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Items: 23

1.

Using the Seven Bridges Cancer Genomics Cloud to Access and Analyze Petabytes of Cancer Data.

Malhotra R, Seth I, Lehnert E, Zhao J, Kaushik G, Williams EH, Sethi A, Davis-Dusenbery BN.

Curr Protoc Bioinformatics. 2017 Dec 8;60:11.16.1-11.16.32. doi: 10.1002/cpbi.39.

PMID:
29220078
2.

The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.

Lau JW, Lehnert E, Sethi A, Malhotra R, Kaushik G, Onder Z, Groves-Kirkby N, Mihajlovic A, DiGiovanna J, Srdic M, Bajcic D, Radenkovic J, Mladenovic V, Krstanovic D, Arsenijevic V, Klisic D, Mitrovic M, Bogicevic I, Kural D, Davis-Dusenbery B; Seven Bridges CGC Team.

Cancer Res. 2017 Nov 1;77(21):e3-e6. doi: 10.1158/0008-5472.CAN-17-0387.

PMID:
29092927
3.

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium.

Grossman RL, Abel B, Angiuoli S, Barrett JC, Bassett D, Bramlett K, Blumenthal GM, Carlsson A, Cortese R, DiGiovanna J, Davis-Dusenbery B, Dittamore R, Eberhard DA, Febbo P, Fitzsimons M, Flamig Z, Godsey J, Goswami J, Gruen A, Ortuño F, Han J, Hayes D, Hicks J, Holloway D, Hovelson D, Johnson J, Juhl H, Kalamegham R, Kamal R, Kang Q, Kelloff GJ, Klozenbuecher M, Kolatkar A, Kuhn P, Langone K, Leary R, Loverso P, Manmathan H, Martin AM, Martini J, Miller D, Mitchell M, Morgan T, Mulpuri R, Nguyen T, Otto G, Pathak A, Peters E, Philip R, Posadas E, Reese D, Reese MG, Robinson D, Dei Rossi A, Sakul H, Schageman J, Singh S, Scher HI, Schmitt K, Silvestro A, Simmons J, Simmons T, Sislow J, Talasaz A, Tang P, Tewari M, Tomlins S, Toukhy H, Tseng HR, Tuck M, Tzou A, Vinson J, Wang Y, Wells W, Welsh A, Wilbanks J, Wolf J, Young L, Lee J, Leiman LC.

Clin Pharmacol Ther. 2017 May;101(5):589-592. doi: 10.1002/cpt.666. Epub 2017 Apr 12. Review.

4.

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

Kaushik G, Ivkovic S, Simonovic J, Tijanic N, Davis-Dusenbery B, Kural D.

Pac Symp Biocomput. 2017;22:154-165. doi: 10.1142/9789813207813_0016.

5.

Reproducible, Scalable Fusion Gene Detection from RNA-Seq.

Arsenijevic V, Davis-Dusenbery BN.

Methods Mol Biol. 2016;1381:223-37. doi: 10.1007/978-1-4939-3204-7_13.

PMID:
26667464
6.

Genetic validation of a therapeutic target in a mouse model of ALS.

de Boer AS, Koszka K, Kiskinis E, Suzuki N, Davis-Dusenbery BN, Eggan K.

Sci Transl Med. 2014 Aug 6;6(248):248ra104. doi: 10.1126/scitranslmed.3009351.

7.

Ketamine exposure in early development impairs specification of the primary germ cell layers.

Akeju O, Davis-Dusenbery BN, Cassel SH, Ichida JK, Eggan K.

Neurotoxicol Teratol. 2014 May-Jun;43:59-68. doi: 10.1016/j.ntt.2014.04.001. Epub 2014 Apr 16.

8.

Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1.

Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K.

Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3.

9.

Nanog-independent reprogramming to iPSCs with canonical factors.

Carter AC, Davis-Dusenbery BN, Koszka K, Ichida JK, Eggan K.

Stem Cell Reports. 2014 Jan 31;2(2):119-26. doi: 10.1016/j.stemcr.2013.12.010. eCollection 2014 Feb 11.

10.

How to make spinal motor neurons.

Davis-Dusenbery BN, Williams LA, Klim JR, Eggan K.

Development. 2014 Feb;141(3):491-501. doi: 10.1242/dev.097410. Review.

11.

Acetylation of p53 stimulates miRNA processing and determines cell survival following genotoxic stress.

Chang J, Davis-Dusenbery BN, Kashima R, Jiang X, Marathe N, Sessa R, Louie J, Gu W, Lagna G, Hata A.

EMBO J. 2013 Dec 11;32(24):3192-205. doi: 10.1038/emboj.2013.242. Epub 2013 Nov 12.

12.

The mouse C9ORF72 ortholog is enriched in neurons known to degenerate in ALS and FTD.

Suzuki N, Maroof AM, Merkle FT, Koszka K, Intoh A, Armstrong I, Moccia R, Davis-Dusenbery BN, Eggan K.

Nat Neurosci. 2013 Dec;16(12):1725-7. doi: 10.1038/nn.3566. Epub 2013 Nov 3.

13.

Atrial natriuretic peptide is negatively regulated by microRNA-425.

Arora P, Wu C, Khan AM, Bloch DB, Davis-Dusenbery BN, Ghorbani A, Spagnolli E, Martinez A, Ryan A, Tainsh LT, Kim S, Rong J, Huan T, Freedman JE, Levy D, Miller KK, Hata A, Del Monte F, Vandenwijngaert S, Swinnen M, Janssens S, Holmes TM, Buys ES, Bloch KD, Newton-Cheh C, Wang TJ.

J Clin Invest. 2013 Aug;123(8):3378-82. doi: 10.1172/JCI67383. Epub 2013 Jul 15.

14.

Inhibition of microRNA-302 (miR-302) by bone morphogenetic protein 4 (BMP4) facilitates the BMP signaling pathway.

Kang H, Louie J, Weisman A, Sheu-Gruttadauria J, Davis-Dusenbery BN, Lagna G, Hata A.

J Biol Chem. 2012 Nov 9;287(46):38656-64. doi: 10.1074/jbc.M112.390898. Epub 2012 Sep 17.

15.

Bone morphogenetic protein signaling in vascular disease: anti-inflammatory action through myocardin-related transcription factor A.

Wang D, Prakash J, Nguyen P, Davis-Dusenbery BN, Hill NS, Layne MD, Hata A, Lagna G.

J Biol Chem. 2012 Aug 10;287(33):28067-77. doi: 10.1074/jbc.M112.379487. Epub 2012 Jun 20.

16.

SnapShot: directed differentiation of pluripotent stem cells.

Williams LA, Davis-Dusenbery BN, Eggan KC.

Cell. 2012 May 25;149(5):1174-1174.e1. doi: 10.1016/j.cell.2012.05.015. No abstract available.

17.

Bone morphogenetic protein 4 promotes vascular smooth muscle contractility by activating microRNA-21 (miR-21), which down-regulates expression of family of dedicator of cytokinesis (DOCK) proteins.

Kang H, Davis-Dusenbery BN, Nguyen PH, Lal A, Lieberman J, Van Aelst L, Lagna G, Hata A.

J Biol Chem. 2012 Feb 3;287(6):3976-86. doi: 10.1074/jbc.M111.303156. Epub 2011 Dec 9.

18.

Micromanaging vascular smooth muscle cell differentiation and phenotypic modulation.

Davis-Dusenbery BN, Wu C, Hata A.

Arterioscler Thromb Vasc Biol. 2011 Nov;31(11):2370-7. doi: 10.1161/ATVBAHA.111.226670. Review.

19.

Hypoxia potentiates microRNA-mediated gene silencing through posttranslational modification of Argonaute2.

Wu C, So J, Davis-Dusenbery BN, Qi HH, Bloch DB, Shi Y, Lagna G, Hata A.

Mol Cell Biol. 2011 Dec;31(23):4760-74. doi: 10.1128/MCB.05776-11. Epub 2011 Oct 3.

20.

down-regulation of Kruppel-like factor-4 (KLF4) by microRNA-143/145 is critical for modulation of vascular smooth muscle cell phenotype by transforming growth factor-beta and bone morphogenetic protein 4.

Davis-Dusenbery BN, Chan MC, Reno KE, Weisman AS, Layne MD, Lagna G, Hata A.

J Biol Chem. 2011 Aug 12;286(32):28097-110. doi: 10.1074/jbc.M111.236950. Epub 2011 Jun 13.

21.

MicroRNA in Cancer: The Involvement of Aberrant MicroRNA Biogenesis Regulatory Pathways.

Davis-Dusenbery BN, Hata A.

Genes Cancer. 2010 Nov;1(11):1100-14. doi: 10.1177/1947601910396213.

22.

Smad-mediated miRNA processing: a critical role for a conserved RNA sequence.

Davis-Dusenbery BN, Hata A.

RNA Biol. 2011 Jan-Feb;8(1):71-6. Epub 2011 Jan 1. Review.

23.

Mechanisms of control of microRNA biogenesis.

Davis-Dusenbery BN, Hata A.

J Biochem. 2010 Oct;148(4):381-92. doi: 10.1093/jb/mvq096. Epub 2010 Sep 9. Review.

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