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D
Rennert H
,
Eng K
,
Zhang T
,
Tan A
,
Xiang J
,
Romanel A
,
Kim R
,
Tam W
,
Liu Y-C
,
Bhinder B
et al.
. 2016.
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. 1
Erler P
,
Keutgen XM
,
Crowley MJ
,
Zetoune T
,
Kundel A
,
Kleiman D
,
Beninato T
,
Scognamiglio T
,
Elemento O
,
Zarnegar R
et al.
. 2014.
Dicer expression and microRNA dysregulation associate with aggressive features in thyroid cancer.
.
Surgery. 156(6):1342-50;discussion1350.
Cox N
,
Crozet L
,
Holtman IR
,
Loyher P-L
,
Lazarov T
,
White JB
,
Mass E
,
E Stanley R
,
Elemento O
,
Glass CK
et al.
. 2021.
Diet-regulated production of PDGFcc by macrophages controls energy storage.
.
Science. 373(6550)
Lourenco ARita
,
Ban Y
,
Crowley MJ
,
Lee SB
,
Ramchandani D
,
Du W
,
Elemento O
,
George JT
,
Jolly MKumar
,
Levine H
et al.
. 2020.
Differential Contributions of Pre- and Post-EMT Tumor Cells in Breast Cancer Metastasis.
.
Cancer Res. 80(2):163-169.
Prasain N
,
Lee MRyul
,
Vemula S
,
Meador JLuke
,
Yoshimoto M
,
Ferkowicz MJ
,
Fett A
,
Gupta M
,
Rapp BM
,
Saadatzadeh MReza
et al.
. 2014.
Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony-forming cells.
.
Nat Biotechnol. 32(11):1151-1157.
Allen JE
,
C Kline LB
,
Prabhu VV
,
Wagner J
,
Ishizawa J
,
Madhukar N
,
Lev A
,
Baumeister M
,
Zhou L
,
Lulla A
et al.
. 2016.
Discovery and clinical introduction of first-in-class imipridone ONC201.
.
Oncotarget. 7(45):74380-74392.
Pan H
,
Renaud L
,
Chaligne R
,
Bloehdorn J
,
Tausch E
,
Mertens D
,
Fink AMaria
,
Fischer K
,
Zhang C
,
Betel D
et al.
. 2021.
Discovery of candidate DNA methylation cancer driver genes.
.
Cancer Discov.
da Piedade I
,
Tang M-HEric
,
Elemento O
. 2009.
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices.
.
BMC Bioinformatics. 10:388.
Vazirani RP
,
Verma A
,
L Sadacca A
,
Buckman MS
,
Picatoste B
,
Beg M
,
Torsitano C
,
Bruno JH
,
Patel RT
,
Simonyte K
et al.
. 2016.
Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance.
.
Diabetes. 65(6):1577-89.
Beltran H
,
Prandi D
,
Mosquera JMiguel
,
Benelli M
,
Puca L
,
Cyrta J
,
Marotz C
,
Giannopoulou E
,
Chakravarthi BVSK
,
Varambally S
et al.
. 2016.
Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.
.
Nat Med. 22(3):298-305.
Dominguez PM
,
Teater M
,
Chambwe N
,
Kormaksson M
,
Redmond D
,
Ishii J
,
Vuong B
,
Chaudhuri J
,
Melnick A
,
Vasanthakumar A
et al.
. 2015.
DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID.
.
Cell Rep. 12(12):2086-98.
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.
Shaknovich R
,
Cerchietti L
,
Tsikitas L
,
Kormaksson M
,
De S
,
Figueroa ME
,
Ballon G
,
Yang SNing
,
Weinhold N
,
Reimers M
et al.
. 2011.
DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation.
.
Blood. 118(13):3559-69.
Thakur BKumar
,
Zhang H
,
Becker A
,
Matei I
,
Huang Y
,
Costa-Silva B
,
Zheng Y
,
Hoshino A
,
Brazier H
,
Xiang J
et al.
. 2014.
Double-stranded DNA in exosomes: a novel biomarker in cancer detection.
.
Cell Res. 24(6):766-9.
Sagardoy A
,
Martinez-Ferrandis JI
,
Roa S
,
Bunting KL
,
Aznar MAngela
,
Elemento O
,
Shaknovich R
,
Fontán L
,
Fresquet V
,
Perez-Roger I
et al.
. 2013.
Downregulation of FOXP1 is required during germinal center B-cell function.
.
Blood. 121(21):4311-20.
Zhu Y
,
Elemento O
,
Pathak J
,
Wang F
. 2019.
Drug knowledge bases and their applications in biomedical informatics research.
.
Brief Bioinform. 20(4):1308-1321.
Gayvert K
,
Elemento O
. 2019.
Drug-Induced Expression-Based Computational Repurposing of Small Molecules Affecting Transcription Factor Activity.
.
Methods Mol Biol. 1903:179-184.
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.
Grive KJ
,
Hu Y
,
Shu E
,
Grimson A
,
Elemento O
,
Grenier JK
,
Cohen PE
. 2019.
Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.
.
PLoS Genet. 15(3):e1007810.
E
Du W
,
Goldstein R
,
Jiang Y
,
Aly O
,
Cerchietti L
,
Melnick A
,
Elemento O
. 2017.
Effective Combination Therapies for B-cell Lymphoma Predicted by a Virtual Disease Model.
.
Cancer Res. 77(8):1818-1830.
Elemento O
,
Gascuel O
. 2002.
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
.
Bioinformatics. 18 Suppl 2:S92-9.
Ginsberg M
,
James D
,
Ding B-S
,
Nolan D
,
Geng F
,
Butler JM
,
Schachterle W
,
Pulijaal VR
,
Mathew S
,
Chasen ST
et al.
. 2012.
Efficient direct reprogramming of mature amniotic cells into endothelial cells by ETS factors and TGFβ suppression.
.
Cell. 151(3):559-75.
Lu Y-C
,
Chang S-H
,
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.
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.
Poulos MG
,
Ramalingam P
,
Gutkin MC
,
Kleppe M
,
Ginsberg M
,
Crowley MJP
,
Elemento O
,
Levine RL
,
Rafii S
,
Kitajewski J
et al.
. 2016.
Endothelial-specific inhibition of NF-κB enhances functional haematopoiesis.
.
Nat Commun. 7:13829.
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