Hodara E, Mades A, Swartz L, Iqbal M, Xu T, Bsteh D, Farnham PJ, Rhie SK, Goldkorn A. m(6)A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer. NAR Cancer 2023 Dec;5(4):zcad054. doi: 10.1093/narcan/zcad054. eCollection 2023 Dec. PMID: 38023731
Reams RR, Odedina FT, Carpten JD, Redda K, Stern MC, Krieger JL, Aparicio J, Hensel B, Askins N, Abreu A, Adams A, Agyare E, Ali J, Allen JM, Aló R, Baezconde-Garbanati L, Brant J, Brown CP, Buxbaum SG, Cohen P, Cozen W, Ezenwa MO, Falzarano S, Fillingim RB, Flores-Rozas H, Fredenburg KM, George T, Han B, Huang Y, Hughes Halbert C, Kiros G-E, Lamango NS, Lee J-H, Lyon DE, Mitchell DA, Mochona B, Nieva JJ, Offringa IA, Okunieff P, Parker A, Rhie SK, Richey JM, Rogers SC, Salhia B, Schmittgen TD, Segal R, Setiawan VW, Smith U, Su L, Suther S, Trevino J, Velazquez-Villarreal EI, Webb FJ, Wu AH, Yao Y, and Wilkie D.J. Florida-California Cancer Research, Education and Engagement (CaRE2) Health Equity Center: Structure, Innovations, and Initial Outcomes. Cancer Control 2023 Jan-Dec;30:10732748231197878. doi: 10.1177/10732748231197878. PMID: 37703814
Tucker DW, Ppangal DJ, Du R, Gogia AS, Tafreshi A, Hurth KT, Triche TJ, Micko A, Carpten JD, Shiroish MS, Carmichael JD, Rhie SK*, Zada G* Validation of Myc-Associated Protein X (MAX) regulation in growth hormone secreting and nonfunctional pituitary adenoma. PLoS One 2023 Apr 27;18(4):e0284949. doi: 10.1371/journal.pone.0284949. PMID: 37104368 *Rhie is a co-corresponding author
Lu YT, Plets M, Morrison G, Cunha AT, Cen SY, Rhie SK, Siegmund KD, Daneshmand S, Quinn DI, Meeks JJ, Lerner SP, Petrylak DP, McConkey D, Flaig TW, Thompson IM Jr, Goldkorn A. Cell-free DNA Methylation as a Predictive Biomarker of Response to Neoadjuvant Chemotherapy for Patients with Muscle-invasive Bladder Cancer in SWOG S1314. Eur Urol Oncol. 2023 Apr 20:S2588-9311(23)00074-3. doi: 10.1016/j.euo.2023.03.008. PMID: 37087309
Liu DH, Dani KA, Reddy SS, Lei X, Demirjian NL, Hwang DH, Varghese BA, Rhie SK, Yap FY, Quinn DI, Siddiqi I, Aron M, Vaishampayan U, Zahoor H, Cen SY, Gill IS, Duddalwar VA. Radiogenomic Associations Clear Cell Renal Cell Carcinoma: An Exploratory Study. 2023;101(6):375-388. doi: 10.1159/000530719. Epub 2023 Apr 20. PMID: 37080171
Ghate NB, Kim S, Shin Y, Kim J, Doche M, Valena S, Situ A, Kim S, Rhie SK, Lenz HJ, Ulmer TS, Mumenthaler SM, An W. Phosphorylation and stabilization of EZH2 by DCAF1/VprBP trigger aberrant gene silencing in colon cancer. Nat Commun. 2023 Apr 17;14(1):2140. doi: 10.1038/s41467-023-37883-1. PMID: 37069142
Chen F, Madduri RK, Rodriguez AA, Darst BF, Chou A, Sheng X, Wang A, Shen J, Saunders EJ, Rhie SK, et al Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry. Eur Urol 2023 S0302-2838(23)02561-7. doi: 10.1016/j.eururo.2023.01.022. PMID: 36872133
Stevens C, Hightower A, Buxbam S, Falzarano S, Rhie SK Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients Frontiers in Oncology 2023 13:1079037 doi:10.3389/fonc.2023.1079037 PMID: 36937425
Epigenetics Chromatin. 2022 Dec 21;15(1):41. doi: 10.1186/s13072-022-00473-4.
Cancers (Basel). 2022 Oct 11;14(20):4979. doi: 10.3390/cancers14204979.
Varghese B Cen S Zahoor H Siddiqui I Aron M Sali A Rhie SK Lei X Rivas M Liu D Hwang D Quinn D Desai M Vaishampayan U Gill I Duddalwar V Feasibility of using CT radiomic signatures for predicting CD8-T cell infiltration and PD-L1 expression in renal cell carcinoma. Eur J Radiol Open. 2022 Sep 2;9:100440. doi: 10.1016/j.ejro.2022.100440.
Wang X Jordahl KM Zhu C Livingstone J Rhie SK Wright JL Grady WM Boutros PC Stanford JL Dai JY Methylation Subtypes of Primary Prostate Cancer Predict Poor Prognosis Cancer Epidemiol Biomarkers Prev 2022 Jul 1;31(7):1473-1482. doi: 10.1158/1055-9965.EPI-22-0007.
Wedemeyer MA Muskens I Strickland BA Aurelio O Martirosian V Wiemels JL Weisenberger DJ Wang K Mukerjee D Rhie SK# Zada G# Epigenetic Dysregulation in Meningiomas Neurooncol Adv. 2022 Jun 6;4(1):vdac084. doi: 10.1093/noajnl/vdac084. #Rhie is a co-corresponding author
Lu YT Xu T Iqbal M Hsieh TC Luo Z Liang G Farnham PJ Rhie SK# Goldkorn A# FOXC1 Binds Enhancers and Promoters Cisplatin Resistance in Bladder Cancer. Cancers (Basel) 2022 Mar 28;14(7):1717. doi: 10.3390/cancers14071717. #Rhie is a co-corresponding author
Shin Y Kim S Ghate NB Rhie SK An W MMP-9 drives melanomagenic transcription program through histone H3 tail proteolysis Oncogene 2021 Nov 16. doi: 10.1038/s41388-021-02109-5.
Demirjian NL Varghese BA Cen SY Hwang DH Aron M Siddiqui I Fields BKK Lei X Yap FY Rivas M Reddy SS Zahoor H Liu DH Desai M Rhie SK Gill IS Duddalwar V CT-based radiomics stratification of tumor grade and TNM stage of clear cell renal cell carcinoma Eur Radiol 2021 Nov 10. doi: 10.1007/s00330-021-08344-4.
Ghate NB Kim S Spiller E Kim S Shin Y Rhie SK Smbatyan G Lenz HJ Mumenthaler SM An W VprBP directs epigenetic gene silencing through histone H2A phosphorylation in colon cancer. Mol Oncol 2021 Oct;15(10):2801-2817. doi: 10.1002/1878-0261.13068.
Hu B Won H Mah W Park RB Kassim B Spiess K Kozlenkov A Crowley CA Pochareddy S; PsychENCODE Consortium (Rhie SK) Li Y Dracheva S Sestan N Akbarian S Geschwind DH Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. Nat Commun. 2021 Jun 25;12(1):3968. doi: 10.1038/s41467-021-24243-0.
Lee BH Rhie SK Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics Chromatin 2021 Mar 19;14(1):14. doi: 10.1186/s13072-021-00390-y
Polfus LM Darst BF Highland H Shen X Ng MCY Below JE Petty L Bien S Sim X Wang W Fontanillas P Patel Y The 23andMe Research Team DIAMANTE Hispanic/Latino Consortium Meta-analysis of type2 Diabetes in African Americans Consortium Preuss M Schurnmann C Du Z Lu Y Rhie SK … Kooperberg C Loos RJF Stram DO Haiman CA Genetic discovery and risk characterization in type 2 diabetes across diverse populations. HGG Advances 2021 Mar 9; doi: 10.1016/xhgg.2021.10029
Graff M Justice AE Young KL Marouli E Zhang X … Rhie SK … Haiman CA Loos R Ng MCY North KE Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry. Am J Hum Genet. 2021 Mar 5; doi: 10.1016/j.ajhg.2021.02.011
Mullen DJ Yan C Kang DL Zhou B Borok Z Marconett CN Farnham PJ Offringa IA Rhie SK TENET 2.0: identification of key transcriptional regulators and enhancers in lung adenocarcinoma Plos Genetics 2020 Sep 14;16(9):e1009023. doi: 10.1371/journal.pgen.1009023
The ENCODE Consortium (Rhie SK) Moore JE Purcaro MJ Pratt HE Epstein CB Shoresh N Adrian J Kawli T Davis CA Dobin A Kaul R Halow J Van Nostrand EL Freese P Gorkin DU He Y Mackiewicz M et al Expanded encyclopaedias of DNA elements in the human and mouse genomes Nature 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4
The ENCODE Consortium (Rhie SK) Snyder MP Gingeras TR Moore JE Weng Z Gerstein MB Ren B Hardison RC Stamatoyannopoulos JA Graveley BR Feingold EA Pazin MJ Pagan M Gilchrist DA Hitz BC Cherry M Bernstein BE Mendenhall EM Zerbino DR Frankish A Flicek P Myers RM Perspectives on ENCODE Nature 2020 Jul;583(7818)693-698. doi: 10.1038/s41586-020-2449-8
Zepeda-Martinez JA Pribitzer C Wang J Bstech D Golumbeanu S Zhao Q Burkard TR Reichholf B Rhie SK Jude J Moussa HF Zuber J Bell O Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells Science Advances 2020 Apr 1:6(14):eaax5692. doi: 10.1126/sciadv.aax5692
Ashton C Rhie SK Carmichael JD Zada G Role of KCNAB2 expression in modulating hormone secretion in somatotroph pituitary adenoma Journal of Neurosurgery 2020 Feb 28:1-7. doi: 10.3171/2019.12.JNS192435.
Xu T Li H Wei J Li M Hsieh T Lu Y Lakshminarasimhan R Xu R Hodara E Morrison G Gujar H Rhie SK Siegmund K Liang G Goldkorn A Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype International Journal of Cancer 2020 Feb 3. doi: 10.1002/ijc.32904
Rhie SK* Perez AA Lay F Schreiner S Shi J Polin J Farnham PJ A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome Nature Communications 2019 Sep 12;10(1):4154. doi: 10.1038/s41467-019-12079-8 *Rhie is a corresponding author
Qian Y Zhang L Cai M Li H Xu H Yang H Zhao Z Rhie SK Farnham PJ Shi J Lu W The prostate cancer risk variant rs55958994 regulates multiple genes expression through extreme long-range chromatin interaction to control tumor progression Science Advances 2019 Jul 17;5(7):eaaw6710. doi: 10.1126/sciadv.aaw6710
O’Geen H Bates S Carter SS Nisson KA Halmai J Fink KD Rhie SK Farnham PJ Segal DJ Engineering epigenetic memory requires co-targeting of histone methylatransferases and DNA methylatransferases Epigenetics Chromatin 2019 May 3;12(1):26. doi: 10.1186/s13072-019-0275-8
Luo Z Rhie SK Farnham PJ The Enigmatic HOX Genes: Can We Crack Their Code? Cancers 2019 Mar 7; 11(3):323 doi.org/10.3390/cancers11030323
The PsychENCODE Consortium (Rhie SK) Revealing the brain’s molecular architecture Science 2018 Dec14; 362(6420):1262-1263 doi: 10.1126/science.362.6420.1262
Wang Liu Warrell Won Shi Navarro Clarke Gu Emani Yang Xu Gandal Lou Zhang Park Yan Rhie SK Manakongtreecheep Zhou Nathan Zhang Peters Mattei Fitzgerald Brunetti Moore Jiang Girdhar Hoffman Kalayci Gümüş Crawford PsychENCODE Consortium Raussos Akbarian Jaffe White Weng Sestan Geschwind Knowles Gerstein Comprehensive functional genomic resource and integrative model for the adult brain Science 2018 2018 Dec14; 362(6420) doi: 10.1126/science.aat8464
Amiri A Coppola G Scuden S Wu F Roychowdhury T Liu F Pochareddy S Shin Y Safi A Song L Zhu Y Sousa AM The PsychENCODE Consortium (Rhie SK) Gerstein M Crawford GE Sestan N Abyzov A Vaccarino FM Transcriptome and epigenome landscape of human cortical development modeled in organoids Science 2018 Dec14; 362(6420) doi: 10.1126/science.aat6720
Li Santpere Kawasawa Evgrafov Gulden Pochareddy Sunkin Li Shin Zhu Sousa Werling Kitchen Kang Pletikos Choi Muchnik Xu Wang Lorente-Galdos Liu Giusti-Rodríguez Won de Leeuw Pardiñas BrainSpan Consortium PsychENCODE Consortium (Rhie SK), PsychENCODE Developmental Subgroup Hu Jin Li Owen O’Donovan Walters Posthuma Levit Weinberger Hyde Kleinman Geschwind Hawrylycz State Sanders Sullivan Gerstein Lein Knowles Sestan Integrative functional genomic analysis of human brain development and neuropsychiatric risks Science 2018 Dec14; 362(6420) doi: 10.1126/science.aat7615
Gandal Zhang Hadjimichael Walker Chen Liu Won van Bakel Varghese Wang Shieh Haney Parhami Belmont Kim Losada Khan Mleczko Xia Dai Wang Yang Xu Fish Hof Warrell Fitzgerald White Jaffe PsychENCODE Consortium (Rhie SK) Peters Gerstein Liu Iakoucheva Pinto Geschwind Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder Science 2018 Dec14; 362(6420) doi: 10.1126/science.aat8127
Rhie SK Schreiner S Witt H Armoskus C Lay F Camarena A Spitsyna VN Guo Y Berman B Evgrafov OV Knowles JA Farnham PJ Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation Science Advances 2018 Dec 13; 4(12) doi: 10.1126/sciadv.aav8550
Guo Y Perez A Hazelett DJ Coetzee GA Rhie SK# Farnham PJ#. CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops. Genome Biology 2018 19(1):160 #Rhie is a co-corresponding author.
Yang C Steve TR Yan C Rhie SK Mullen DJ Luo J Zhou B Borok Z Marconett CN Offringa IA Positional investigation of lung adenocarcinoma susceptibility loci with primary human alveolar cell epigenomes Epigenomics 2018 10(9):1167-1187
Wedge Gundem Mitchell Woodcock Martincorena Ghori Zamora Butler Whitaker Kote-Jarai Alexandrov Van Massie Dentro Warren Verrill Berney Dennis Merson Hawkins Howat Lu Lambert Kay Kremeyer Karaszi Luxton Camacho Marsden Edwards Matthews Bo Leongamornlert McLaren Ng Yu Zhang Dadaev Thomas Easton Ahmed Bancroft Fisher Livni Nicol Tavare Gill Greenman Khoo Van As Kumar Ogden Cahill Thompson Mayer Rowe Dudderidge Gnanapragasam Shah Raine Jones Menzies Stebbings Teague Hazell Corbishley CAMCAP Study Group De Bono Attard Isaacs Visakorpi Fraser Boutros Bristow Workman Sander TCGA Consortium (Rhie SK) Hamdy Futreal McDermott AI-Lazikani Lynch Bova Foster Brewer Neal Cooper Eeles Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets Nature Genetics 2018 May;50(5):682-692
Rhie SK Yao L Luo Z Witt H Schreiner S Guo Y Perez AA Farnham PJ ZFX acts as a transcription activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters Genome Res 2018 Feb 2;28:310-320
Rhie SK Schreiner S Farnham PJ Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) Methods Mol Biol 2018 1766:209-229
Luo Z Rhie SK Lay F Guo P Farnham PJ A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13 Cell Rep 2017 Nov 7;21(6):1411-1417 *Rhie led Hi-C analysis
Feng Y^ Rhie SK^ Huo D Ruiz-Narvaez EA Haddad S Ambrosome AB et al Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry Cancer Epidemiol Biomarkers Prev 2017 July;26(7):1016-1026 ^Rhie is a co-first author
Farshidfar Zheng Gingrans Newton Shih Robertson Hinoue Hoadley Gibb Roszik Covington Wu Shinbrot Stransky Hegde Yang Reznik Sadeghi Pedamallu Ojesna Hess Auman Rhie SK Bowlby Borad et al Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles Cell Rep 2017 Jun 27;19(13):2878-2880
Huo D Hu H Rhie SK Gamazon ER Cherniack AD Liu J Yoshimatsu TF Pitt JJ Hoadley KA Troester M et al Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas JAMA Oncology 2017 Dec 1;3(12):1654-1662 *Rhie led DNA methylation analysis
Rhie SK Guo Y Tak YG Yao L Shen H Coetzee GA Laird PW Farnham PJ Identification of activated enhancers and linked transcription factors in breast prostate and kidney tumors by Tracing Enhancer Networks using Epigenetic Traits Epigenetics Chromatin 2016 Nov 9;9:50
Cancer Genome Atlas Research Network (Rhie SK) The Molecular Taxonomy of Primary Prostate Cancer Cell 2015 Nov 5;163(4):1011-25 *Rhie led DNA methylation analysis (TCGA PRAD Research Network group is assigned as a first-author)
Ciriello G Gatza ML Beck AH Wilkerson MD Rhie SK Pastore A Zhang H McLellan M Yau C et al Comprehensive Molecular Portraits of Invasive Lobular breast cancer Cell 2015 Oct 8;163(2):506-19 *Rhie led DNA methylation analysis
Coetzee SG Shen HC Hazelett DJ Lawrenson K Kuchenbaecker K Tyrer J Rhie SK Levanon K Karst A Drapkin R Ramus SJ; Ovarian Cancer Association Consortium; Consortium of Investigators of Modifiers of BRCA1/2 Couch FJ et al Cell Type Specific Enrichment Of Risk Associated Regulatory Elements At Ovarian Cancer Susceptibility Loci Human Molecular Genetics 2015 Jul 1;24(13):3595-607
Hoadley Yau Wolf Cherniack Tamborero Ng Leiserson Niu McLelian Uzuangelov Zhang Kandoth Akbani Shen Omberg Chu Margolin Van’t Veer Lopez-Bigas Laird Raphael Ding Robertson Byers Mills Weinstein Van Waes Chen Collisson Cancer Genome Atlas Research Network (Rhie SK) Benz Perou Stuart Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin Cell 2014 Aug 14; 158(4): 929-44
Rhie SK Hazelett DJ Coetzee SG Yan C Noushmehr H Coetzee GA Nucleosome Positioning and Histone Modifications Define Relationships between Regulatory Elements and Nearby Gene Expression in Breast Epithelial Cells BMC Genomics 2014 May 2; 15:331
Feng Y Stram DO Rhie SK Millikan RC Ambrosone CB John EM Bernstein L Zheng W Olshan AF Hu JJ Ziegler RG et al A comprehensive examination of breast cancer risk loci in African American women Human Molecular Genetics 2014 Oct 15; 23(20): 5518-26
Hazelett DJ Rhie SK Gaddis M Yan C Lakeland DL Coetzee SG Henderson BE Noushmehr H Cozen W Kote-Jarai Z Eeles RA Easton DF Haiman CA Lu W Farnham PJ Coetzee GA Comprehensive Functional Annotation of Seventy-seven Prostate Cancer Risk Loci Plos Genetics 2014 10 (1) e1004102
Cancer Genome Atlas Research Network (Rhie SK) Weinstein JN Collisson EA Mills GB Shaw KR Ozenberger BA Ellrott K Shmulevich I Sander C Stuart JM The Cancer Genome Atlas Pan-Cancer analysis project Nature Genetics 2013 Oct; 45(10):1113-20
Rhie SK Coetzee SG Noushmehr H Yan C Kim JM Haiman CA Coetzee GA Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci Plos One 2013 8 (5) e64925 *Selected as the top 25% most cited articles
Monda KL Chen GK Taylor KC Palmer C Lange L Edwards TL Ng MC Adeyemo AA Allison MA Bielak LF Chen G Graff M Irvin MR Rhie SK Li G Liu Y et al A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry Nature Genetics 2013 Jun;45(6):690-6
Garcia-Closas M Couch FJ Lindstrom S Michailidou K Schmidt MK Orr N Rhie SK Riboli E Feigelson HS Marchand LL et al Genome-wide association studies identify four ER-negative specific breast cancer risk loci Nature Genetics 2013 Mar 27; 45:392–398
Siddiq A Couch FJ Chen GK Lindstrom S Eccles D Millikan RC Michailidou K Stram DO Beckmann L Rhie SK Ambrosone CB Aittomaki K Amiano P et al A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11 Human Molecular Genetics 2012 Dec 15;21(24):5373-84
Chen Chen Stram Millikan Ambrosone John Bernstein Zheng Palmer Hu Rebbeck Ziegler Nyante Bandera Ingles Press Ruiz-Narvaez Deming Rodriguez-Gil DeMichele Chanock Blot Signorello Cai Li Long Huo Zheng Cox Olopade Ogundiran Adebamowo Nathanson Domchek Simon Hennis Nemesure Wu Leske Ambs Hutter Young Kooperberg Peters Rhie SK Wan Sheng Pooler Van Den Berg Marchand Kolonel Henderson Haiman A genome-wide association study of breast cancer in women of African ancestry Human Genetics 2013 Jan;132(1):39-48
Noushmehr H Coetzee SG Rhie SK Yan C Coetzee GA Chapter 6 The Functionality of Prostate Cancer Predisposition Risk Regions is revealed by AR Enhancers Androgen-Responsive Genes in Prostate Cancer Regulation Function and Clinical Applications 2013 59-84
Coetzee SG Rhie SK Berman B Coetzee GA Noushmehr H FunciSNP: An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Nucleic Acids Research 2012 Oct 1;40(18):e139
Peter AK Ko CY Kim MH Hsu N Ouchi N Rhie S Izumiya Y Walsh K Crosbie RH Myogenic Akt Signaling Upregulates Utrophin and Integrin Complexes that Promote Sarcolemma Stability in Muscular Dystrophy Human Molecular Genetics 2009 Jan 15; 18(2):318-27