Publications

Bhinder B, Elemento O.  2017.  Towards a better cancer precision medicine: systems biology meets immunotherapy.. Curr Opin Syst Biol. 2:67-73.

Bhinder B, Elemento O.  2020.  Computational methods in tumor immunology.. Methods Enzymol. 636:209-259.

Bhinder B, Gilvary C, Madhukar NS, Elemento O.  2021.  Artificial Intelligence in Cancer Research and Precision Medicine.. Cancer Discov. 11(4):900-915.

Bödör C, Grossmann V, Popov N, Okosun J, O'Riain C, Tan K, Marzec J, Araf S, Wang J, Lee AM et al..  2013.  EZH2 mutations are frequent and represent an early event in follicular lymphoma.. Blood. 122(18):3165-8.

Boehm KMichael, Bhinder B, Raja VJoseph, Dephoure N, Elemento O.  2019.  Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome.. BMC Bioinformatics. 20(1):7.

Boi M, Todaro M, Vurchio V, Yang SNing, Moon J, Kwee I, Rinaldi A, Pan H, Crescenzo R, Cheng M et al..  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.

Brady NJ, Bagadion AM, Singh R, Conteduca V, Van Emmenis L, Arceci E, Pakula H, Carelli R, Khani F, Bakht M et al..  2021.  Temporal evolution of cellular heterogeneity during the progression to advanced AR-negative prostate cancer.. Nat Commun. 12(1):3372.

Bruno NE, Nwachukwu JC, Srinivasan S, Nettles CC, Izard T, Jin Z, Nowak J, Cameron MD, Boregowda SV, Phinney DG et al..  2021.  Chemical systems biology reveals mechanisms of glucocorticoid receptor signaling.. Nat Chem Biol. 17(3):307-316.

Bunting KL, T Soong D, Singh R, Jiang Y, Béguelin W, Poloway DW, Swed BL, Hatzi K, Reisacher W, Teater M et al..  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.

Buqué A, Bloy N, Perez-Lanzón M, Iribarren K, Humeau J, Pol JG, Levesque S, Mondragon L, Yamazaki T, Sato A et al..  2020.  Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer.. Nat Commun. 11(1):3819.

Buqué A, Bloy N, Perez-Lanzón M, Iribarren K, Humeau J, Pol JG, Levesque S, Mondragon L, Yamazaki T, Sato A et al..  2020.  Publisher Correction: Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer.. Nat Commun. 11(1):4787.

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.

Cárdenas MG, Yu W, Béguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang S-N, Cohen J et al..  2016.  Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.. J Clin Invest. 126(9):3351-62.

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TChedraoui, Wong CK, Choi HYoung, Felau I, A Robertson G et al..  2021.  Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.. Cell Rep. 34(8):108784.

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TChedraoui, Wong CK, Choi HYoung, Felau I, A Robertson G et al..  2021.  Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.. Cell Rep. 34(5):108707.

Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS.  2017.  An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data.. Nat Commun. 8:15454.

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

Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A.  2020.  ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA.. Bioinformatics. 36(9):2665-2674.

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.

Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JMiguel, Pauwels J, Park K, Kossai M et al..  2014.  The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer.. Nat Commun. 5:5383.

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

Chang C-Y, H Pasolli A, 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.

Chang S-H, Lu Y-C, Li X, Hsieh W-Y, 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.

Chang S-H, 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.

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