NEW: The ChIPseeqer paper is out and highlighted as
Click here for our most recent list of publications from pubmed

Gayvert K, Elemento O. 2017. Mining for Therapeutic Targets using Gene Expression Profiling, submitted.

Du W, Goldstein R, Jiang Y, Aly O, Cerchietti L, Melnick AM, Elemento O. 2017. Effective combination therapies for B cell lymphoma predicted by a virtual disease model. Cancer Res online early publication

Doane AS, Elemento O. 2017. Regulatory elements in molecular networks. Wiley Interdiscip Rev Syst Biol Med online early publication

Schachterle W, Badwe CR, Palikuqi B, Kunar B, Ginsberg M, Lis R, Yokoyama M, Elemento O, Scandura JM, Rafii S. 2017. Sox17 drives functional engraftment of endothelium converted from non-vascular cells. Nat Commun 8: 13963.

Gayvert KM, Aly O, Platt J, Bosenberg MW, Stern DF, Elemento O. 2017. A Computational Approach for Identifying Synergistic Drug Combinations. PLoS Comput Biol 13(1): e1005308.

Nwachukwu JC, Srinivasan S, Bruno NE, Nowak J, Wright NJ, Minutolo F, Rangarajan ES, Izard T, Yao XQ, Grant BJ, Kojetin DJ, Elemento O, Katzenellenbogen JA, Nettles KW. 2017. Systems Structural Biology Analysis of Ligand Effects on ERα Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies. Cell Chem Biol 24(1): 35-45.

Dave B, Gonzalez DD, Liu ZB, Li X, Wong H, Granados S, Ezzedine NE, Sieglaff DH, Ensor JE, Miller KD, Radovich M, KarinaEtrovic A, Gross SS, Elemento O, Mills GB, Gilcrease MZ, Chang JC. 2017. Role of RPL39 in Metaplastic Breast Cancer. J Natl Cancer Inst 109(6).

Mauer J, Luo X, Blanjoie A, Jiao X, Grozhik AV, Patil DP, Linder B, Pickering BF, Vasseur JJ, Chen Q, Gross SS, Elemento O, Debart F, Kiledjian M, Jaffrey SR. 2017. Reversible methylation of m6Am in the 5' cap controls mRNA stability. Nature 541(7637): 371-375.

Poulos MG, Ramalingam P, Gutkin MC, Kleppe M, Ginsberg M, Crowley MJ, Elemento O, Levine RL, Rafii S, Kitajewski J, Greenblatt MB, Shim JH, Butler JM. 2016. Endothelial-specific inhibition of NF-κB enhances functional haematopoiesis. Nat Commun 7: 13829.

Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim K, Tam W, Beltran H, Robinson B, Mosquera JM, Fernandes H, Demichelis F, Sboner A, Kluk M, Rubin M*, and Elemento O*. 2016. Development and Validation of a Whole Exome Sequencing Test-1 (EXaCT-1) for Simultaneous Detection of Point Mutation, Indels and Copy Number Alterations for Precision Cancer Care. NPJ Genomic Medicine. * senior authors

Amengual JE, Prabhu SA, Lombardo M, Zullo KM, Johannet PM, Gonzalez Y, Scotto L, Jirau-Serrano X, Wei Y, Duong JK, Nandakumar R, Cremers S, Verma A, Elemento O, O'Connor OA. 2016. Mechanisms of Acquired Drug Resistance to the HDAC6 Selective Inhibitor Ricolinostat Reveals Rational Drug : Drug Combination with Ibrutinib. Clin Cancer Res online early publication

Giannopoulou E, Elemento O. 2017. Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets. Methods Mol Biol 1507: 43-58.

Faltas BM, Prandi D, Tagawa ST, Molina AM, Nanus DM, Sternberg C, Rosenberg J, Mosquera JM, Robinson B, Elemento O, Sboner A, Beltran H, Demichelis F, Rubin MA. 2016. Clonal evolution of chemotherapy-resistant urothelial carcinoma. Nat Genet 48(12): 1490-1499.

Boi M, Todaro M, Vurchio V, Yang SN, Moon J, Kwee I, Rinaldi A, Pan H, Crescenzo R, Cheng M, Cerchietti L, Elemento O, Riveiro ME, Cvitkovic E, Bertoni F, Inghirami G, AIRC 5xMille Consortium ‘Genetics-Driven Targeted Management of Lymphoid Malignancies’.. 2016. Therapeutic efficacy of the bromodomain inhibitor OTX015/MK-8628 in ALK-positive anaplastic large cell lymphoma: an alternative modality to overcome resistant phenotypes. Oncotarget 7(48): 79637-79653.

Huang L, Fernandes H, Zia H, Tavassoli P, Rennert H, Pisapia D, Imielinski M, Sboner A, Rubin MA, Kluk M, Elemento O. 2016. The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations. J Am Med Inform Assoc online early publication

Gayvert KM, Madhukar NS, Elemento O. 2016. A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials. Cell Chem Biol 23(10): 1294-1301.

Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM. 2017. CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas. Cancer Discov 7(1): 38-53.

Dardenne E, Beltran H, Benelli M, Gayvert K, Berger A, Puca L, Cyrta J, Sboner A, Noorzad Z, MacDonald T, Cheung C, Yuen KS, Gao D, Chen Y, Eilers M, Mosquera JM, Robinson BD, Elemento O, Rubin MA, Demichelis F, Rickman DS. 2016. N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer. Cancer Cell 30(4): 563-577.

Bunting KL, Soong TD, Singh R, Jiang Y, Béguelin W, Poloway DW, Swed BL, Hatzi K, Reisacher W, Teater M, Elemento O, Melnick AM. 2016. Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region. Immunity 45(3): 497-512.

Allen JE, Kline CL, Prabhu VV, Wagner J, Ishizawa J, Madhukar N, Lev A, Baumeister M, Zhou L, Lulla A, Stogniew M, Schalop L, Benes C, Kaufman HL, Pottorf RS, Nallaganchu BR, Olson GL, Al-Mulla F, Duvic M, Wu GS, Dicker DT, Talekar MK, Lim B, Elemento O, Oster W, Bertino J, Flaherty K, Wang ML, Borthakur G, Andreeff M, Stein M, El-Deiry WS. 2016. Discovery and clinical introduction of first-in-class imipridone ONC201. Oncotarget 7(45): 74380-74392.

Xylinas E, Hassler MR, Zhuang D, Krzywinski M, Erdem Z, Robinson BD, Elemento O, Clozel T, Shariat SF. 2016. An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer. Biomolecules 6(3).

Page DB, Yuan J, Redmond D, Wen YH, Durack JC, Emerson R, Solomon S, Dong Z, Wong P, Comstock C, Diab A, Sung J, Maybody M, Morris E, Brogi E, Morrow M, Sacchini V, Elemento O, Robins H, Patil S, Allison JP, Wolchok JD, Hudis C, Norton L, McArthur HL. 2016. Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy. Cancer Immunol Res 4(10): 835-844.

Béguelin W, Teater M, Gearhart MD, Calvo Fernández MT, Goldstein RL, Cárdenas MG, Hatzi K, Rosen M, Shen H, Corcoran CM, Hamline MY, Gascoyne RD, Levine RL, Abdel-Wahab O, Licht JD, Shaknovich R, Elemento O, Bardwell VJ, Melnick AM. 2016. EZH2 and BCL6 Cooperate to Assemble CBX8-BCOR Complex to Repress Bivalent Promoters, Mediate Germinal Center Formation and Lymphomagenesis. Cancer Cell 30(2): 197-213.

Elemento O. 2016. KLF4: A new player in plasma cell development. Cell Cycle 15(20): 2691-2.

Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang SN, Cohen J, Shaknovich R, Vanommeslaeghe K, Cheng H, Liang D, Cho HJ, Abbott J, Tam W, Du W, Leonard JP, Elemento O, Cerchietti L, Cierpicki T, Xue F, MacKerell AD Jr, Melnick AM. 2016. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest 126(9): 3351-62.

Redmond D, Poran A, Elemento O. 2016. Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med 8(1): 80.

Pritchard CC, Mateo J, Walsh MF, De Sarkar N, Abida W, Beltran H, Garofalo A, Gulati R, Carreira S, Eeles R, Elemento O, Rubin MA, Robinson D, Lonigro R, Hussain M, Chinnaiyan A, Vinson J, Filipenko J, Garraway L, Taplin ME, AlDubayan S, Han GC, Beightol M, Morrissey C, Nghiem B, Cheng HH, Montgomery B, Walsh T, Casadei S, Berger M, Zhang L, Zehir A, Vijai J, Scher HI, Sawyers C, Schultz N, Kantoff PW, Solit D, Robson M, Van Allen EM, Offit K, de Bono J, Nelson PS. 2016. Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer. N Engl J Med 375(5): 443-53.

Gayvert KM, Dardenne E, Cheung C, Boland MR, Lorberbaum T, Wanjala J, Chen Y, Rubin MA, Tatonetti NP, Rickman DS, Elemento O. 2016. A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors. Cell Rep 15(11): 2348-56.

Vazirani RP, Verma A, Sadacca LA, Buckman MS, Picatoste B, Beg M, Torsitano C, Bruno JH, Patel RT, Simonyte K, Camporez JP, Moreira G, Falcone DJ, Accili D, Elemento O, Shulman GI, Kahn BB, McGraw TE. 2016. Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance. Diabetes 65(6): 1577-89.

Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M. 2016. Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. Nat Commun 7: 11275.

Nwachukwu JC, Srinivasan S, Zheng Y, Wang S, Min J, Dong C, Liao Z, Nowak J, Wright NJ, Houtman R, Carlson KE, Josan JS, Elemento O, Katzenellenbogen JA, Zhou HB, Nettles KW. 2016. Predictive features of ligand-specific signaling through the estrogen receptor. Mol Syst Biol 12(4): 864.

Carty MA, Elemento O. 2016. Practical Analysis of Genome Contact Interaction Experiments. Methods Mol Biol 1418: 177-89.

Takemoto A, Kawashima SA, Li JJ, Jeffery L, Yamatsugu K, Elemento O, Nurse P. 2016. Nuclear envelope expansion is crucial for proper chromosomal segregation during a closed mitosis. J Cell Sci 129(6): 1250-9.

Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F. 2016. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med 22(3): 298-305.

Jiang Y, Nie K, Redmond D, Melnick AM, Tam W, Elemento O. 2015. VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma. J Vis Exp e53215.

Crowley MJ, Scognamiglio T, Liu YF, Kleiman DA, Beninato T, Aronova A, Liu H, Jhanwar YS, Molina A, Tagawa ST, Bander NH, Zarnegar R, Elemento O, Fahey TJ 3rd. 2016. Prostate-Specific Membrane Antigen Is a Potential Antiangiogenic Target in Adrenocortical Carcinoma. J Clin Endocrinol Metab 101(3): 981-7.

Culjkovic-Kraljacic B, Fernando TM, Marullo R, Calvo-Vidal N, Verma A, Yang S, Tabbò F, Gaudiano M, Zahreddine H, Goldstein RL, Patel J, Taldone T, Chiosis G, Ladetto M, Ghione P, Machiorlatti R, Elemento O, Inghirami G, Melnick A, Borden KL, Cerchietti L. 2016. Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphomas. Blood 127(7): 858-68.

Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR. 2015. 5' UTR m(6)A Promotes Cap-Independent Translation. Cell 163(4): 999-1010.

Madhukar NS, Elemento O, Pandey G. 2015. Prediction of Genetic Interactions Using Machine Learning and Network Properties. Front Bioeng Biotechnol 3: 172.

Yun J, Mullarky E, Lu C, Bosch KN, Kavalier A, Rivera K, Roper J, Chio II, Giannopoulou EG, Rago C, Muley A, Asara JM, Paik J, Elemento O, Chen Z, Pappin DJ, Dow LE, Papadopoulos N, Gross SS, Cantley LC. 2015. Vitamin C selectively kills KRAS and BRAF mutant colorectal cancer cells by targeting GAPDH. Science 350(6266): 1391-6.

Ma J, Nie K, Redmond D, Liu Y, Elemento O, Knowles DM, Tam W. 2016. EBV-miR-BHRF1-2 targets PRDM1/Blimp1: potential role in EBV lymphomagenesis. Leukemia 30(3): 594-604.

Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O. 2015. Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma. Genome Med 7: 110.

Poulos MG, Crowley MJ, Gutkin MC, Ramalingam P, Schachterle W, Thomas JL, Elemento O, Butler JM. 2015. Vascular Platform to Define Hematopoietic Stem Cell Factors and Enhance Regenerative Hematopoiesis. Stem Cell Reports 5(5): 881-94.

Ortega-Molina A, Boss IW, Canela A, Pan H, Jiang Y, Zhao C, Jiang M, Hu D, Agirre X, Niesvizky I, Lee JE, Chen HT, Ennishi D, Scott DW, Mottok A, Hother C, Liu S, Cao XJ, Tam W, Shaknovich R, Garcia BA, Gascoyne RD, Ge K, Shilatifard A, Elemento O, Nussenzweig A, Melnick AM, Wendel HG. 2015. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat Med 21(10): 1199-208.

Dominguez PM, Teater M, Chambwe N, Kormaksson M, Redmond D, Ishii J, Vuong B, Chaudhuri J, Melnick A, Vasanthakumar A, Godley LA, Papavasiliou FN, Elemento O, Shaknovich R. 2015. DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID. Cell Rep 12(12): 2086-98.

Seo BR, Bhardwaj P, Choi S, Gonzalez J, Andresen Eguiluz RC, Wang K, Mohanan S, Morris PG, Du B, Zhou XK, Vahdat LT, Verma A, Elemento O, Hudis CA, Williams RM, Gourdon D, Dannenberg AJ, Fischbach C. 2015. Obesity-dependent changes in interstitial ECM mechanics promote breast tumorigenesis. Sci Transl Med 7(301): 301ra130.

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA. 2015. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Oncol 1(4): 466-74.

Giannopoulou EG, Elemento O, Ivashkiv LB. 2015. Use of RNA sequencing to evaluate rheumatic disease patients. Arthritis Res Ther 17: 167.

Rickman KA, Lach FP, Abhyankar A, Donovan FX, Sanborn EM, Kennedy JA, Sougnez C, Gabriel SB, Elemento O, Chandrasekharappa SC, Schindler D, Auerbach AD, Smogorzewska A. 2015. Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia. Cell Rep 12(1): 35-41.

Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, Wu YG, Elemento O, Tavazoie SF. 2015. Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. Nat Cell Biol 17(7): 943-52.

Sboner A, Elemento O. 2016. A primer on precision medicine informatics. Brief Bioinform 17(1): 145-53.

Durrans A, Gao D, Gupta R, Fischer KR, Choi H, El Rayes T, Ryu S, Nasar A, Spinelli CF, Andrews W, Elemento O, Nolan D, Stiles B, Rafii S, Narula N, Davuluri R, Altorki NK, Mittal V. 2015. Identification of Reprogrammed Myeloid Cell Transcriptomes in NSCLC. PLoS One 10(6): e0129123.

Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM. 2015. Integrative clinical genomics of advanced prostate cancer. Cell 161(5): 1215-28.

Zhao X, Chen-Kiang S, Shetty S, Di Liberto M, Bodo J, Durkin L, Eng K, Elemento O, Smith MR, Hsi ED. 2015. CCMCL1: a new model of aggressive mantle cell lymphoma. Blood 125(17): 2730-2.

Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M, Reyes JC. 2015. The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PLoS Genet 11(4): e1005174.

Pan H, Jiang Y, Boi M, Tabbò F, Redmond D, Nie K, Ladetto M, Chiappella A, Cerchietti L, Shaknovich R, Melnick AM, Inghirami GG, Tam W, Elemento O. 2015. Epigenomic evolution in diffuse large B-cell lymphomas. Nat Commun 6: 6921.

Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera Mdel C, Bothmer A, Fung J, Langellotto F, Rodig SJ, Elemento O, Shipp MA, Adams DJ, Chiarle R, Pandolfi PP. 2015. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 161(2): 319-32.

Alinari L, Mahasenan KV, Yan F, Karkhanis V, Chung JH, Smith EM, Quinion C, Smith PL, Kim L, Patton JT, Lapalombella R, Yu B, Wu Y, Roy S, De Leo A, Pileri S, Agostinelli C, Ayers L, Bradner JE, Chen-Kiang S, Elemento O, Motiwala T, Majumder S, Byrd JC, Jacob S, Sif S, Li C, Baiocchi RA. 2015. Selective inhibition of protein arginine methyltransferase 5 blocks initiation and maintenance of B-cell transformation. Blood 125(16): 2530-43.

Choi H, Sheng J, Gao D, Li F, Durrans A, Ryu S, Lee SB, Narula N, Rafii S, Elemento O, Altorki NK, Wong ST, Mittal V. 2015. Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model. Cell Rep 10(7): 1187-201.

Gori JL, Butler JM, Chan YY, Chandrasekaran D, Poulos MG, Ginsberg M, Nolan DJ, Elemento O, Wood BL, Adair JE, Rafii S, Kiem HP. 2015. Vascular niche promotes hematopoietic multipotent progenitor formation from pluripotent stem cells. J Clin Invest 125(3): 1243-54.

Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T. 2014. ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. Cell Rep 9(6): 2330-43.

Geyer JT, Subramaniyam S, Jiang Y, Elemento O, Ferry JA, de Leval L, Nakashima MO, Liu YC, Martin P, Mathew S, Orazi A, Tam W. 2015. Lymphoblastic transformation of follicular lymphoma: a clinicopathologic and molecular analysis of 7 patients. Hum Pathol 46(2): 260-71.

Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. 2015. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood 125(7): 1061-72.

Erler P, Keutgen XM, Crowley MJ, Zetoune T, Kundel A, Kleiman D, Beninato T, Scognamiglio T, Elemento O, Zarnegar R, Fahey TJ 3rd. 2014. Dicer expression and microRNA dysregulation associate with aggressive features in thyroid cancer. Surgery 156(6): 1342-50; discussion 1350.

Chang SH, Elemento O, Zhang J, Zhuang ZW, Simons M, Hla T. 2014. ELAVL1 regulates alternative splicing of eIF4E transporter to promote postnatal angiogenesis. Proc Natl Acad Sci U S A 111(51): 18309-14.

Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM, Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, Rubin MA. 2014. The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun 5: 5383.

Prasain N, Lee MR, Vemula S, Meador JL, Yoshimoto M, Ferkowicz MJ, Fett A, Gupta M, Rapp BM, Saadatzadeh MR, Ginsberg M, Elemento O, Lee Y, Voytik-Harbin SL, Chung HM, Hong KS, Reid E, O'Neill CL, Medina RJ, Stitt AW, Murphy MP, Rafii S, Broxmeyer HE, Yoder MC. 2014. Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony-forming cells. Nat Biotechnol 32(11): 1151-7.

Diman NY, Brooks G, Kruithof BP, Elemento O, Seidman JG, Seidman CE, Basson CT, Hatcher CJ. 2014. Tbx5 is required for avian and Mammalian epicardial formation and coronary vasculogenesis. Circ Res 115(10): 834-44.

Du W, Elemento O. 2015. Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies. Oncogene 34(25): 3215-25.

Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC, Hua Y, Bulic M, Jiang Y, Carrara M, Calogero RA, Kath WL, Kelleher NL, Wang JP, Elemento O, Licht JD. 2014. Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation. PLoS Genet 10(9): e1004566.

Jiang Y, Elemento O. 2014. Tracing the roots of cancer evolution. Cancer Discov 4(9): 995-7.

Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LH, Melnick AM, Tam W, Elemento O. 2014. Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas. Genome Biol 15(8): 432.

Chiron D, Di Liberto M, Martin P, Huang X, Sharman J, Blecua P, Mathew S, Vijay P, Eng K, Ali S, Johnson A, Chang B, Ely S, Elemento O, Mason CE, Leonard JP, Chen-Kiang S. 2014. Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma. Cancer Discov 4(9): 1022-35.

Sandler VM, Lis R, Liu Y, Kedem A, James D, Elemento O, Butler JM, Scandura JM, Rafii S. 2014. Reprogramming human endothelial cells to haematopoietic cells requires vascular induction. Nature 511(7509): 312-8.

de Martino M, Zhuang D, Klatte T, Rieken M, Rouprêt M, Xylinas E, Clozel T, Krzywinski M, Elemento O, Shariat SF. 2014. Impact of ERBB2 mutations on in vitro sensitivity of bladder cancer to lapatinib. Cancer Biol Ther 15(9): 1239-47.

Kasap C, Elemento O, Kapoor TM. 2014. DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets. Nat Chem Biol 10(8): 626-8.

Kleiman DA, Beninato T, Sultan S, Crowley MJ, Finnerty B, Kumar R, Panarelli NC, Liu YF, Lieberman MD, Seandel M, Evans T, Elemento O, Zarnegar R, Fahey TJ 3rd. 2014. Silencing of UCHL1 by CpG promoter hyper-methylation is associated with metastatic gastroenteropancreatic well-differentiated neuroendocrine (carcinoid) tumors. Ann Surg Oncol 21 Suppl 4: S672-9.

Wen D, Banaszynski LA, Liu Y, Geng F, Noh KM, Xiang J, Elemento O, Rosenwaks Z, Allis CD, Rafii S. 2014. Histone variant H3.3 is an essential maternal factor for oocyte reprogramming. Proc Natl Acad Sci U S A 111(20): 7325-30.

Yerushalmi GM, Salmon-Divon M, Yung Y, Maman E, Kedem A, Ophir L, Elemento O, Coticchio G, Dal Canto M, Mignini Renzinu M, Fadini R, Hourvitz A. 2014. Characterization of the human cumulus cell transcriptome during final follicular maturation and ovulation. Mol Hum Reprod 20(8): 719-35.

Thakur BK, Zhang H, Becker A, Matei I, Huang Y, Costa-Silva B, Zheng Y, Hoshino A, Brazier H, Xiang J, Williams C, Rodriguez-Barrueco R, Silva JM, Zhang W, Hearn S, Elemento O, Paknejad N, Manova-Todorova K, Welte K, Bromberg J, Peinado H, Lyden D. 2014. Double-stranded DNA in exosomes: a novel biomarker in cancer detection. Cell Res 24(6): 766-9.

Walker SR, Liu S, Xiang M, Nicolais M, Hatzi K, Giannopoulou E, Elemento O, Cerchietti L, Melnick A, Frank DA. 2015. The transcriptional modulator BCL6 as a molecular target for breast cancer therapy. Oncogene 34(9): 1073-82.

Tan AY, Michaeel A, Liu G, Elemento O, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H. 2014. Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing. J Mol Diagn 16(2): 216-28.

Rath P, Huang C, Wang T, Wang T, Li H, Prados-Rosales R, Elemento O, Casadevall A, Nathan CF. 2013. Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 110(49): E4790-7.

Bödör C, Grossmann V, Popov N, Okosun J, O'Riain C, Tan K, Marzec J, Araf S, Wang J, Lee AM, Clear A, Montoto S, Matthews J, Iqbal S, Rajnai H, Rosenwald A, Ott G, Campo E, Rimsza LM, Smeland EB, Chan WC, Braziel RM, Staudt LM, Wright G, Lister TA, Elemento O, Hills R, Gribben JG, Chelala C, Matolcsy A, Kohlmann A, Haferlach T, Gascoyne RD, Fitzgibbon J. 2013. EZH2 mutations are frequent and represent an early event in follicular lymphoma. Blood 122(18): 3165-8.

Qiao Y, Giannopoulou EG, Chan CH, Park SH, Gong S, Chen J, Hu X, Elemento O, Ivashkiv LB. 2013. Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling. Immunity 39(3): 454-69.

Israely E, Ginsberg M, Nolan D, Ding BS, James D, Elemento O, Rafii S, Rabbany SY. 2014. Akt suppression of TGFβ signaling contributes to the maintenance of vascular identity in embryonic stem cell-derived endothelial cells. Stem Cells 32(1): 177-90.

Hatzi K, Jiang Y, Huang C, Garrett-Bakelman F, Gearhart MD, Giannopoulou EG, Zumbo P, Kirouac K, Bhaskara S, Polo JM, Kormaksson M, MacKerell AD Jr, Xue F, Mason CE, Hiebert SW, Prive GG, Cerchietti L, Bardwell VJ, Elemento O, Melnick A. 2013. A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep 4(3): 578-88.

Nolan DJ, Ginsberg M, Israely E, Palikuqi B, Poulos MG, James D, Ding BS, Schachterle W, Liu Y, Rosenwaks Z, Butler JM, Xiang J, Rafii A, Shido K, Rabbany SY, Elemento O, Rafii S. 2013. Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration. Dev Cell 26(2): 204-19.

Hess ME, Hess S, Meyer KD, Verhagen LA, Koch L, Brönneke HS, Dietrich MO, Jordan SD, Saletore Y, Elemento O, Belgardt BF, Franz T, Horvath TL, Rüther U, Jaffrey SR, Kloppenburg P, Brüning JC. 2013. The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nat Neurosci 16(8): 1042-8.

Sun XJ, Wang Z, Wang L, Jiang Y, Kost N, Soong TD, Chen WY, Tang Z, Nakadai T, Elemento O, Fischle W, Melnick A, Patel DJ, Nimer SD, Roeder RG. 2013. A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature 500(7460): 93-7.

Kumar R, DiMenna L, Schrode N, Liu TC, Franck P, Muñoz-Descalzo S, Hadjantonakis AK, Zarrin AA, Chaudhuri J, Elemento O, Evans T. 2013. AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes. Nature 500(7460): 89-92.

Béguelin W, Popovic R, Teater M, Jiang Y, Bunting KL, Rosen M, Shen H, Yang SN, Wang L, Ezponda T, Martinez-Garcia E, Zhang H, Zheng Y, Verma SK, McCabe MT, Ott HM, Van Aller GS, Kruger RG, Liu Y, McHugh CF, Scott DW, Chung YR, Kelleher N, Shaknovich R, Creasy CL, Gascoyne RD, Wong KK, Cerchietti L, Levine RL, Abdel-Wahab O, Licht JD, Elemento O, Melnick AM. 2013. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23(5): 677-92.

Lu Y, Soong TD, Elemento O. 2013. A novel approach for characterizing microsatellite instability in cancer cells. PLoS One 8(5): e63056.

Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. 2013. Punctuated evolution of prostate cancer genomes. Cell 153(3): 666-77.

Sagardoy A, Martinez-Ferrandis JI, Roa S, Bunting KL, Aznar MA, Elemento O, Shaknovich R, Fontán L, Fresquet V, Perez-Roger I, Robles EF, De Smedt L, Sagaert X, Melnick A, Martinez-Climent JA. 2013. Downregulation of FOXP1 is required during germinal center B-cell function. Blood 121(21): 4311-20.

Lin PC, Giannopoulou EG, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA, Elemento O. 2013. Epigenomic alterations in localized and advanced prostate cancer. Neoplasia 15(4): 373-83.

Giannopoulou EG, Elemento O. 2013. Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res 23(8): 1295-306.

Chaudhri VK, Salzler GG, Dick SA, Buckman MS, Sordella R, Karoly ED, Mohney R, Stiles BM, Elemento O, Altorki NK, McGraw TE. 2013. Metabolic alterations in lung cancer-associated fibroblasts correlated with increased glycolytic metabolism of the tumor. Mol Cancer Res 11(6): 579-92.

Chang CY, Pasolli HA, Giannopoulou EG, Guasch G, Gronostajski RM, Elemento O, Fuchs E. 2013. NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche. Nature 495(7439): 98-102.

De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F. 2013. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet 9(1): e1003137.

Lin PC, Chiu YL, Banerjee S, Park K, Mosquera JM, Giannopoulou E, Alves P, Tewari AK, Gerstein MB, Beltran H, Melnick AM, Elemento O, Demichelis F, Rubin MA. 2013. Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Res 73(3): 1232-44.

Chang SH, Lu YC, Li X, Hsieh WY, Xiong Y, Ghosh M, Evans T, Elemento O, Hla T. 2013. Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of vascular endothelial growth factor-A expression and angiogenesis. J Biol Chem 288(7): 4908-21.

Rafii S, Kloss CC, Butler JM, Ginsberg M, Gars E, Lis R, Zhan Q, Josipovic P, Ding BS, Xiang J, Elemento O, Zaninovic N, Rosenwaks Z, Sadelain M, Rafii JA, James D. 2013. Human ESC-derived hemogenic endothelial cells undergo distinct waves of endothelial to hematopoietic transition. Blood 121(5): 770-80.

Geng H, Brennan S, Milne TA, Chen WY, Li Y, Hurtz C, Kweon SM, Zickl L, Shojaee S, Neuberg D, Huang C, Biswas D, Xin Y, Racevskis J, Ketterling RP, Luger SM, Lazarus H, Tallman MS, Rowe JM, Litzow MR, Guzman ML, Allis CD, Roeder RG, Müschen M, Paietta E, Elemento O, Melnick AM. 2012. Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. Cancer Discov 2(11): 1004-23.

Ginsberg M, James D, Ding BS, Nolan D, Geng F, Butler JM, Schachterle W, Pulijaal VR, Mathew S, Chasen ST, Xiang J, Rosenwaks Z, Shido K, Elemento O, Rabbany SY, Rafii S. 2012. Efficient direct reprogramming of mature amniotic cells into endothelial cells by ETS factors and TGFβ suppression. Cell 151(3): 559-75.

Elemento O, Rubin MA, Rickman DS. 2012. Oncogenic transcription factors as master regulators of chromatin topology: a new role for ERG in prostate cancer. Cell Cycle 11(18): 3380-3.

Jiang Y, Soong TD, Wang L, Melnick AM, Elemento O. 2012. Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma. PLoS One 7(7): e40332.

Rickman DS, Soong TD, Moss B, Mosquera JM, Dlabal J, Terry S, MacDonald TY, Tripodi J, Bunting K, Najfeld V, Demichelis F, Melnick AM, Elemento O, Rubin MA. 2012. Oncogene-mediated alterations in chromatin conformation. Proc Natl Acad Sci U S A 109(23): 9083-8.

Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. 2012. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 149(7): 1635-46.

Gollamudi S, Johri A, Calingasan NY, Yang L, Elemento O, Beal MF. 2012. Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease. PLoS One 7(5): e36191.

Demichelis F, Setlur SR, Banerjee S, Chakravarty D, Chen JY, Chen CX, Huang J, Beltran H, Oldridge DA, Kitabayashi N, Stenzel B, Schaefer G, Horninger W, Bektic J, Chinnaiyan AM, Goldenberg S, Siddiqui J, Regan MM, Kearney M, Soong TD, Rickman DS, Elemento O, Wei JT, Scherr DS, Sanda MA, Bartsch G, Lee C, Klocker H, Rubin MA. 2012. Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. Proc Natl Acad Sci U S A 109(17): 6686-91.

Keutgen XM, Buitrago D, Filicori F, Kundel A, Elemento O, Fahey TJ 3rd, Zarnegar R. 2012. Calcimimetics versus parathyroidectomy for treatment of primary hyperparathyroidism: retrospective chart analysis of a prospective database. Ann Surg 255(5): 981-5.

Mason CE, Elemento O. 2012. Faster sequencers, larger datasets, new challenges. Genome Biol 13(3): 314.

Keutgen XM, Filicori F, Crowley MJ, Wang Y, Scognamiglio T, Hoda R, Buitrago D, Cooper D, Zeiger MA, Zarnegar R, Elemento O, Fahey TJ 3rd. 2012. A panel of four miRNAs accurately differentiates malignant from benign indeterminate thyroid lesions on fine needle aspiration. Clin Cancer Res 18(7): 2032-8.

Wacker SA, Houghtaling BR, Elemento O, Kapoor TM. 2012. Using transcriptome sequencing to identify mechanisms of drug action and resistance. Nat Chem Biol 8(3): 235-7.

Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. 2011. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 118(13): 3559-69.

Giannopoulou EG, Elemento O. 2011. An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics 12: 277.

Lieber DS, Elemento O, Tavazoie S. 2010. Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One 5(12): e14444.

Rajadhyaksha AM, Elemento O, Puffenberger EG, Schierberl KC, Xiang JZ, Putorti ML, Berciano J, Poulin C, Brais B, Michaelides M, Weleber RG, Higgins JJ. 2010. Mutations in FLVCR1 cause posterior column ataxia and retinitis pigmentosa. Am J Hum Genet 87(5): 643-54.

Campbell TL, De Silva EK, Olszewski KL, Elemento O, Llinás M. 2010. Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog 6(10): e1001165.

Velichutina I, Shaknovich R, Geng H, Johnson NA, Gascoyne RD, Melnick AM, Elemento O. 2010. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood 116(24): 5247-55.

Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A. 2010. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood 116(20): e81-9.

Goodarzi H, Elemento O, Tavazoie S. 2009. Revealing global regulatory perturbations across human cancers. Mol Cell 36(5): 900-11.

da Piedade I, Tang MH, Elemento O. 2009. DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. BMC Bioinformatics 10: 388.

Lu X, Li JM, Elemento O, Tavazoie S, Wieschaus EF. 2009. Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition. Development 136(12): 2101-10.

Ci W, Polo JM, Cerchietti L, Shaknovich R, Wang L, Yang SN, Ye K, Farinha P, Horsman DE, Gascoyne RD, Elemento O, Melnick A. 2009. The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL. Blood 113(22): 5536-48.

Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA. 2009. let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. J Biol Chem 284(11): 6605-9.

Elemento O, Tavazoie S. 2007. Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation. Methods Mol Biol 395: 349-66.

Elemento O, Slonim N, Tavazoie S. 2007. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28(2): 337-50.

Elemento O. 2007. Developing a systems-level understanding of gene expression. Genome Biol 8(4): 304.

De Renzis S, Elemento O, Tavazoie S, Wieschaus EF. 2007. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol 5(5): e117.

Slonim N, Elemento O, Tavazoie S. 2006. Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol 2: 2006.0005.

Chan CS, Elemento O, Tavazoie S. 2005. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol 1(7): e69.

Elemento O, Tavazoie S. 2005. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 6(2): R18.

Elemento O, Lefranc MP. 2003. IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes. Dev Comp Immunol 27(9): 763-79.

Elemento O, Gascuel O. 2002. An efficient and accurate distance based algorithm to reconstruct tandem duplication trees. Bioinformatics 18 Suppl 2: S92-9.

Elemento O, Gascuel O, Lefranc MP. 2002. Reconstructing the duplication history of tandemly repeated genes. Mol Biol Evol 19(3): 278-88.