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O
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.
Rickman DS
,
T Soong D
,
Moss B
,
Mosquera JMiguel
,
Dlabal J
,
Terry S
,
MacDonald TY
,
Tripodi J
,
Bunting K
,
Najfeld V
et al.
. 2012.
Oncogene-mediated alterations in chromatin conformation.
.
Proc Natl Acad Sci U S A. 109(23):9083-8.
Karass M
,
Bareja R
,
Shelkey E
,
Vlachostergios PJ
,
Robinson BD
,
Khani F
,
Mosquera JMiguel
,
Scherr DS
,
Sboner A
,
Tagawa ST
et al.
. 2019.
Oncogenic Addiction to ERBB2 Signaling Predicts Response to Trastuzumab in Urothelial Cancer.
.
J Natl Compr Canc Netw. 17(3):194-200.
Anelli V
,
Villefranc JA
,
Chhangawala S
,
Martinez-McFaline R
,
Riva E
,
Nguyen A
,
Verma A
,
Bareja R
,
Chen Z
,
Scognamiglio T
et al.
. 2017.
Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression.
.
Elife. 6
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.
Sivakumar R
,
Chan M
,
Shin JStella
,
Nishida-Aoki N
,
Kenerson HL
,
Elemento O
,
Beltran H
,
Yeung R
,
Gujral TS
. 2019.
Organotypic tumor slice cultures provide a versatile platform for immuno-oncology and drug discovery.
.
Oncoimmunology. 8(12):e1670019.
P
Keutgen XM
,
Filicori F
,
Crowley MJ
,
Wang Y
,
Scognamiglio T
,
Hoda R
,
Buitrago D
,
Cooper D
,
Zeiger MA
,
Zarnegar R
et al.
. 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.
Puca L
,
Bareja R
,
Prandi D
,
Shaw R
,
Benelli M
,
Karthaus WR
,
Hess J
,
Sigouros M
,
Donoghue A
,
Kossai M
et al.
. 2018.
Patient derived organoids to model rare prostate cancer phenotypes.
.
Nat Commun. 9(1):2404.
Park K
,
Tran H
,
Eng KW
,
Ramazanoglu S
,
Rolon RMMarrero
,
Scognamiglio T
,
Borczuk A
,
Mosquera JMiguel
,
Pan Q
,
Sboner A
et al.
. 2020.
Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome.
.
Arch Pathol Lab Med.
Pauli C
,
Hopkins BD
,
Prandi D
,
Shaw R
,
Fedrizzi T
,
Sboner A
,
Sailer V
,
Augello M
,
Puca L
,
Rosati R
et al.
. 2017.
Personalized and Cancer Models to Guide Precision Medicine.
.
Cancer Discov. 7(5):462-477.
Lundquist MR
,
Goncalves MD
,
Loughran RM
,
Possik E
,
Vijayaraghavan T
,
Yang A
,
Pauli C
,
Ravi A
,
Verma A
,
Yang Z
et al.
. 2018.
Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy.
.
Mol Cell. 70(3):531-544.e9.
Carty MA
,
Elemento O
. 2016.
Practical Analysis of Genome Contact Interaction Experiments.
.
Methods Mol Biol. 1418:177-89.
Hajirasouliha I
,
Elemento O
. 2020.
Precision medicine and artificial intelligence: overview and relevance to reproductive medicine.
.
Fertil Steril. 114(5):908-913.
Lue JK
,
Prabhu SA
,
Liu Y
,
Gonzalez Y
,
Verma A
,
Mundi PS
,
Abshiru N
,
Camarillo JM
,
Mehta S
,
Chen EI
et al.
. 2019.
Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas.
.
Clin Cancer Res. 25(17):5271-5283.
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.
Madhukar NS
,
Elemento O
,
Pandey G
. 2015.
Prediction of Genetic Interactions Using Machine Learning and Network Properties.
.
Front Bioeng Biotechnol. 3:172.
Nwachukwu JC
,
Srinivasan S
,
Zheng Y
,
Wang S
,
Min J
,
Dong C
,
Liao Z
,
Nowak J
,
Wright NJ
,
Houtman R
et al.
. 2016.
Predictive features of ligand-specific signaling through the estrogen receptor.
.
Mol Syst Biol. 12(4):864.
Liberti MV
,
Dai Z
,
Wardell SE
,
Baccile JA
,
Liu X
,
Gao X
,
Baldi R
,
Mehrmohamadi M
,
Johnson MO
,
Madhukar NS
et al.
. 2017.
A Predictive Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural Product.
.
Cell Metab. 26(4):648-659.e8.
Curchoe CLynn
,
Malmsten J
,
Bormann C
,
Shafiee H
,
Farias AFlores-Sai
,
Mendizabal G
,
Chavez-Badiola A
,
Sigaras A
,
Alshubbar H
,
Chambost J
et al.
. 2020.
Predictive modeling in reproductive medicine: Where will the future of artificial intelligence research take us?
Fertil Steril. 114(5):934-940.
Sboner A
,
Elemento O
. 2016.
A primer on precision medicine informatics.
.
Brief Bioinform. 17(1):145-53.
Rendeiro AF
,
Casano J
,
Vorkas CKyriakos
,
Singh H
,
Morales A
,
DeSimone RA
,
Ellsworth GB
,
Soave R
,
Kapadia SN
,
Saito K
et al.
. 2021.
Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression.
.
Life Sci Alliance. 4(2)
Subbaramaiah K
,
Iyengar NM
,
Morrow M
,
Elemento O
,
Zhou XKathy
,
Dannenberg AJ
. 2019.
Prostaglandin E down-regulates sirtuin 1 (SIRT1), leading to elevated levels of aromatase, providing insights into the obesity-breast cancer connection.
.
J Biol Chem. 294(1):361-371.
Crowley MJP
,
Scognamiglio T
,
Liu Y-F
,
Kleiman DA
,
Beninato T
,
Aronova A
,
Liu H
,
Jhanwar YS
,
Molina A
,
Tagawa ST
et al.
. 2016.
Prostate-Specific Membrane Antigen Is a Potential Antiangiogenic Target in Adrenocortical Carcinoma.
.
J Clin Endocrinol Metab. 101(3):981-7.
Segal E
,
Zhang F
,
Lin X
,
King G
,
Shalem O
,
Shilo S
,
Allen WE
,
Alquaddoomi F
,
Altae-Tran H
,
Anders S
et al.
. 2020.
Publisher Correction: Building an international consortium for tracking coronavirus health status.
.
Nat Med. 26(8):1309.
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.
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