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Items: 1 to 20 of 57

1.

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges.

Pejaver V, Mooney SD, Radivojac P.

Hum Mutat. 2017 May 16. doi: 10.1002/humu.23258. [Epub ahead of print]

PMID:
28508593
2.

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Hsieh CL, Wiklund F, Catalona WJ, Foulkes WD, Mandal D, Eeles RA, Kote-Jarai Z, Bustamante CD, Schaid DJ, Hastie T, Ostrander EA, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W.

Am J Hum Genet. 2016 Oct 6;99(4):877-885. doi: 10.1016/j.ajhg.2016.08.016. Epub 2016 Sep 22.

3.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

4.

USE OF GENOME DATA IN NEWBORNS AS A STARTING POINT FOR LIFE-LONG PRECISION MEDICINE.

Brenner SE, Kingsmore S, Mooney SD, Nussbaum R, Puck J.

Pac Symp Biocomput. 2016;21:568-75.

5.

Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides.

Li Z, Dilger JM, Pejaver V, Smiley D, Arnold RJ, Mooney SD, Mukhopadhyay S, Radivojac P, Clemmer DE.

Int J Mass Spectrom. 2014 Jul 15;368:6-14.

6.

Ten simple rules for a community computational challenge.

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

PLoS Comput Biol. 2015 Apr 23;11(4):e1004150. doi: 10.1371/journal.pcbi.1004150. eCollection 2015 Apr. No abstract available.

7.

Mitochondrial DNA Sequence Variation Associated With Peripheral Nerve Function in the Elderly.

Katzman SM, Strotmeyer ES, Nalls MA, Zhao Y, Mooney S, Schork N, Newman AB, Harris TB, Yaffe K, Cummings SR, Liu Y, Tranah GJ; Health, Aging, and Body Composition Study.

J Gerontol A Biol Sci Med Sci. 2015 Nov;70(11):1400-8. doi: 10.1093/gerona/glu175. Epub 2014 Nov 13.

8.

Progress towards the integration of pharmacogenomics in practice.

Mooney SD.

Hum Genet. 2015 May;134(5):459-65. doi: 10.1007/s00439-014-1484-7. Epub 2014 Sep 11. Review.

9.

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.

Jiang Y, Clark WT, Friedberg I, Radivojac P.

Bioinformatics. 2014 Sep 1;30(17):i609-16. doi: 10.1093/bioinformatics/btu472.

10.

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.

11.

Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations.

Morrone A, Tylee KL, Al-Sayed M, Brusius-Facchin AC, Caciotti A, Church HJ, Coll MJ, Davidson K, Fietz MJ, Gort L, Hegde M, Kubaski F, Lacerda L, Laranjeira F, Leistner-Segal S, Mooney S, Pajares S, Pollard L, Ribeiro I, Wang RY, Miller N.

Mol Genet Metab. 2014 Jun;112(2):160-70. doi: 10.1016/j.ymgme.2014.03.004. Epub 2014 Mar 20. Erratum in: Mol Genet Metab. 2014 Nov;113(3):237.

12.

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):2091-2. doi: 10.1093/bioinformatics/btu117. Epub 2014 Mar 3. No abstract available.

13.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

OMICS. 2014 Jan;18(1):10-4. doi: 10.1089/omi.2013.0149.

14.

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. doi: 10.1186/gb-2014-15-1-r19.

15.

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.

16.

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.

17.

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
18.

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.

19.

Towards precision medicine: advances in computational approaches for the analysis of human variants.

Peterson TA, Doughty E, Kann MG.

J Mol Biol. 2013 Nov 1;425(21):4047-63. doi: 10.1016/j.jmb.2013.08.008. Epub 2013 Aug 17. Review.

20.

A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations.

Peterson TA, Park D, Kann MG.

BMC Genomics. 2013;14 Suppl 3:S5. doi: 10.1186/1471-2164-14-S3-S5. Epub 2013 May 28.

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