) AML cells. Leukemia. 2017 09; 31(9):1951-1961. PMID: 28042144.
      View in: PubMed
    63. Blessing AM, Rajapakshe K, Reddy Bollu L, Shi Y, White MA, Pham AH, Lin C, Jonsson P, Cortes CJ, Cheung E, La Spada AR, Bast RC, Merchant FA, Coarfa C, Frigo DE. Transcriptional regulation of core autophagy and lysosomal genes by the androgen receptor promotes prostate cancer progression. Autophagy. 2017 Mar 04; 13(3):506-521. PMID: 27977328.
      View in: PubMed
    64. Kettner NM, Voicu H, Finegold MJ, Coarfa C, Sreekumar A, Putluri N, Katchy CA, Lee C, Moore DD, Fu L. Circadian Homeostasis of Liver Metabolism Suppresses Hepatocarcinogenesis. Cancer Cell. 2016 Dec 12; 30(6):909-924. PMID: 27889186.
      View in: PubMed
    65. Su X, Napoli M, Abbas HA, Venkatanarayan A, Bui NHB, Coarfa C, Gi YJ, Kittrell F, Gunaratne PH, Medina D, Rosen JM, Behbod F, Flores ER. TAp63 suppresses mammary tumorigenesis through regulation of the Hippo pathway. Oncogene. 2017 04 27; 36(17):2377-2393. PMID: 27869165.
      View in: PubMed
    66. Saenz DT, Fiskus W, Manshouri T, Rajapakshe K, Krieger S, Sun B, Mill CP, DiNardo C, Pemmaraju N, Kadia T, Parmar S, Sharma S, Coarfa C, Qiu P, Verstovsek S, Bhalla KN. BET protein bromodomain inhibitor-based combinations are highly active against post-myeloproliferative neoplasm secondary AML cells. Leukemia. 2017 03; 31(3):678-687. PMID: 27677740.
      View in: PubMed
    67. Basu-Roy U, Han E, Rattanakorn K, Gadi A, Verma N, Maurizi G, Gunaratne PH, Coarfa C, Kennedy OD, Garabedian MJ, Basilico C, Mansukhani A. PPAR? agonists promote differentiation of cancer stem cells by restraining YAP transcriptional activity. Oncotarget. 2016 Sep 20; 7(38):60954-60970. PMID: 27528232.
      View in: PubMed
    68. Ware MJ, Keshishian V, Law JJ, Ho JC, Favela CA, Rees P, Smith B, Mohammad S, Hwang RF, Rajapakshe K, Coarfa C, Huang S, Edwards DP, Corr SJ, Godin B, Curley SA. Generation of an in vitro 3D PDAC stroma rich spheroid model. Biomaterials. 2016 11; 108:129-42. PMID: 27627810.
      View in: PubMed
    69. Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016 08 30; 7:12601. PMID: 27574101.
      View in: PubMed
    70. Iwamori N, Tominaga K, Sato T, Riehle K, Iwamori T, Ohkawa Y, Coarfa C, Ono E, Matzuk MM. MRG15 is required for pre-mRNA splicing and spermatogenesis. Proc Natl Acad Sci U S A. 2016 09 13; 113(37):E5408-15. PMID: 27573846.
      View in: PubMed
    71. Fleet T, Stashi E, Zhu B, Rajapakshe K, Marcelo KL, Kettner NM, Gorman BK, Coarfa C, Fu L, O'Malley BW, York B. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology. J Biol Rhythms. 2016 10; 31(5):443-60. PMID: 27432117.
      View in: PubMed
    72. Ochsner SA, Tsimelzon A, Dong J, Coarfa C, McKenna NJ. Research Resource: A Reference Transcriptome for Constitutive Androstane Receptor and Pregnane X Receptor Xenobiotic Signaling. Mol Endocrinol. 2016 Aug; 30(8):937-48. PMID: 27409825.
      View in: PubMed
    73. Napoli M, Venkatanarayan A, Raulji P, Meyers BA, Norton W, Mangala LS, Sood AK, Rodriguez-Aguayo C, Lopez-Berestein G, Vin H, Duvic M, Tetzlaff MB, Curry JL, Rook AH, Abbas HA, Coarfa C, Gunaratne PH, Tsai KY, Flores ER. ?Np63/DGCR8-Dependent MicroRNAs Mediate Therapeutic Efficacy of HDAC Inhibitors in Cancer. Cancer Cell. 2016 06 13; 29(6):874-888. PMID: 27300436.
      View in: PubMed
    74. Adelmann CH, Truong KA, Liang RJ, Bansal V, Gandee L, Saporito RC, Lee W, Du L, Nicholas C, Napoli M, Mino B, South AP, Proby CM, Leigh IM, Coarfa C, Flores ER, Tsai KY. MEK Is a Therapeutic and Chemopreventative Target in Squamous Cell Carcinoma. J Invest Dermatol. 2016 09; 136(9):1920-1924. PMID: 27293029.
      View in: PubMed
    75. Hamilton MP, Rajapakshe KI, Bader DA, Cerne JZ, Smith EA, Coarfa C, Hartig SM, McGuire SE. The Landscape of microRNA Targeting in Prostate Cancer Defined by AGO-PAR-CLIP. Neoplasia. 2016 06; 18(6):356-70. PMID: 27292025.
      View in: PubMed
    76. 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. Reprogramming of the Epigenome by MLL1 Links Early-Life Environmental Exposures to Prostate Cancer Risk. Mol Endocrinol. 2016 Aug; 30(8):856-71. PMID: 27219490.
      View in: PubMed
    77. Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH. miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2016 May 03; 7(18):25930-48. PMID: 27036018.
      View in: PubMed
    78. Shivanna B, Maity S, Zhang S, Patel A, Jiang W, Wang L, Welty SE, Belmont J, Coarfa C, Moorthy B. Gene Expression Profiling Identifies Cell Proliferation and Inflammation as the Predominant Pathways Regulated by Aryl Hydrocarbon Receptor in Primary Human Fetal Lung Cells Exposed to Hyperoxia. Toxicol Sci. 2016 07; 152(1):155-68. PMID: 27103661.
      View in: PubMed
    79. Eclarinal JD, Zhu S, Baker MS, Piyarathna DB, Coarfa C, Fiorotto ML, Waterland RA. Maternal exercise during pregnancy promotes physical activity in adult offspring. FASEB J. 2016 07; 30(7):2541-8. PMID: 27033262.
      View in: PubMed
    80. Park JH, Vithayathil S, Kumar S, Sung PL, Dobrolecki LE, Putluri V, Bhat VB, Bhowmik SK, Gupta V, Arora K, Wu D, Tsouko E, Zhang Y, Maity S, Donti TR, Graham BH, Frigo DE, Coarfa C, Yotnda P, Putluri N, Sreekumar A, Lewis MT, Creighton CJ, Wong LC, Kaipparettu BA. Fatty Acid Oxidation-Driven Src Links Mitochondrial Energy Reprogramming and Oncogenic Properties in Triple-Negative Breast Cancer. Cell Rep. 2016 Mar 08; 14(9):2154-2165. PMID: 26923594.
      View in: PubMed
    81. von Rundstedt FC, Rajapakshe K, Ma J, Arnold JM, Gohlke J, Putluri V, Krishnapuram R, Piyarathna DB, Lotan Y, Gödde D, Roth S, Störkel S, Levitt JM, Michailidis G, Sreekumar A, Lerner SP, Coarfa C, Putluri N. Integrative Pathway Analysis of Metabolic Signature in Bladder Cancer: A Linkage to The Cancer Genome Atlas Project and Prediction of Survival. J Urol. 2016 06; 195(6):1911-9. PMID: 26802582.
      View in: PubMed
    82. Foulds CE, Panigrahi AK, Coarfa C, Lanz RB, O'Malley BW. Long Noncoding RNAs as Targets and Regulators of Nuclear Receptors. Curr Top Microbiol Immunol. 2016; 394:143-76. PMID: 26362934.
      View in: PubMed
    83. Thomas AL, Coarfa C, Qian J, Wilkerson JJ, Rajapakshe K, Krett NL, Gunaratne PH, Rosen ST. Identification of potential glucocorticoid receptor therapeutic targets in multiple myeloma. Nucl Recept Signal. 2015; 13:e006. PMID: 26715915.
      View in: PubMed
    84. Zhang S, Wei JS, Li SQ, Badgett TC, Song YK, Agarwal S, Coarfa C, Tolman C, Hurd L, Liao H, He J, Wen X, Liu Z, Thiele CJ, Westermann F, Asgharzadeh S, Seeger RC, Maris JM, Guidry Auvil JM, Smith MA, Kolaczyk ED, Shohet J, Khan J. MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma. Cancer Lett. 2016 Feb 28; 371(2):214-24. PMID: 26683771.
      View in: PubMed
    85. Holdman XB, Welte T, Rajapakshe K, Pond A, Coarfa C, Mo Q, Huang S, Hilsenbeck SG, Edwards DP, Zhang X, Rosen JM. Upregulation of EGFR signaling is correlated with tumor stroma remodeling and tumor recurrence in FGFR1-driven breast cancer. Breast Cancer Res. 2015 Nov 18; 17:141. PMID: 26581390.
      View in: PubMed
    86. Kessler NJ, Van Baak TE, Baker MS, Laritsky E, Coarfa C, Waterland RA. CpG methylation differences between neurons and glia are highly conserved from mouse to human. Hum Mol Genet. 2016 Jan 15; 25(2):223-32. PMID: 26566671.
      View in: PubMed
    87. Fleet T, Zhang B, Lin F, Zhu B, Dasgupta S, Stashi E, Tackett B, Thevananther S, Rajapakshe KI, Gonzales N, Dean A, Mao J, Timchenko N, Malovannaya A, Qin J, Coarfa C, DeMayo F, Dacso CC, Foulds CE, O'Malley BW, York B. SRC-2 orchestrates polygenic inputs for fine-tuning glucose homeostasis. Proc Natl Acad Sci U S A. 2015 Nov 03; 112(44):E6068-77. PMID: 26487680.
      View in: PubMed
    88. Kannan K, Kordestani GK, Galagoda A, Coarfa C, Yen L. Aberrant MUC1-TRIM46-KRTCAP2 Chimeric RNAs in High-Grade Serous Ovarian Carcinoma. Cancers (Basel). 2015 Oct 19; 7(4):2083-93. PMID: 26492273.
      View in: PubMed
    89. Shafi AA, Putluri V, Arnold JM, Tsouko E, Maity S, Roberts JM, Coarfa C, Frigo DE, Putluri N, Sreekumar A, Weigel NL. Differential regulation of metabolic pathways by androgen receptor (AR) and its constitutively active splice variant, AR-V7, in prostate cancer cells. Oncotarget. 2015 Oct 13; 6(31):31997-2012. PMID: 26378018.
      View in: PubMed
    90. Marcelo KL, Lin F, Rajapakshe K, Dean A, Gonzales N, Coarfa C, Means AR, Goldie LC, York B. Deciphering hepatocellular responses to metabolic and oncogenic stress. J Biol Methods. 2015; 2(3). PMID: 26504887.
      View in: PubMed
    91. Jonsson P, Coarfa C, Mesmar F, Raz T, Rajapakshe K, Thompson JF, Gunaratne PH, Williams C. Single-Molecule Sequencing Reveals Estrogen-Regulated Clinically Relevant lncRNAs in Breast Cancer. Mol Endocrinol. 2015 Nov; 29(11):1634-45. PMID: 26426411.
      View in: PubMed
    92. Coarfa C, Fiskus W, Eedunuri VK, Rajapakshe K, Foley C, Chew SA, Shah SS, Geng C, Shou J, Mohamed JS, O'Malley BW, Mitsiades N. Comprehensive proteomic profiling identifies the androgen receptor axis and other signaling pathways as targets of microRNAs suppressed in metastatic prostate cancer. Oncogene. 2016 05 05; 35(18):2345-56. PMID: 26364608.
      View in: PubMed
    93. Blessing AM, Ganesan S, Rajapakshe K, Ying Sung Y, Reddy Bollu L, Shi Y, Cheung E, Coarfa C, Chang JT, McDonnell DP, Frigo DE. Identification of a Novel Coregulator, SH3YL1, That Interacts With the Androgen Receptor N-Terminus. Mol Endocrinol. 2015 Oct; 29(10):1426-39. PMID: 26305679.
      View in: PubMed
    94. Chang CH, Zhang M, Rajapakshe K, Coarfa C, Edwards D, Huang S, Rosen JM. Mammary Stem Cells and Tumor-Initiating Cells Are More Resistant to Apoptosis and Exhibit Increased DNA Repair Activity in Response to DNA Damage. Stem Cell Reports. 2015 Sep 08; 5(3):378-91. PMID: 26300228.
      View in: PubMed
    95. Sun B, Shah B, Fiskus W, Qi J, Rajapakshe K, Coarfa C, Li L, Devaraj SG, Sharma S, Zhang L, Wang ML, Saenz DT, Krieger S, Bradner JE, Bhalla KN. Synergistic activity of BET protein antagonist-based combinations in mantle cell lymphoma cells sensitive or resistant to ibrutinib. Blood. 2015 Sep 24; 126(13):1565-74. PMID: 26254443.
      View in: PubMed
    96. Eedunuri VK, Rajapakshe K, Fiskus W, Geng C, Chew SA, Foley C, Shah SS, Shou J, Mohamed JS, Coarfa C, O'Malley BW, Mitsiades N. miR-137 Targets p160 Steroid Receptor Coactivators SRC1, SRC2, and SRC3 and Inhibits Cell Proliferation. Mol Endocrinol. 2015 Aug; 29(8):1170-83. PMID: 26066330.
      View in: PubMed
    97. Silver MJ, Kessler NJ, Hennig BJ, Dominguez-Salas P, Laritsky E, Baker MS, Coarfa C, Hernandez-Vargas H, Castelino JM, Routledge MN, Gong YY, Herceg Z, Lee YS, Lee K, Moore SE, Fulford AJ, Prentice AM, Waterland RA. Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment. Genome Biol. 2015 Jun 11; 16:118. PMID: 26062908.
      View in: PubMed
    98. Bhardwaj A, Ganesan N, Tachibana K, Rajapakshe K, Albarracin CT, Gunaratne PH, Coarfa C, Bedrosian I. Annexin A1 Preferentially Predicts Poor Prognosis of Basal-Like Breast Cancer Patients by Activating mTOR-S6 Signaling. PLoS One. 2015; 10(5):e0127678. PMID: 26000884.
      View in: PubMed
    99. Lin F, Marcelo KL, Rajapakshe K, Coarfa C, Dean A, Wilganowski N, Robinson H, Sevick E, Bissig KD, Goldie LC, Means AR, York B. The camKK2/camKIV relay is an essential regulator of hepatic cancer. Hepatology. 2015 Aug; 62(2):505-20. PMID: 25847065.
      View in: PubMed
    100. Kannan K, Coarfa C, Chao PW, Luo L, Wang Y, Brinegar AE, Hawkins SM, Milosavljevic A, Matzuk MM, Yen L. Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):E1272-7. PMID: 25733895.
      View in: PubMed
    101. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563.
      View in: PubMed
    102. Amin V, Harris RA, Onuchic V, Jackson AR, Charnecki T, Paithankar S, Lakshmi Subramanian S, Riehle K, Coarfa C, Milosavljevic A. Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs. Nat Commun. 2015 Feb 18; 6:6370. PMID: 25691256.
      View in: PubMed
    103. Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18; 6:6363. PMID: 25691127.
      View in: PubMed
    104. Dasgupta S, Putluri N, Long W, Zhang B, Wang J, Kaushik AK, Arnold JM, Bhowmik SK, Stashi E, Brennan CA, Rajapakshe K, Coarfa C, Mitsiades N, Ittmann MM, Chinnaiyan AM, Sreekumar A, O'Malley BW. Coactivator SRC-2-dependent metabolic reprogramming mediates prostate cancer survival and metastasis. J Clin Invest. 2015 Mar 02; 125(3):1174-88. PMID: 25664849.
      View in: PubMed
    105. He B, Lanz RB, Fiskus W, Geng C, Yi P, Hartig SM, Rajapakshe K, Shou J, Wei L, Shah SS, Foley C, Chew SA, Eedunuri VK, Bedoya DJ, Feng Q, Minami T, Mitsiades CS, Frolov A, Weigel NL, Hilsenbeck SG, Rosen DG, Palzkill T, Ittmann MM, Song Y, Coarfa C, O'Malley BW, Mitsiades N. GATA2 facilitates steroid receptor coactivator recruitment to the androgen receptor complex. Proc Natl Acad Sci U S A. 2014 Dec 23; 111(51):18261-6. PMID: 25489091.
      View in: PubMed
    106. Venkatanarayan A, Raulji P, Norton W, Chakravarti D, Coarfa C, Su X, Sandur SK, Ramirez MS, Lee J, Kingsley CV, Sananikone EF, Rajapakshe K, Naff K, Parker-Thornburg J, Bankson JA, Tsai KY, Gunaratne PH, Flores ER. IAPP-driven metabolic reprogramming induces regression of p53-deficient tumours in vivo. Nature. 2015 Jan 29; 517(7536):626-30. PMID: 25409149.
      View in: PubMed
    107. Menon DU, Coarfa C, Xiao W, Gunaratne PH, Meller VH. siRNAs from an X-linked satellite repeat promote X-chromosome recognition in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2014 Nov 18; 111(46):16460-5. PMID: 25368194.
      View in: PubMed
    108. Geng C, Rajapakshe K, Shah SS, Shou J, Eedunuri VK, Foley C, Fiskus W, Rajendran M, Chew SA, Zimmermann M, Bond R, He B, Coarfa C, Mitsiades N. Androgen receptor is the key transcriptional mediator of the tumor suppressor SPOP in prostate cancer. Cancer Res. 2014 Oct 01; 74(19):5631-43. PMID: 25274033.
      View in: PubMed
    109. Bliss-Moreau M, Coarfa C, Gunaratne PH, Guitart J, Krett NL, Rosen ST. Identification of p38ß as a therapeutic target for the treatment of Sézary syndrome. J Invest Dermatol. 2015 Feb; 135(2):599-608. PMID: 25148579.
      View in: PubMed
    110. Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, de Hoon MJ. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc Natl Acad Sci U S A. 2014 Aug 05; 111(31):11467-72. PMID: 25049417.
      View in: PubMed
    111. Feng Q, Zhang Z, Shea MJ, Creighton CJ, Coarfa C, Hilsenbeck SG, Lanz R, He B, Wang L, Fu X, Nardone A, Song Y, Bradner J, Mitsiades N, Mitsiades CS, Osborne CK, Schiff R, O'Malley BW. An epigenomic approach to therapy for tamoxifen-resistant breast cancer. Cell Res. 2014 Jul; 24(7):809-19. PMID: 24874954.
      View in: PubMed
    112. Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A. Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools. BMC Bioinformatics. 2014; 15 Suppl 7:S2. PMID: 25080362.
      View in: PubMed
    113. Ma J, Coarfa C, Qin X, Bonnen PE, Milosavljevic A, Versalovic J, Aagaard K. mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities. BMC Genomics. 2014 Apr 03; 15:257. PMID: 24694284.
      View in: PubMed
    114. Kannan K, Coarfa C, Rajapakshe K, Hawkins SM, Matzuk MM, Milosavljevic A, Yen L. CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. PLoS Genet. 2014 Mar; 10(3):e1004216. PMID: 24675677.
      View in: PubMed
    115. Chakravarti D, Su X, Cho MS, Bui NH, Coarfa C, Venkatanarayan A, Benham AL, Flores González RE, Alana J, Xiao W, Leung ML, Vin H, Chan IL, Aquino A, Müller N, Wang H, Cooney AJ, Parker-Thornburg J, Tsai KY, Gunaratne PH, Flores ER. Induced multipotency in adult keratinocytes through down-regulation of ?Np63 or DGCR8. Proc Natl Acad Sci U S A. 2014 Feb 04; 111(5):E572-81. PMID: 24449888.
      View in: PubMed
    116. Motamed M, Rajapakshe KI, Hartig SM, Coarfa C, Moses RE, Lonard DM, O'Malley BW. Steroid receptor coactivator 1 is an integrator of glucose and NAD+/NADH homeostasis. Mol Endocrinol. 2014 Mar; 28(3):395-405. PMID: 24438340.
      View in: PubMed
    117. Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res. 2014 Apr; 42(6):e43. PMID: 24391148.
      View in: PubMed
    118. Tennakoon JB, Wang H, Coarfa C, Cooney AJ, Gunaratne PH. Chromatin changes in dicer-deficient mouse embryonic stem cells in response to retinoic acid induced differentiation. PLoS One. 2013; 8(9):e74556. PMID: 24040281.
      View in: PubMed
    119. Seo E, Basu-Roy U, Gunaratne PH, Coarfa C, Lim DS, Basilico C, Mansukhani A. SOX2 regulates YAP1 to maintain stemness and determine cell fate in the osteo-adipo lineage. Cell Rep. 2013 Jun 27; 3(6):2075-87. PMID: 23791527.
      View in: PubMed
    120. Cheng JC, McBrayer SK, Coarfa C, Dalva-Aydemir S, Gunaratne PH, Carpten JD, Keats JK, Rosen ST, Shanmugam M. Expression and phosphorylation of the AS160_v2 splice variant supports GLUT4 activation and the Warburg effect in multiple myeloma. Cancer Metab. 2013 May 29; 1(1):14. PMID: 24280290.
      View in: PubMed
    121. Hsu DM, Agarwal S, Benham A, Coarfa C, Trahan DN, Chen Z, Stowers PN, Courtney AN, Lakoma A, Barbieri E, Metelitsa LS, Gunaratne P, Kim ES, Shohet JM. G-CSF receptor positive neuroblastoma subpopulations are enriched in chemotherapy-resistant or relapsed tumors and are highly tumorigenic. Cancer Res. 2013 Jul 01; 73(13):4134-46. PMID: 23687340.
      View in: PubMed
    122. Geng C, He B, Xu L, Barbieri CE, Eedunuri VK, Chew SA, Zimmermann M, Bond R, Shou J, Li C, Blattner M, Lonard DM, Demichelis F, Coarfa C, Rubin MA, Zhou P, O'Malley BW, Mitsiades N. Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover. Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):6997-7002. PMID: 23559371.
      View in: PubMed
    123. Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. PLoS Genet. 2013; 9(2):e1003333. PMID: 23468659.
      View in: PubMed
    124. Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat Commun. 2013; 4:2730. PMID: 24220575.
      View in: PubMed
    125. Plé H, Landry P, Benham A, Coarfa C, Gunaratne PH, Provost P. The repertoire and features of human platelet microRNAs. PLoS One. 2012; 7(12):e50746. PMID: 23226537.
      View in: PubMed
    126. Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F. Atlas2 Cloud: a framework for personal genome analysis in the cloud. BMC Genomics. 2012; 13 Suppl 6:S19. PMID: 23134663.
      View in: PubMed
    127. Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. BMC Bioinformatics. 2012; 13 Suppl 13:S11. PMID: 23320832.
      View in: PubMed
    128. Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Sarraj S, Dobson R, Schalkwyk LC, Mill J. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol. 2012 Jun 15; 13(6):R43. PMID: 22703893.
      View in: PubMed
    129. Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One. 2012; 7(6):e36466. PMID: 22719832.
      View in: PubMed
    130. Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet. 2012; 8(5):e1002692. PMID: 22615578.
      View in: PubMed
    131. Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics. 2012 Jan 12; 13:8. PMID: 22239737.
      View in: PubMed
    132. Gunaratne PH, Coarfa C, Soibam B, Tandon A. miRNA data analysis: next-gen sequencing. Methods Mol Biol. 2012; 822:273-88. PMID: 22144206.
      View in: PubMed
    133. Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Den Hollander P, Schoenherr C, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ, Milosavljevic A. Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines. Cancer Genet. 2011 Aug; 204(8):447-57. PMID: 21962895.
      View in: PubMed
    134. Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91. PMID: 21741921.
      View in: PubMed
    135. Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S, Clayton DF. Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics. 2011 May 31; 12(1):277. PMID: 21627805.
      View in: PubMed
    136. Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski DN, Milosavljevic A, Kim ES, Gunaratne PH. A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma. Cancer Res. 2011 Jun 01; 71(11):3841-51. PMID: 21498633.
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    137. Miller CA, Hampton O, Coarfa C, Milosavljevic A. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011 Jan 31; 6(1):e16327. PMID: 21305028.
      View in: PubMed
    138. Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM. Analysis of microRNA expression in the prepubertal testis. PLoS One. 2010 Dec 29; 5(12):e15317. PMID: 21206922.
      View in: PubMed
    139. Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics. 2010 Nov 23; 11:572. PMID: 21092284.
      View in: PubMed
    140. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635.
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    141. Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, Gunaratne PH, Corry DB. Proinflammatory role for let-7 microRNAS in experimental asthma. J Biol Chem. 2010 Sep 24; 285(39):30139-49. PMID: 20630862.
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    142. Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod. 2010 Jul; 16(7):463-71. PMID: 20215419.
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    143. Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 Feb; 20(2):273-80. PMID: 20019143.
      View in: PubMed
    144. Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, Han DY, Harris RA, Coarfa C, Gunaratne PH, Yan W, Matzuk MM. GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLoS Genet. 2009 Sep; 5(9):e1000635. PMID: 19730684.
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    145. Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res. 2009 Feb; 19(2):167-77. PMID: 19056696.
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    146. Coarfa C, Milosavljevic A. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput. 2008; 102-13. PMID: 18229679.
      View in: PubMed
    147. Dotsenko Y, Coarfa C, Nakhleh L, Mellor-Crummey J, Roshan U. PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. Int J Bioinform Res Appl. 2006; 2(4):407-19. PMID: 18048181.
      View in: PubMed
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