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158. Pyenson NC, Gayvert K, Varble A, Elemento O, Marraffini LA. Broad Targeting Specificity during Bacterial Type III CRISPR-Cas Immunity Constrains Viral Escape. Cell Host Microbe. 2017 Sep 13;22(3):343-353.e3. doi: 10.1016/j.chom.2017.07.016. Epub 2017 Aug 17.

157. Prabhu VV, Lulla AR, Madhukar NS, Ralff MD, Zhao D, Kline CLB, Van den Heuvel APJ, Lev A, Garnett MJ, McDermott U, Benes CH, Batchelor TT, Chi AS, Elemento O, Allen JE, El-Deiry WS. Cancer stem cell-related gene expression as a potential biomarker of response for first-in-class imipridone ONC201 in solid tumors. PLoS One. 2017 Aug 2;12(8):e0180541. doi: 10.1371/journal.pone.0180541. eCollection 2017.

156. Han T, Schatoff EM, Murphy C, Zafra MP, Wilkinson JE, Elemento O, Dow LE. R-Spondin chromosome rearrangements drive Wnt-dependent tumour initiation and maintenance in the intestine. Nat Commun. 2017 Jul 11;8:15945. doi: 10.1038/ncomms15945.

155. Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F. Inherited determinants of early recurrent somatic mutations in prostate cancer. Nat Commun. 2017 Jun 29;8(1):48. doi: 10.1038/s41467-017-00046-0.

154. Reichel JB, McCormick J, Fromm JR, Elemento O, Cesarman E, Roshal M. Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma. J Vis Exp. 2017 Jun 10;(124). doi: 10.3791/54399.

153. Bose R, Karthaus WR, Armenia J, Abida W, Iaquinta PJ, Zhang Z, Wongvipat J, Wasmuth EV, Shah N, Sullivan PS, Doran MG, Wang P, Patruno A, Zhao Y, Zheng D, Schultz N, Sawyers CL. ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis. Nature. 2017 Jun 29;546(7660):671-675. doi: 10.1038/nature22820. Epub 2017 Jun 14.

152. Mendoza A, Fang V, Chen C, Serasinghe M, Verma A, Muller J, Chaluvadi VS, Dustin ML, Hla T, Elemento O, Chipuk JE, Schwab SR. Lymphatic endothelial S1P promotes mitochondrial function and survival in naive T cells. Nature. 2017 Jun 1;546(7656):158-161. doi: 10.1038/nature22352. Epub 2017 May 24.

151. Benedicto I, Lehmann GL, Ginsberg M, Nolan DJ, Bareja R, Elemento O, Salfati Z, Alam NM, Prusky GT, Llanos P, Rabbany SY, Maminishkis A, Miller SS, Rafii S, Rodriguez-Boulan E. Concerted regulation of retinal pigment epithelium basement membrane and barrier function by angiocrine factors. Nat Commun. 2017 May 19;8:15374. doi: 10.1038/ncomms15374.

150. Liu Y, Pelham-Webb B, Di Giammartino DC, Li J, Kim D, Kita K, Saiz N, Garg V, Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E. Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells. Cell Rep. 2017 May 16;19(7):1283-1293. doi: 10.1016/j.celrep.2017.04.067.

149. Lis R, Karrasch CC, Poulos MG, Kunar B, Redmond D, Duran JGB, Badwe CR, Schachterle W, Ginsberg M, Xiang J, Tabrizi AR, Shido K, Rosenwaks Z, Elemento O, Speck NA, Butler JM, Scandura JM, Rafii S. Conversion of adult endothelium to immunocompetent haematopoietic stem cells. Nature. 2017 May 25;545(7655):439-445. doi: 10.1038/nature22326. Epub 2017 May 17.

148. Carty M, Zamparo L, Sahin M, Gonzalez A, Pelossof R, Elemento O, Leslie CS. An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data. Nat Commun. 2017 May 17;8:15454. doi: 10.1038/ncomms15454.

147. Nayar U, Sadek J, Reichel J, Hernandez-Hopkins D, Akar G, Barelli PJ, Sahai MA, Zhou H, Totonchy J, Jayabalan D, Niesvizky R, Guasparri I, Hassane D, Liu Y, Sei S, Shoemaker RH, Warren JD, Elemento O, Kaye KM, Cesarman E. Identification of a nucleoside analog active against adenosine kinase-expressing plasma cell malignancies. J Clin Invest. 2017 Jun 1;127(6):2066-2080. doi: 10.1172/JCI83936. Epub 2017 May 15.

146. Kassambara A, Jourdan M, Bruyer A, Robert N, Pantesco V, Elemento O, Klein B, Moreaux J. Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell. Nucleic Acids Res. 2017 Jun 2;45(10):5639-5652. doi: 10.1093/nar/gkx327.

145. Ge Y, Gomez NC, Adam RC, Nikolova M, Yang H, Verma A, Lu CP, Polak L, Yuan S, Elemento O, Fuchs E. Stem Cell Lineage Infidelity Drives Wound Repair and Cancer. Cell. 2017 May 4;169(4):636-650.e14. doi: 10.1016/j.cell.2017.03.042. Epub 2017 Apr 20.

144. Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME. Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Cancer Discov. 2017 Aug;7(8):868-883. doi: 10.1158/2159-8290.CD-16-1032. Epub 2017 Apr 13.

143. Romanel A, Zhang T, Elemento O, Demichelis F. EthSEQ: ethnicity annotation from whole exome sequencing data. Bioinformatics. 2017 Aug 1;33(15):2402-2404. doi: 10.1093/bioinformatics/btx165.

142. Anelli V, Villefranc JA, Chhangawala S, Martinez-McFaline R, Riva E, Nguyen A, Verma A, Bareja R, Chen Z, Scognamiglio T, Elemento O, Houvras Y. Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression. Elife. 2017 Mar 28;6. pii: e20728. doi: 10.7554/eLife.20728.

141. Pauli C, Hopkins BD, Prandi D, Shaw R, Fedrizzi T, Sboner A, Sailer V, Augello M, Puca L, Rosati R, McNary TJ, Churakova Y, Cheung C, Triscott J, Pisapia D, Rao R, Mosquera JM, Robinson B, Faltas BM, Emerling BE, Gadi VK, Bernard B, Elemento O, Beltran H, Demichelis F, Kemp CJ, Grandori C, Cantley LC, Rubin MA. Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine. Cancer Discov. 2017 May;7(5):462-477. doi: 10.1158/2159-8290.CD-16-1154. Epub 2017 Mar 22.

140. Patnaik A, Swanson KD, Csizmadia E, Solanki A, Landon-Brace N, Gehring MP, Helenius K, Olson BM, Pyzer AR, Wang LC, Elemento O, Novak J, Thornley TB, Asara JM, Montaser L, Timmons JJ, Morgan TM, Wang Y, Levantini E, Clohessy JG, Kelly K, Pandolfi PP, Rosenblatt JM, Avigan DE, Ye H, Karp JM, Signoretti S, Balk SP, Cantley LC. Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity. Cancer Discov. 2017 Jul;7(7):750-765. doi: 10.1158/2159-8290.CD-16-0778. Epub 2017 Mar 8.

139. Valls E, Lobry C, Geng H, Wang L, Cardenas M, Rivas M, Cerchietti L, Oh P, Yang SN, Oswald E, Graham CW, Jiang Y, Hatzi K, Agirre X, Perkey E, Li Z, Tam W, Bhatt K, Leonard JP, Zweidler-McKay PA, Maillard I, Elemento O, Ci W, Aifantis I, Melnick A. BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells. Cancer Discov. 2017 May;7(5):506-521. doi: 10.1158/2159-8290.CD-16-1189. Epub 2017 Feb 23.

138. Kansler ER, Verma A, Langdon EM, Simon-Vermot T, Yin A, Lee W, Attiyeh M, Elemento O, White RM. Melanoma genome evolution across species. BMC Genomics. 2017 Feb 7;18(1):136. doi: 10.1186/s12864-017-3518-8.

137. Du W, Goldstein R, Jiang Y, Aly O, Cerchietti L, Melnick A, Elemento O. Effective Combination Therapies for B-cell Lymphoma Predicted by a Virtual Disease Model. Cancer Res. 2017 Apr 15;77(8):1818-1830. doi: 10.1158/0008-5472.CAN-16-0476. Epub 2017 Jan 27.

136. Doane AS, Elemento O. Regulatory elements in molecular networks. Wiley Interdiscip Rev Syst Biol Med. 2017 May;9(3). doi: 10.1002/wsbm.1374. Epub 2017 Jan 17.

135. Schachterle W, Badwe CR, Palikuqi B, Kunar B, Ginsberg M, Lis R, Yokoyama M, Elemento O, Scandura JM, Rafii S. Sox17 drives functional engraftment of endothelium converted from non-vascular cells. Nat Commun. 2017 Jan 16;8:13963. doi: 10.1038/ncomms13963.

134. Gayvert KM, Aly O, Platt J, Bosenberg MW, Stern DF, Elemento O. A Computational Approach for Identifying Synergistic Drug Combinations. PLoS Comput Biol. 2017 Jan 13;13(1):e1005308. doi: 10.1371/journal.pcbi.1005308. eCollection 2017 Jan.

133. 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. Systems Structural Biology Analysis of Ligand Effects on ERalpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies. Cell Chem Biol. 2017 Jan 19;24(1):35-45. doi: 10.1016/j.chembiol.2016.11.014. Epub 2016 Dec 29.

132. 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. Role of RPL39 in Metaplastic Breast Cancer. J Natl Cancer Inst. 2016 Dec 31;109(6). pii: djw292. doi: 10.1093/jnci/djw292. Print 2017 Jun.

131. 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. Reversible methylation of m6Am in the 5' cap controls mRNA stability. Nature. 2017 Jan 19;541(7637):371-375. doi: 10.1038/nature21022. Epub 2016 Dec 21.

130. 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. Endothelial-specific inhibition of NF-kappaB enhances functional haematopoiesis. Nat Commun. 2016 Dec 21;7:13829. doi: 10.1038/ncomms13829.

129. Amengual JE, Prabhu SA, Lombardo M, Zullo K, Johannet PM, Gonzalez Y, Scotto L, Serrano XJ, Wei Y, Duong J, Nandakumar R, Cremers S, Verma A, Elemento O, O'Connor OA. Mechanisms of Acquired Drug Resistance to the HDAC6 Selective Inhibitor Ricolinostat Reveals Rational Drug-Drug Combination with Ibrutinib. Clin Cancer Res. 2017 Jun 15;23(12):3084-3096. doi: 10.1158/1078-0432.CCR-16-2022. Epub 2016 Dec 19.

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

127. 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. Clonal evolution of chemotherapy-resistant urothelial carcinoma. Nat Genet. 2016 Dec;48(12):1490-1499. doi: 10.1038/ng.3692. Epub 2016 Oct 17.

126. 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. Therapeutic efficacy of the bromodomain inhibitor OTX015/MK-8628 in ALK-positive anaplastic large cell lymphoma: an alternative modality to overcome resistant phenotypes. Oncotarget. 2016 Nov 29;7(48):79637-79653. doi: 10.18632/oncotarget.12876.

125. Huang L, Fernandes H, Zia H, Tavassoli P, Rennert H, Pisapia D, Imielinski M, Sboner A, Rubin MA, Kluk M, Elemento O. The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations. J Am Med Inform Assoc. 2017 May 1;24(3):513-519. doi: 10.1093/jamia/ocw148.

124. Gayvert KM, Madhukar NS, Elemento O. A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials. Cell Chem Biol. 2016 Oct 20;23(10):1294-1301. doi: 10.1016/j.chembiol.2016.07.023. Epub 2016 Sep 15.

123. 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. CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas. Cancer Discov. 2017 Jan;7(1):38-53. doi: 10.1158/2159-8290.CD-16-0975. Epub 2016 Oct 12.

122. 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. N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer. Cancer Cell. 2016 Oct 10;30(4):563-577. doi: 10.1016/j.ccell.2016.09.005.

121. Bunting KL, Soong TD, Singh R, Jiang Y, Beguelin W, Poloway DW, Swed BL, Hatzi K, Reisacher W, Teater M, Elemento O, Melnick AM. Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region. Immunity. 2016 Sep 20;45(3):497-512. doi: 10.1016/j.immuni.2016.08.012. Epub 2016 Sep 13.

120. 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. Discovery and clinical introduction of first-in-class imipridone ONC201. Oncotarget. 2016 Nov 8;7(45):74380-74392. doi: 10.18632/oncotarget.11814.

119. Xylinas E, Hassler MR, Zhuang D, Krzywinski M, Erdem Z, Robinson BD, Elemento O, Clozel T, Shariat SF. An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer. Biomolecules. 2016 Sep 2;6(3). pii: E37. doi: 10.3390/biom6030037.

118. 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. Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy. Cancer Immunol Res. 2016 Oct;4(10):835-844. Epub 2016 Sep 1.

117. Beguelin W, Teater M, Gearhart MD, Calvo Fernandez MT, Goldstein RL, Cardenas 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. EZH2 and BCL6 Cooperate to Assemble CBX8-BCOR Complex to Repress Bivalent Promoters, Mediate Germinal Center Formation and Lymphomagenesis. Cancer Cell. 2016 Aug 8;30(2):197-213. doi: 10.1016/j.ccell.2016.07.006.

116. Elemento O. KLF4: A new player in plasma cell development. Cell Cycle. 2016 Oct 17;15(20):2691-2. doi: 10.1080/15384101.2016.1214048. Epub 2016 Aug 2.

115. 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. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest. 2016 Sep 1;126(9):3351-62. doi: 10.1172/JCI85795. Epub 2016 Aug 2.

114. Redmond D, Poran A, Elemento O. Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med. 2016 Jul 27;8(1):80. doi: 10.1186/s13073-016-0335-7.

113. 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. Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer. N Engl J Med. 2016 Aug 4;375(5):443-53. doi: 10.1056/NEJMoa1603144. Epub 2016 Jul 6.

112. Gayvert KM, Dardenne E, Cheung C, Boland MR, Lorberbaum T, Wanjala J, Chen Y, Rubin MA, Tatonetti NP, Rickman DS, Elemento O. A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors. Cell Rep. 2016 Jun 14;15(11):2348-56. doi: 10.1016/j.celrep.2016.05.037. Epub 2016 Jun 2.

111. 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. Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance. Diabetes. 2016 Jun;65(6):1577-89. doi: 10.2337/db15-1128. Epub 2016 Mar 25.

110. Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M. Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. Nat Commun. 2016 Apr 27;7:11275. doi: 10.1038/ncomms11275.

109. 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. Predictive features of ligand-specific signaling through the estrogen receptor. Mol Syst Biol. 2016 Apr 22;12(4):864. doi: 10.15252/msb.20156701.

108. Carty MA, Elemento O. Practical Analysis of Genome Contact Interaction Experiments. Methods Mol Biol. 2016;1418:177-89. doi: 10.1007/978-1-4939-3578-9_9.

107. Takemoto A, Kawashima SA, Li JJ, Jeffery L, Yamatsugu K, Elemento O, Nurse P. Nuclear envelope expansion is crucial for proper chromosomal segregation during a closed mitosis. J Cell Sci. 2016 Mar 15;129(6):1250-9. doi: 10.1242/jcs.181560. Epub 2016 Feb 11.

106. 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. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Mar;22(3):298-305. doi: 10.1038/nm.4045. Epub 2016 Feb 8.

105. Jiang Y, Nie K, Redmond D, Melnick AM, Tam W, Elemento O. VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma. J Vis Exp. 2015 Dec 28;(106):e53215. doi: 10.3791/53215.

104. 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. Prostate-Specific Membrane Antigen Is a Potential Antiangiogenic Target in Adrenocortical Carcinoma. J Clin Endocrinol Metab. 2016 Mar;101(3):981-7. doi: 10.1210/jc.2015-4021. Epub 2016 Jan 15.

103. Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim R, Tam W, Liu YC, Bhinder B, Cyrta J, Beltran H, Robinson B, Mosquera JM, Fernandes H, Demichelis F, Sboner A, Kluk M, Rubin MA, Elemento O. Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care. NPJ Genom Med. 2016;1. pii: 16019. doi: 10.1038/npjgenmed.2016.19. Epub 2016 Jul 20.

102. Culjkovic-Kraljacic B, Fernando TM, Marullo R, Calvo-Vidal N, Verma A, Yang S, Tabbo 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. Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphomas. Blood. 2016 Feb 18;127(7):858-68. doi: 10.1182/blood-2015-05-645069. Epub 2015 Nov 24.

101. Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR. 5' UTR m(6)A Promotes Cap-Independent Translation. Cell. 2015 Nov 5;163(4):999-1010. doi: 10.1016/j.cell.2015.10.012. Epub 2015 Oct 22.

100. Madhukar NS, Elemento O, Pandey G. Prediction of Genetic Interactions Using Machine Learning and Network Properties. Front Bioeng Biotechnol. 2015 Oct 26;3:172. doi: 10.3389/fbioe.2015.00172. eCollection 2015.

99. 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. Vitamin C selectively kills KRAS and BRAF mutant colorectal cancer cells by targeting GAPDH. Science. 2015 Dec 11;350(6266):1391-6. doi: 10.1126/science.aaa5004. Epub 2015 Nov 5.

98. Ma J, Nie K, Redmond D, Liu Y, Elemento O, Knowles DM, Tam W. EBV-miR-BHRF1-2 targets PRDM1/Blimp1: potential role in EBV lymphomagenesis. Leukemia. 2016 Mar;30(3):594-604. doi: 10.1038/leu.2015.285. Epub 2015 Nov 4.

97. Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O. Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma. Genome Med. 2015 Nov 1;7:110. doi: 10.1186/s13073-015-0230-7.

96. Poulos MG, Crowley MJ, Gutkin MC, Ramalingam P, Schachterle W, Thomas JL, Elemento O, Butler JM. Vascular Platform to Define Hematopoietic Stem Cell Factors and Enhance Regenerative Hematopoiesis. Stem Cell Reports. 2015 Nov 10;5(5):881-94. doi: 10.1016/j.stemcr.2015.08.018. Epub 2015 Oct 1.

95. 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. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat Med. 2015 Oct;21(10):1199-208. doi: 10.1038/nm.3943. Epub 2015 Sep 14.

94. 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. DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID. Cell Rep. 2015 Sep 29;12(12):2086-98. doi: 10.1016/j.celrep.2015.08.036. Epub 2015 Sep 10.

93. 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. Obesity-dependent changes in interstitial ECM mechanics promote breast tumorigenesis. Sci Transl Med. 2015 Aug 19;7(301):301ra130. doi: 10.1126/scitranslmed.3010467.

92. 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. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.

91. 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, Sboner A, 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. Integrative Clinical Genomics of Advanced Prostate Cancer. Cell. 2015 Jul 16;162(2):454. doi: 10.1016/j.cell.2015.06.053. Epub 2015 Jul 16.

90. Giannopoulou EG, Elemento O, Ivashkiv LB. Use of RNA sequencing to evaluate rheumatic disease patients. Arthritis Res Ther. 2015 Jul 1;17:167. doi: 10.1186/s13075-015-0677-3.

89. 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. Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia. Cell Rep. 2015 Jul 7;12(1):35-41. doi: 10.1016/j.celrep.2015.06.014. Epub 2015 Jun 25.

88. Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, Wu YG, Elemento O, Tavazoie SF. Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. Nat Cell Biol. 2015 Jul;17(7):943-52. doi: 10.1038/ncb3194. Epub 2015 Jun 22.

87. Sboner A, Elemento O. A primer on precision medicine informatics. Brief Bioinform. 2016 Jan;17(1):145-53. doi: 10.1093/bib/bbv032. Epub 2015 Jun 5.

86. 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. Identification of Reprogrammed Myeloid Cell Transcriptomes in NSCLC. PLoS One. 2015 Jun 5;10(6):e0129123. doi: 10.1371/journal.pone.0129123. eCollection 2015.

85. 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. Integrative clinical genomics of advanced prostate cancer. Cell. 2015 May 21;161(5):1215-1228. doi: 10.1016/j.cell.2015.05.001.

84. Zhao X, Chen-Kiang S, Shetty S, Di Liberto M, Bodo J, Durkin L, Eng K, Elemento O, Smith MR, Hsi ED. CCMCL1: a new model of aggressive mantle cell lymphoma. Blood. 2015 Apr 23;125(17):2730-2. doi: 10.1182/blood-2015-01-622795.

83. Ceballos-Chavez M, Subtil-Rodriguez A, Giannopoulou EG, Soronellas D, Vazquez-Chavez E, Vicent GP, Elemento O, Beato M, Reyes JC. The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PLoS Genet. 2015 Apr 20;11(4):e1005174. doi: 10.1371/journal.pgen.1005174. eCollection 2015 Apr.

82. Pan H, Jiang Y, Boi M, Tabbo F, Redmond D, Nie K, Ladetto M, Chiappella A, Cerchietti L, Shaknovich R, Melnick AM, Inghirami GG, Tam W, Elemento O. Epigenomic evolution in diffuse large B-cell lymphomas. Nat Commun. 2015 Apr 20;6:6921. doi: 10.1038/ncomms7921.

81. Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Leopold 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. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.

80. 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. Selective inhibition of protein arginine methyltransferase 5 blocks initiation and maintenance of B-cell transformation. Blood. 2015 Apr 16;125(16):2530-43. doi: 10.1182/blood-2014-12-619783. Epub 2015 Mar 5.

79. 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. Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model. Cell Rep. 2015 Feb 24;10(7):1187-201. doi: 10.1016/j.celrep.2015.01.040. Epub 2015 Feb 19.

78. Gori JL, Butler JM, Chan YY, Chandrasekaran D, Poulos MG, Ginsberg M, Nolan DJ, Elemento O, Wood BL, Adair JE, Rafii S, Kiem HP. Vascular niche promotes hematopoietic multipotent progenitor formation from pluripotent stem cells. J Clin Invest. 2015 Mar 2;125(3):1243-54. doi: 10.1172/JCI79328. Epub 2015 Feb 9.

77. Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T. ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. Cell Rep. 2014 Dec 24;9(6):2330-43. doi: 10.1016/j.celrep.2014.11.030. Epub 2014 Dec 18.

76. 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. Lymphoblastic transformation of follicular lymphoma: a clinicopathologic and molecular analysis of 7 patients. Hum Pathol. 2015 Feb;46(2):260-71. doi: 10.1016/j.humpath.2014.10.021. Epub 2014 Nov 13.

75. 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. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061-72. doi: 10.1182/blood-2014-11-610436. Epub 2014 Dec 8.

74. Erler P, Keutgen XM, Crowley MJ, Zetoune T, Kundel A, Kleiman D, Beninato T, Scognamiglio T, Elemento O, Zarnegar R, Fahey TJ 3rd. Dicer expression and microRNA dysregulation associate with aggressive features in thyroid cancer. Surgery. 2014 Dec;156(6):1342-50; discussion 1350. doi: 10.1016/j.surg.2014.08.007. Epub 2014 Nov 11.

73. Chang SH, Elemento O, Zhang J, Zhuang ZW, Simons M, Hla T. ELAVL1 regulates alternative splicing of eIF4E transporter to promote postnatal angiogenesis. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18309-14. doi: 10.1073/pnas.1412172111. Epub 2014 Nov 24.

72. 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. The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun. 2014 Nov 21;5:5383. doi: 10.1038/ncomms6383.

71. 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. Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony-forming cells. Nat Biotechnol. 2014 Nov;32(11):1151-1157. doi: 10.1038/nbt.3048. Epub 2014 Oct 12.

70. Diman NY, Brooks G, Kruithof BP, Elemento O, Seidman JG, Seidman CE, Basson CT, Hatcher CJ. Tbx5 is required for avian and Mammalian epicardial formation and coronary vasculogenesis. Circ Res. 2014 Oct 24;115(10):834-44. doi: 10.1161/CIRCRESAHA.115.304379. Epub 2014 Sep 22.

69. Du W, Elemento O. Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies. Oncogene. 2015 Jun;34(25):3215-25. doi: 10.1038/onc.2014.291. Epub 2014 Sep 15.

68. 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. Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation. PLoS Genet. 2014 Sep 4;10(9):e1004566. doi: 10.1371/journal.pgen.1004566. eCollection 2014 Sep.

67. Jiang Y, Elemento O. Tracing the roots of cancer evolution. Cancer Discov. 2014 Sep;4(9):995-7. doi: 10.1158/2159-8290.CD-14-0743.

66. Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LH, Melnick AM, Tam W, Elemento O. Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas. Genome Biol. 2014 Aug 15;15(8):432. doi: 10.1186/s13059-014-0432-0.

65. 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. Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma. Cancer Discov. 2014 Sep;4(9):1022-35. doi: 10.1158/2159-8290.CD-14-0098. Epub 2014 Jul 31.

64. Sandler VM, Lis R, Liu Y, Kedem A, James D, Elemento O, Butler JM, Scandura JM, Rafii S. Reprogramming human endothelial cells to haematopoietic cells requires vascular induction. Nature. 2014 Jul 17;511(7509):312-8. doi: 10.1038/nature13547. Epub 2014 Jul 2.

63. de Martino M, Zhuang D, Klatte T, Rieken M, Roupret M, Xylinas E, Clozel T, Krzywinski M, Elemento O, Shariat SF. Impact of ERBB2 mutations on in vitro sensitivity of bladder cancer to lapatinib. Cancer Biol Ther. 2014 Sep;15(9):1239-47. doi: 10.4161/cbt.29687. Epub 2014 Jul 14.

62. Kasap C, Elemento O, Kapoor TM. DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets. Nat Chem Biol. 2014 Aug;10(8):626-8. doi: 10.1038/nchembio.1551. Epub 2014 Jun 15.

61. 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. Silencing of UCHL1 by CpG promoter hyper-methylation is associated with metastatic gastroenteropancreatic well-differentiated neuroendocrine (carcinoid) tumors. Ann Surg Oncol. 2014 Dec;21 Suppl 4:S672-9. doi: 10.1245/s10434-014-3787-2. Epub 2014 May 23.

60. Wen D, Banaszynski LA, Liu Y, Geng F, Noh KM, Xiang J, Elemento O, Rosenwaks Z, Allis CD, Rafii S. Histone variant H3.3 is an essential maternal factor for oocyte reprogramming. Proc Natl Acad Sci U S A. 2014 May 20;111(20):7325-30. doi: 10.1073/pnas.1406389111. Epub 2014 May 5.

59. 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. Characterization of the human cumulus cell transcriptome during final follicular maturation and ovulation. Mol Hum Reprod. 2014 Aug;20(8):719-35. doi: 10.1093/molehr/gau031. Epub 2014 Apr 25.

58. 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. Double-stranded DNA in exosomes: a novel biomarker in cancer detection. Cell Res. 2014 Jun;24(6):766-9. doi: 10.1038/cr.2014.44. Epub 2014 Apr 8.

57. Walker SR, Liu S, Xiang M, Nicolais M, Hatzi K, Giannopoulou E, Elemento O, Cerchietti L, Melnick A, Frank DA. The transcriptional modulator BCL6 as a molecular target for breast cancer therapy. Oncogene. 2015 Feb 26;34(9):1073-82. doi: 10.1038/onc.2014.61. Epub 2014 Mar 24.

56. Tan AY, Michaeel A, Liu G, Elemento O, Blumenfeld J, Donahue S, Parker T, Levine D, Rennert H. Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing. J Mol Diagn. 2014 Mar;16(2):216-28. doi: 10.1016/j.jmoldx.2013.10.005. Epub 2013 Dec 27.

55. Rath P, Huang C, Wang T, Wang T, Li H, Prados-Rosales R, Elemento O, Casadevall A, Nathan CF. Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4790-7. doi: 10.1073/pnas.1320118110. Epub 2013 Nov 18.

54. Bodor 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. EZH2 mutations are frequent and represent an early event in follicular lymphoma. Blood. 2013 Oct 31;122(18):3165-8. doi: 10.1182/blood-2013-04-496893. Epub 2013 Sep 19.

53. Qiao Y, Giannopoulou EG, Chan CH, Park SH, Gong S, Chen J, Hu X, Elemento O, Ivashkiv LB. Synergistic activation of inflammatory cytokine genes by interferon-gamma-induced chromatin remodeling and toll-like receptor signaling. Immunity. 2013 Sep 19;39(3):454-69. doi: 10.1016/j.immuni.2013.08.009. Epub 2013 Sep 5.

52. Israely E, Ginsberg M, Nolan D, Ding BS, James D, Elemento O, Rafii S, Rabbany SY. Akt suppression of TGFbeta signaling contributes to the maintenance of vascular identity in embryonic stem cell-derived endothelial cells. Stem Cells. 2014 Jan;32(1):177-90. doi: 10.1002/stem.1521.

51. 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. A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep. 2013 Aug 15;4(3):578-88. doi: 10.1016/j.celrep.2013.06.016. Epub 2013 Aug 1.

50. 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. Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration. Dev Cell. 2013 Jul 29;26(2):204-19. doi: 10.1016/j.devcel.2013.06.017. Epub 2013 Jul 18.

49. Hess ME, Hess S, Meyer KD, Verhagen LA, Koch L, Bronneke HS, Dietrich MO, Jordan SD, Saletore Y, Elemento O, Belgardt BF, Franz T, Horvath TL, Ruther U, Jaffrey SR, Kloppenburg P, Bruning JC. The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nat Neurosci. 2013 Aug;16(8):1042-8. doi: 10.1038/nn.3449. Epub 2013 Jun 30.

48. 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. A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature. 2013 Aug 1;500(7460):93-7. doi: 10.1038/nature12287. Epub 2013 Jun 30.

47. Kumar R, DiMenna L, Schrode N, Liu TC, Franck P, Munoz-Descalzo S, Hadjantonakis AK, Zarrin AA, Chaudhuri J, Elemento O, Evans T. AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes. Nature. 2013 Aug 1;500(7460):89-92. doi: 10.1038/nature12299. Epub 2013 Jun 26.

46. Beguelin 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. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell. 2013 May 13;23(5):677-92. doi: 10.1016/j.ccr.2013.04.011.

45. Lu Y, Soong TD, Elemento O. A novel approach for characterizing microsatellite instability in cancer cells. PLoS One. 2013 May 6;8(5):e63056. doi: 10.1371/journal.pone.0063056. Print 2013.

44. 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. Punctuated evolution of prostate cancer genomes. Cell. 2013 Apr 25;153(3):666-77. doi: 10.1016/j.cell.2013.03.021.

43. Sagardoy A, Martinez-Ferrandis JI, Roa S, Bunting KL, Aznar MA, Elemento O, Shaknovich R, Fontan L, Fresquet V, Perez-Roger I, Robles EF, De Smedt L, Sagaert X, Melnick A, Martinez-Climent JA. Downregulation of FOXP1 is required during germinal center B-cell function. Blood. 2013 May 23;121(21):4311-20. doi: 10.1182/blood-2012-10-462846. Epub 2013 Apr 11.

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

41. Giannopoulou EG, Elemento O. Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res. 2013 Aug;23(8):1295-306. doi: 10.1101/gr.149419.112. Epub 2013 Apr 3.

40. Chaudhri VK, Salzler GG, Dick SA, Buckman MS, Sordella R, Karoly ED, Mohney R, Stiles BM, Elemento O, Altorki NK, McGraw TE. Metabolic alterations in lung cancer-associated fibroblasts correlated with increased glycolytic metabolism of the tumor. Mol Cancer Res. 2013 Jun;11(6):579-92. doi: 10.1158/1541-7786.MCR-12-0437-T. Epub 2013 Mar 8.

39. Chang CY, Pasolli HA, Giannopoulou EG, Guasch G, Gronostajski RM, Elemento O, Fuchs E. NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche. Nature. 2013 Mar 7;495(7439):98-102. doi: 10.1038/nature11847. Epub 2013 Feb 6.

38. 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. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet. 2013;9(1):e1003137. doi: 10.1371/journal.pgen.1003137. Epub 2013 Jan 10.

37. 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. Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Res. 2013 Feb 1;73(3):1232-44. doi: 10.1158/0008-5472.CAN-12-2968. Epub 2012 Dec 11.

36. Chang SH, Lu YC, Li X, Hsieh WY, Xiong Y, Ghosh M, Evans T, Elemento O, Hla T. 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. 2013 Feb 15;288(7):4908-21. doi: 10.1074/jbc.M112.423871. Epub 2012 Dec 6.

35. 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. Human ESC-derived hemogenic endothelial cells undergo distinct waves of endothelial to hematopoietic transition. Blood. 2013 Jan 31;121(5):770-80. doi: 10.1182/blood-2012-07-444208. Epub 2012 Nov 20.

34. 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, Muschen M, Paietta E, Elemento O, Melnick AM. Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. Cancer Discov. 2012 Nov;2(11):1004-23. doi: 10.1158/2159-8290.CD-12-0208. Epub 2012 Oct 29.

33. 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. Efficient direct reprogramming of mature amniotic cells into endothelial cells by ETS factors and TGFbeta suppression. Cell. 2012 Oct 26;151(3):559-75. doi: 10.1016/j.cell.2012.09.032. Epub 2012 Oct 18.

32. Elemento O, Rubin MA, Rickman DS. Oncogenic transcription factors as master regulators of chromatin topology: a new role for ERG in prostate cancer. Cell Cycle. 2012 Sep 15;11(18):3380-3. doi: 10.4161/cc.21401. Epub 2012 Aug 23.

31. Jiang Y, Soong TD, Wang L, Melnick AM, Elemento O. Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma. PLoS One. 2012;7(7):e40332. doi: 10.1371/journal.pone.0040332. Epub 2012 Jul 12.

30. 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. Oncogene-mediated alterations in chromatin conformation. Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9083-8. doi: 10.1073/pnas.1112570109. Epub 2012 May 21.

29. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell. 2012 Jun 22;149(7):1635-46. doi: 10.1016/j.cell.2012.05.003. Epub 2012 May 17.

28. Gollamudi S, Johri A, Calingasan NY, Yang L, Elemento O, Beal MF. Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease. PLoS One. 2012;7(5):e36191. doi: 10.1371/journal.pone.0036191. Epub 2012 May 1.

27. 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. 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. 2012 Apr 24;109(17):6686-91. doi: 10.1073/pnas.1117405109. Epub 2012 Apr 10.

26. Keutgen XM, Buitrago D, Filicori F, Kundel A, Elemento O, Fahey TJ 3rd, Zarnegar R. Calcimimetics versus parathyroidectomy for treatment of primary hyperparathyroidism: retrospective chart analysis of a prospective database. Ann Surg. 2012 May;255(5):981-5. doi: 10.1097/SLA.0b013e31824c5252.

25. Mason CE, Elemento O. Faster sequencers, larger datasets, new challenges. Genome Biol. 2012;13(3):314. doi: 10.1186/gb-2012-13-3-314.

24. 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. A panel of four miRNAs accurately differentiates malignant from benign indeterminate thyroid lesions on fine needle aspiration. Clin Cancer Res. 2012 Apr 1;18(7):2032-8. doi: 10.1158/1078-0432.CCR-11-2487. Epub 2012 Feb 20.

23. Wacker SA, Houghtaling BR, Elemento O, Kapoor TM. Using transcriptome sequencing to identify mechanisms of drug action and resistance. Nat Chem Biol. 2012 Feb 12;8(3):235-7. doi: 10.1038/nchembio.779.

22. 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. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 2011 Sep 29;118(13):3559-69. doi: 10.1182/blood-2011-06-357996. Epub 2011 Aug 9.

21. Giannopoulou EG, Elemento O. An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics. 2011 Jul 7;12:277. doi: 10.1186/1471-2105-12-277.

20. Lieber DS, Elemento O, Tavazoie S. Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One. 2010 Dec 29;5(12):e14444. doi: 10.1371/journal.pone.0014444.

19. Rajadhyaksha AM, Elemento O, Puffenberger EG, Schierberl KC, Xiang JZ, Putorti ML, Berciano J, Poulin C, Brais B, Michaelides M, Weleber RG, Higgins JJ. Mutations in FLVCR1 cause posterior column ataxia and retinitis pigmentosa. Am J Hum Genet. 2010 Nov 12;87(5):643-54. doi: 10.1016/j.ajhg.2010.10.013.

18. Campbell TL, De Silva EK, Olszewski KL, Elemento O, Llinas M. Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog. 2010 Oct 28;6(10):e1001165. doi: 10.1371/journal.ppat.1001165.

17. Velichutina I, Shaknovich R, Geng H, Johnson NA, Gascoyne RD, Melnick AM, Elemento O. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood. 2010 Dec 9;116(24):5247-55. doi: 10.1182/blood-2010-04-280149. Epub 2010 Aug 24.

16. Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood. 2010 Nov 18;116(20):e81-9. doi: 10.1182/blood-2010-05-285320. Epub 2010 Jul 7.

15. Goodarzi H, Elemento O, Tavazoie S. Revealing global regulatory perturbations across human cancers. Mol Cell. 2009 Dec 11;36(5):900-11. doi: 10.1016/j.molcel.2009.11.016.

14. da Piedade I, Tang MH, Elemento O. DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. BMC Bioinformatics. 2009 Nov 26;10:388. doi: 10.1186/1471-2105-10-388.

13. Lu X, Li JM, Elemento O, Tavazoie S, Wieschaus EF. Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition. Development. 2009 Jun;136(12):2101-10. doi: 10.1242/dev.034421.

12. Ci W, Polo JM, Cerchietti L, Shaknovich R, Wang L, Yang SN, Ye K, Farinha P, Horsman DE, Gascoyne RD, Elemento O, Melnick A. The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL. Blood. 2009 May 28;113(22):5536-48. doi: 10.1182/blood-2008-12-193037. Epub 2009 Mar 23.

11. Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA. 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. 2009 Mar 13;284(11):6605-9. doi: 10.1074/jbc.C900002200. Epub 2009 Jan 6.

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

9. Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell. 2007 Oct 26;28(2):337-50.

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

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

6. Slonim N, Elemento O, Tavazoie S. Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol. 2006;2:2006.0005. Epub 2006 Jan 31.

5. Chan CS, Elemento O, Tavazoie S. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol. 2005 Dec;1(7):e69. Epub 2005 Dec 9.

4. Elemento O, Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol. 2005;6(2):R18. Epub 2005 Jan 26.

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

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

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