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Results: 1 to 20 of 52

1.

In silico comparative characterization of pharmacogenomic missense variants.

Li B, Seligman C, Thusberg J, Miller JL, Auer J, Whirl-Carrillo M, Capriotti E, Klein TE, Mooney SD.

BMC Genomics. 2014;15 Suppl 4:S4. doi: 10.1186/1471-2164-15-S4-S4. Epub 2014 May 20.

PMID:
25057096
[PubMed - in process]
Free PMC Article
2.

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I.

Bioinformatics. 2014 Jul 15;30(14):2091-2092. Epub 2014 Mar 3.

PMID:
24590444
[PubMed - as supplied by publisher]
3.

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing.

Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD.

Genome Biol. 2014 Jan 13;15(1):R19. [Epub ahead of print]

PMID:
24451234
[PubMed - as supplied by publisher]
Free PMC Article
4.

A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease.

Tourette C, Li B, Bell R, O'Hare S, Kaltenbach LS, Mooney SD, Hughes RE.

J Biol Chem. 2014 Mar 7;289(10):6709-26. doi: 10.1074/jbc.M113.523696. Epub 2014 Jan 9.

PMID:
24407293
[PubMed - indexed for MEDLINE]
5.

Genome-wide DNA methylation changes with age in disease-free human skeletal muscle.

Zykovich A, Hubbard A, Flynn JM, Tarnopolsky M, Fraga MF, Kerksick C, Ogborn D, MacNeil L, Mooney SD, Melov S.

Aging Cell. 2014 Apr;13(2):360-6. doi: 10.1111/acel.12180. Epub 2013 Dec 2.

PMID:
24304487
[PubMed - in process]
6.

Genome and proteome annotation using automatically recognized concepts and functional networks.

Bivol A, Wittkop T, Davis D, Mooney SD.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:26. eCollection 2013.

PMID:
24303290
[PubMed]
Free PMC Article
7.

Medium-chain acyl-CoA deficiency: outlines from newborn screening, in silico predictions, and molecular studies.

Catarzi S, Caciotti A, Thusberg J, Tonin R, Malvagia S, la Marca G, Pasquini E, Cavicchi C, Ferri L, Donati MA, Baronio F, Guerrini R, Mooney SD, Morrone A.

ScientificWorldJournal. 2013 Oct 31;2013:625824. doi: 10.1155/2013/625824. eCollection 2013.

PMID:
24294134
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Reply to Brook et al: No empirical evidence for human overkill of megafauna in Sahul.

Wroe S, Field JH, Archer M, Grayson DK, Price GJ, Louys J, Faith JT, Webb GE, Davidson I, Mooney SD.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3369. No abstract available.

PMID:
24137797
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Late-life rapamycin treatment reverses age-related heart dysfunction.

Flynn JM, O'Leary MN, Zambataro CA, Academia EC, Presley MP, Garrett BJ, Zykovich A, Mooney SD, Strong R, Rosen CJ, Kapahi P, Nelson MD, Kennedy BK, Melov S.

Aging Cell. 2013 Oct;12(5):851-62. doi: 10.1111/acel.12109. Epub 2013 Jul 7.

PMID:
23734717
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Climate change frames debate over the extinction of megafauna in Sahul (Pleistocene Australia-New Guinea).

Wroe S, Field JH, Archer M, Grayson DK, Price GJ, Louys J, Faith JT, Webb GE, Davidson I, Mooney SD.

Proc Natl Acad Sci U S A. 2013 May 28;110(22):8777-81. doi: 10.1073/pnas.1302698110. Epub 2013 May 6.

PMID:
23650401
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways.

Rardin MJ, Newman JC, Held JM, Cusack MP, Sorensen DJ, Li B, Schilling B, Mooney SD, Kahn CR, Verdin E, Gibson BW.

Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6601-6. doi: 10.1073/pnas.1302961110. Epub 2013 Apr 1.

PMID:
23576753
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.

Wittkop T, TerAvest E, Evani US, Fleisch KM, Berman AE, Powell C, Shah NH, Mooney SD.

BMC Bioinformatics. 2013 Feb 14;14:53. doi: 10.1186/1471-2105-14-53.

PMID:
23409969
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

PMID:
23353650
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A genome-scale RNA-interference screen identifies RRAS signaling as a pathologic feature of Huntington's disease.

Miller JP, Yates BE, Al-Ramahi I, Berman AE, Sanhueza M, Kim E, de Haro M, DeGiacomo F, Torcassi C, Holcomb J, Gafni J, Mooney SD, Botas J, Ellerby LM, Hughes RE.

PLoS Genet. 2012;8(11):e1003042. doi: 10.1371/journal.pgen.1003042. Epub 2012 Nov 29.

PMID:
23209424
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Collaborative software for traditional and translational research.

Berman AE, Barnett WK, Mooney SD.

Hum Genomics. 2012 Sep 25;6:21. doi: 10.1186/1479-7364-6-21. Review.

PMID:
23157911
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Tor1 regulates protein solubility in Saccharomyces cerevisiae.

Peters TW, Rardin MJ, Czerwieniec G, Evani US, Reis-Rodrigues P, Lithgow GJ, Mooney SD, Gibson BW, Hughes RE.

Mol Biol Cell. 2012 Dec;23(24):4679-88. doi: 10.1091/mbc.E12-08-0620. Epub 2012 Oct 24.

PMID:
23097491
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions.

Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RM, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV.

Hum Mutat. 2013 Jan;34(1):255-65. doi: 10.1002/humu.22214. Epub 2012 Oct 22.

PMID:
22949387
[PubMed - indexed for MEDLINE]
18.

Comparative protein interactomics of neuroglobin and myoglobin.

Haines BA, Davis DA, Zykovich A, Peng B, Rao R, Mooney SD, Jin K, Greenberg DA.

J Neurochem. 2012 Oct;123(1):192-8. doi: 10.1111/j.1471-4159.2012.07881.x. Epub 2012 Aug 14.

PMID:
22816983
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

DEFOG: discrete enrichment of functionally organized genes.

Wittkop T, Berman AE, Fleisch KM, Mooney SD.

Integr Biol (Camb). 2012 Jul;4(7):795-804. doi: 10.1039/c2ib00136e. Epub 2012 Jun 18.

PMID:
22706384
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Functional organization and its implication in evolution of the human protein-protein interaction network.

Zhao Y, Mooney SD.

BMC Genomics. 2012 Apr 24;13:150. doi: 10.1186/1471-2164-13-150.

PMID:
22530615
[PubMed - indexed for MEDLINE]
Free PMC Article

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