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B
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.
C
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.
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