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Items: 1 to 50 of 245

1.

CIC is a critical regulator of neuronal differentiation.

Hwang I, Pan H, Yao J, Elemento O, Zheng H, Paik J.

JCI Insight. 2020 Mar 31. pii: 135826. doi: 10.1172/jci.insight.135826. [Epub ahead of print]

2.

Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid.

Lehmann GL, Hanke-Gogokhia C, Hu Y, Bareja R, Salfati Z, Ginsberg M, Nolan DJ, Mendez-Huergo SP, Dalotto-Moreno T, Wojcinski A, Ochoa F, Zeng S, Cerliani JP, Panagis L, Zager PJ, Mullins RF, Ogura S, Lutty GA, Bang J, Zippin JH, Romano C, Rabinovich GA, Elemento O, Joyner AL, Rafii S, Rodriguez-Boulan E, Benedicto I.

J Exp Med. 2020 Jun 1;217(6). pii: e20190730. doi: 10.1084/jem.20190730.

PMID:
32196081
3.

Computational methods in tumor immunology.

Bhinder B, Elemento O.

Methods Enzymol. 2020;636:209-259. doi: 10.1016/bs.mie.2020.01.001. Epub 2020 Jan 25.

PMID:
32178820
4.

Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration.

De Micheli AJ, Laurilliard EJ, Heinke CL, Ravichandran H, Fraczek P, Soueid-Baumgarten S, De Vlaminck I, Elemento O, Cosgrove BD.

Cell Rep. 2020 Mar 10;30(10):3583-3595.e5. doi: 10.1016/j.celrep.2020.02.067.

5.

Epigenetic reprogramming sensitizes immunologically silent EBV+ lymphomas to viral directed immunotherapy.

Dalton T, Doubrovina E, Pankov D, Reynolds RC, Scholze H, Selvakumar A, Vizconde T, Savalia B, Dyomin V, Weigel C, Oakes CC, Alonso A, Elemento O, Pan H, Phillip JM, O'Reilly RJ, Gewurz BE, Cesarman E, Giulino-Roth L.

Blood. 2020 Mar 10. pii: blood.2019004126. doi: 10.1182/blood.2019004126. [Epub ahead of print]

PMID:
32157281
6.

SLFN11 expression in advanced prostate cancer and response to platinum-based chemotherapy.

Conteduca V, Ku SY, Puca L, Slade M, Fernandez L, Hess J, Bareja R, Vlachostergios PJ, Sigouros M, Mosquera JM, Sboner A, Nanus DM, Elemento O, Dittamore R, Tagawa ST, Beltran H.

Mol Cancer Ther. 2020 Mar 3. pii: molcanther.0926.2019. doi: 10.1158/1535-7163.MCT-19-0926. [Epub ahead of print]

PMID:
32127465
7.

The novel lncRNA BlackMamba controls the neoplastic phenotype of ALK- anaplastic large cell lymphoma by regulating the DNA helicase HELLS.

Fragliasso V, Verma A, Manzotti G, Tameni A, Bareja R, Heavican TB, Iqbal J, Wang R, Fiore D, Mularoni V, Chan WC, Lhoumaud P, Skok J, Zanetti E, Merli F, Ciarrocchi A, Elemento O, Inghirami G.

Leukemia. 2020 Mar 2. doi: 10.1038/s41375-020-0754-8. [Epub ahead of print]

PMID:
32123306
8.

Urinary cell transcriptomics and acute rejection in human kidney allografts.

Verma A, Muthukumar T, Yang H, Lubetzky M, Cassidy MF, Lee JR, Dadhania DM, Snopkowski C, Shankaranarayanan D, Salvatore SP, Sharma VK, Xiang JZ, De Vlaminck I, Seshan SV, Mueller FB, Suhre K, Elemento O, Suthanthiran M.

JCI Insight. 2020 Feb 27;5(4). pii: 131552. doi: 10.1172/jci.insight.131552.

9.

The aging skin microenvironment dictates stem cell behavior.

Ge Y, Miao Y, Gur-Cohen S, Gomez N, Yang H, Nikolova M, Polak L, Hu Y, Verma A, Elemento O, Krueger JG, Fuchs E.

Proc Natl Acad Sci U S A. 2020 Mar 10;117(10):5339-5350. doi: 10.1073/pnas.1901720117. Epub 2020 Feb 24.

PMID:
32094197
10.

Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer.

Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F.

J Clin Invest. 2020 Apr 1;130(4):1653-1668. doi: 10.1172/JCI131041.

11.

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.

Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W.

Arch Pathol Lab Med. 2020 Feb 11. doi: 10.5858/arpa.2019-0162-OA. [Epub ahead of print]

PMID:
32045275
12.

Inhibition of EZH2 Catalytic Activity Selectively Targets a Metastatic Subpopulation in Triple-Negative Breast Cancer.

Yomtoubian S, Lee SB, Verma A, Izzo F, Markowitz G, Choi H, Cerchietti L, Vahdat L, Brown KA, Andreopoulou E, Elemento O, Chang J, Inghirami G, Gao D, Ryu S, Mittal V.

Cell Rep. 2020 Jan 21;30(3):755-770.e6. doi: 10.1016/j.celrep.2019.12.056.

13.

ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA.

Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A.

Bioinformatics. 2020 Jan 10. pii: btaa016. doi: 10.1093/bioinformatics/btaa016. [Epub ahead of print]

PMID:
31922552
14.

Stable reduction of STARD4 alters cholesterol regulation and lipid homeostasis.

Iaea DB, Spahr ZR, Singh RK, Chan RB, Zhou B, Bareja R, Elemento O, Di Paolo G, Zhang X, Maxfield FR.

Biochim Biophys Acta Mol Cell Biol Lipids. 2020 Apr;1865(4):158609. doi: 10.1016/j.bbalip.2020.158609. Epub 2020 Jan 7.

PMID:
31917335
15.

A Bayesian machine learning approach for drug target identification using diverse data types.

Madhukar NS, Khade PK, Huang L, Gayvert K, Galletti G, Stogniew M, Allen JE, Giannakakou P, Elemento O.

Nat Commun. 2019 Nov 19;10(1):5221. doi: 10.1038/s41467-019-12928-6.

16.

Organotypic tumor slice cultures provide a versatile platform for immuno-oncology and drug discovery.

Sivakumar R, Chan M, Shin JS, Nishida-Aoki N, Kenerson HL, Elemento O, Beltran H, Yeung R, Gujral TS.

Oncoimmunology. 2019 Oct 10;8(12):e1670019. doi: 10.1080/2162402X.2019.1670019. eCollection 2019.

17.

Differential Contributions of Pre- and Post-EMT Tumor Cells in Breast Cancer Metastasis.

Lourenco AR, Ban Y, Crowley MJ, Lee SB, Ramchandani D, Du W, Elemento O, George JT, Jolly MK, Levine H, Sheng J, Wong ST, Altorki NK, Gao D.

Cancer Res. 2020 Jan 15;80(2):163-169. doi: 10.1158/0008-5472.CAN-19-1427. Epub 2019 Nov 8.

18.

Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer.

Sailer V, Eng KW, Zhang T, Bareja R, Pisapia DJ, Sigaras A, Bhinder B, Romanel A, Wilkes D, Sticca E, Cyrta J, Rao R, Sahota S, Pauli C, Beg S, Motanagh S, Kossai M, Fontunge J, Puca L, Rennert H, Zhaoying Xiang J, Greco N, Kim R, MacDonald TY, McNary T, Blattner-Johnson M, Schiffman MH, Faltas BM, Greenfield JP, Rickman D, Andreopoulou E, Holcomb K, Vahdat LT, Scherr DS, van Besien K, Barbieri CE, Robinson BD, Fine HA, Ocean AJ, Molina A, Shah MA, Nanus DM, Pan Q, Demichelis F, Tagawa ST, Song W, Mosquera JM, Sboner A, Rubin MA, Elemento O, Beltran H.

JCO Precis Oncol. 2019;3. doi: 10.1200/PO.19.00047. Epub 2019 Sep 20.

19.

Deep learning-based classification of mesothelioma improves prediction of patient outcome.

Courtiol P, Maussion C, Moarii M, Pronier E, Pilcer S, Sefta M, Manceron P, Toldo S, Zaslavskiy M, Le Stang N, Girard N, Elemento O, Nicholson AG, Blay JY, Galateau-Sallé F, Wainrib G, Clozel T.

Nat Med. 2019 Oct;25(10):1519-1525. doi: 10.1038/s41591-019-0583-3. Epub 2019 Oct 7.

PMID:
31591589
20.

Clinical features of neuroendocrine prostate cancer.

Conteduca V, Oromendia C, Eng KW, Bareja R, Sigouros M, Molina A, Faltas BM, Sboner A, Mosquera JM, Elemento O, Nanus DM, Tagawa ST, Ballman KV, Beltran H.

Eur J Cancer. 2019 Nov;121:7-18. doi: 10.1016/j.ejca.2019.08.011. Epub 2019 Sep 13.

21.

Cancer-Specific Thresholds Adjust for Whole Exome Sequencing-based Tumor Mutational Burden Distribution.

Fernandez EM, Eng K, Beg S, Beltran H, Faltas BM, Mosquera JM, Nanus DM, Pisapia DJ, Rao RA, Robinson BD, Rubin MA, Elemento O, Sboner A, Shah MA, Song W.

JCO Precis Oncol. 2019;3. doi: 10.1200/PO.18.00400. Epub 2019 Jul 31.

22.

Exploring tumor clonal evolution in bone marrow of patients with diffuse large B-cell lymphoma by deep IGH sequencing and its potential relevance in relapse.

Ma J, Redmond D, Miyaguchi A, Nam AS, Nie K, Mathew S, Elemento O, Tam W.

Blood Cancer J. 2019 Aug 21;9(9):69. doi: 10.1038/s41408-019-0229-1. No abstract available.

23.

Obesity-Associated Extracellular Matrix Remodeling Promotes a Macrophage Phenotype Similar to Tumor-Associated Macrophages.

Springer NL, Iyengar NM, Bareja R, Verma A, Jochelson MS, Giri DD, Zhou XK, Elemento O, Dannenberg AJ, Fischbach C.

Am J Pathol. 2019 Oct;189(10):2019-2035. doi: 10.1016/j.ajpath.2019.06.005. Epub 2019 Jul 16.

PMID:
31323189
24.

Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization.

Khosravi P, Kazemi E, Zhan Q, Malmsten JE, Toschi M, Zisimopoulos P, Sigaras A, Lavery S, Cooper LAD, Hickman C, Meseguer M, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I.

NPJ Digit Med. 2019 Apr 4;2:21. doi: 10.1038/s41746-019-0096-y. eCollection 2019.

25.

Landscape of innate immune system transcriptome and acute T cell-mediated rejection of human kidney allografts.

Mueller FB, Yang H, Lubetzky M, Verma A, Lee JR, Dadhania DM, Xiang JZ, Salvatore SP, Seshan SV, Sharma VK, Elemento O, Suthanthiran M, Muthukumar T.

JCI Insight. 2019 Jul 11;4(13). pii: 128014. doi: 10.1172/jci.insight.128014. eCollection 2019 Jul 11.

26.

Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling.

Robinson BD, Vlachostergios PJ, Bhinder B, Liu W, Li K, Moss TJ, Bareja R, Park K, Tavassoli P, Cyrta J, Tagawa ST, Nanus DM, Beltran H, Molina AM, Khani F, Miguel Mosquera J, Xylinas E, Shariat SF, Scherr DS, Rubin MA, Lerner SP, Matin SF, Elemento O, Faltas BM.

Nat Commun. 2019 Jul 5;10(1):2977. doi: 10.1038/s41467-019-10873-y.

27.

The Missing Pieces of Artificial Intelligence in Medicine.

Gilvary C, Madhukar N, Elkhader J, Elemento O.

Trends Pharmacol Sci. 2019 Aug;40(8):555-564. doi: 10.1016/j.tips.2019.06.001. Epub 2019 Jul 2. Review.

PMID:
31277839
28.

Artificial intelligence: its applications in reproductive medicine and the assisted reproductive technologies.

Zaninovic N, Elemento O, Rosenwaks Z.

Fertil Steril. 2019 Jul;112(1):28-30. doi: 10.1016/j.fertnstert.2019.05.019. No abstract available.

PMID:
31277764
29.

N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer.

Berger A, Brady NJ, Bareja R, Robinson B, Conteduca V, Augello MA, Puca L, Ahmed A, Dardenne E, Lu X, Hwang I, Bagadion AM, Sboner A, Elemento O, Paik J, Yu J, Barbieri CE, Dephoure N, Beltran H, Rickman DS.

J Clin Invest. 2019 Jul 1;130:3924-3940. doi: 10.1172/JCI127961.

30.

Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system.

Lhuillier C, Rudqvist NP, Elemento O, Formenti SC, Demaria S.

Genome Med. 2019 Jun 20;11(1):40. doi: 10.1186/s13073-019-0653-7. Review.

31.

Graph convolutional networks for computational drug development and discovery.

Sun M, Zhao S, Gilvary C, Elemento O, Zhou J, Wang F.

Brief Bioinform. 2019 Jun 3. pii: bbz042. doi: 10.1093/bib/bbz042. [Epub ahead of print]

PMID:
31155636
32.

Imipridone ONC212 activates orphan G protein-coupled receptor GPR132 and integrated stress response in acute myeloid leukemia.

Nii T, Prabhu VV, Ruvolo V, Madhukar N, Zhao R, Mu H, Heese L, Nishida Y, Kojima K, Garnett MJ, McDermott U, Benes CH, Charter N, Deacon S, Elemento O, Allen JE, Oster W, Stogniew M, Ishizawa J, Andreeff M.

Leukemia. 2019 Dec;33(12):2805-2816. doi: 10.1038/s41375-019-0491-z. Epub 2019 May 24.

33.

CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE.

Cancer Cell. 2019 May 13;35(5):817-819. doi: 10.1016/j.ccell.2019.04.012. No abstract available.

PMID:
31085180
34.

Function and clinical relevance of RHAMM isoforms in pancreatic tumor progression.

Choi S, Wang D, Chen X, Tang LH, Verma A, Chen Z, Kim BJ, Selesner L, Robzyk K, Zhang G, Pang S, Han T, Chan CS, Fahey TJ 3rd, Elemento O, Du YN.

Mol Cancer. 2019 May 9;18(1):92. doi: 10.1186/s12943-019-1018-y.

35.

Supplemental estrogen and caloric restriction reduce obesity-induced periprostatic white adipose inflammation in mice.

Bhardwaj P, Ikeda T, Zhou XK, Wang H, Zheng XE, Giri DD, Elemento O, Verma A, Miyazawa M, Mukherjee S, Falcone DJ, Wendel NK, Scherr DS, Dannenberg AJ.

Carcinogenesis. 2019 Jul 20;40(7):914-923. doi: 10.1093/carcin/bgz088.

PMID:
31067318
36.

A Recurrent Activating Missense Mutation in Waldenström Macroglobulinemia Affects the DNA Binding of the ETS Transcription Factor SPI1 and Enhances Proliferation.

Roos-Weil D, Decaudin C, Armand M, Della-Valle V, Diop MK, Ghamlouch H, Ropars V, Hérate C, Lara D, Durot E, Haddad R, Mylonas E, Damm F, Pflumio F, Stoilova B, Metzner M, Elemento O, Dessen P, Camara-Clayette V, Cosset FL, Verhoeyen E, Leblond V, Ribrag V, Cornillet-Lefebvre P, Rameau P, Azar N, Charlotte F, Morel P, Charbonnier JB, Vyas P, Mercher T, Aoufouchi S, Droin N, Guillouf C, Nguyen-Khac F, Bernard OA.

Cancer Discov. 2019 Jun;9(6):796-811. doi: 10.1158/2159-8290.CD-18-0873. Epub 2019 Apr 24.

PMID:
31018969
37.

Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas.

Lue JK, Prabhu SA, Liu Y, Gonzalez Y, Verma A, Mundi PS, Abshiru N, Camarillo JM, Mehta S, Chen EI, Qiao C, Nandakumar R, Cremers S, Kelleher NL, Elemento O, Amengual JE.

Clin Cancer Res. 2019 Sep 1;25(17):5271-5283. doi: 10.1158/1078-0432.CCR-18-3989. Epub 2019 Apr 12.

PMID:
30979734
38.

CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis.

Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE.

Cancer Cell. 2019 Apr 15;35(4):603-617.e8. doi: 10.1016/j.ccell.2019.03.001. Epub 2019 Mar 28. Erratum in: Cancer Cell. 2019 May 13;35(5):817-819.

PMID:
30930119
39.

Identification of a therapeutic target using molecular sequencing for treatment of recurrent uterine serous adenocarcinoma.

Musselman K, Glynn S, Mosquera JM, Elemento O, Sboner A, Beltran H, Holcomb K.

Gynecol Oncol Rep. 2019 Feb 21;28:54-57. doi: 10.1016/j.gore.2019.01.013. eCollection 2019 May.

40.

Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer.

Puca L, Gavyert K, Sailer V, Conteduca V, Dardenne E, Sigouros M, Isse K, Kearney M, Vosoughi A, Fernandez L, Pan H, Motanagh S, Hess J, Donoghue AJ, Sboner A, Wang Y, Dittamore R, Rickman D, Nanus DM, Tagawa ST, Elemento O, Mosquera JM, Saunders L, Beltran H.

Sci Transl Med. 2019 Mar 20;11(484). pii: eaav0891. doi: 10.1126/scitranslmed.aav0891.

41.

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing.

Grive KJ, Hu Y, Shu E, Grimson A, Elemento O, Grenier JK, Cohen PE.

PLoS Genet. 2019 Mar 20;15(3):e1007810. doi: 10.1371/journal.pgen.1007810. eCollection 2019 Mar.

42.

Oncogenic Addiction to ERBB2 Signaling Predicts Response to Trastuzumab in Urothelial Cancer.

Karass M, Bareja R, Shelkey E, Vlachostergios PJ, Robinson BD, Khani F, Mosquera JM, Scherr DS, Sboner A, Tagawa ST, Molina AM, Elemento O, Nanus DM, Faltas BM.

J Natl Compr Canc Netw. 2019 Mar 1;17(3):194-200. doi: 10.6004/jnccn.2018.7264.

PMID:
30865916
43.

Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance.

Vikova V, Jourdan M, Robert N, Requirand G, Boireau S, Bruyer A, Vincent L, Cartron G, Klein B, Elemento O, Kassambara A, Moreaux J.

Theranostics. 2019 Jan 1;9(2):540-553. doi: 10.7150/thno.28374. eCollection 2019.

44.

Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response.

Agirre X, Meydan C, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O, Mason CE, Prosper F, Melnick A.

Nat Commun. 2019 Feb 18;10(1):821. doi: 10.1038/s41467-019-08679-z.

45.

Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells.

Chen HJ, Poran A, Unni AM, Huang SX, Elemento O, Snoeck HW, Varmus H.

J Exp Med. 2019 Mar 4;216(3):674-687. doi: 10.1084/jem.20181155. Epub 2019 Feb 8.

46.

The application of precision medicine in diagnosing familial Mediterranean fever.

Glynn S, Lipkin S, Zhang T, Sboner A, Elemento O, Van Besien K, Beltran H.

Leuk Lymphoma. 2019 Aug;60(8):2091-2093. doi: 10.1080/10428194.2019.1571204. Epub 2019 Jan 30. No abstract available.

PMID:
30698071
47.

The Transcriptional Regulator Sin3A Contributes to the Oncogenic Potential of STAT3.

Gambi G, Di Simone E, Basso V, Ricci L, Wang R, Verma A, Elemento O, Ponzoni M, Inghirami G, Icardi L, Mondino A.

Cancer Res. 2019 Jun 15;79(12):3076-3087. doi: 10.1158/0008-5472.CAN-18-0359. Epub 2019 Jan 28.

PMID:
30692217
48.

UCHL1 loss alters the cell-cycle in metastatic pancreatic neuroendocrine tumors.

Finnerty BM, Moore MD, Verma A, Aronova A, Huang S, Edwards DP, Chen Z, Seandel M, Scognamiglio T, Du YN, Elemento O, Zarnegar R, Min IM, Fahey TJ.

Endocr Relat Cancer. 2019 Apr 1;26(4):411-423. doi: 10.1530/ERC-18-0507. Epub 2019 Jan 1.

PMID:
30689542
49.

TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis.

Lan Y, Pan H, Li C, Banks KM, Sam J, Ding B, Elemento O, Goll MG, Evans T.

Cell Rep. 2019 Jan 15;26(3):720-732.e4. doi: 10.1016/j.celrep.2018.12.076.

50.

Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome.

Boehm KM, Bhinder B, Raja VJ, Dephoure N, Elemento O.

BMC Bioinformatics. 2019 Jan 5;20(1):7. doi: 10.1186/s12859-018-2561-z.

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