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Results: 1 to 20 of 68

1.

The structural and functional signatures of proteins that undergo multiple events of post-translational modification.

Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P.

Protein Sci. 2014 Aug;23(8):1077-93. doi: 10.1002/pro.2494. Epub 2014 Jun 11.

PMID:
24888500
[PubMed - in process]
2.

Bioinformatics curriculum guidelines: toward a definition of core competencies.

Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV.

PLoS Comput Biol. 2014 Mar 6;10(3):e1003496. doi: 10.1371/journal.pcbi.1003496. eCollection 2014 Mar. No abstract available.

PMID:
24603430
[PubMed - in process]
Free PMC Article
3.

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]
4.

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
5.

Vector quantization kernels for the classification of protein sequences and structures.

Clark WT, Radivojac P.

Pac Symp Biocomput. 2014:316-27.

PMID:
24297558
[PubMed - in process]
Free Article
6.

ISCB computational biology Wikipedia competition.

Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.

PLoS Comput Biol. 2013;9(9):e1003242. doi: 10.1371/journal.pcbi.1003242. Epub 2013 Sep 19. No abstract available.

PMID:
24068913
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Information-theoretic evaluation of predicted ontological annotations.

Clark WT, Radivojac P.

Bioinformatics. 2013 Jul 1;29(13):i53-61. doi: 10.1093/bioinformatics/btt228.

PMID:
23813009
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Quantitative measurement of phosphoproteome response to osmotic stress in arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC).

Xue L, Wang P, Wang L, Renzi E, Radivojac P, Tang H, Arnold R, Zhu JK, Tao WA.

Mol Cell Proteomics. 2013 Aug;12(8):2354-69. doi: 10.1074/mcp.O113.027284. Epub 2013 May 8.

PMID:
23660473
[PubMed - indexed for MEDLINE]
9.

Evaluating purifying selection in the mitochondrial DNA of various mammalian species.

Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L.

PLoS One. 2013;8(3):e58993. doi: 10.1371/journal.pone.0058993. Epub 2013 Mar 22.

PMID:
23533597
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra.

Ji C, Arnold RJ, Sokoloski KJ, Hardy RW, Tang H, Radivojac P.

Proteomics. 2013 Mar;13(5):756-65. doi: 10.1002/pmic.201100670. Epub 2013 Feb 4.

PMID:
23303707
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Computational approaches to protein inference in shotgun proteomics.

Li YF, Radivojac P.

BMC Bioinformatics. 2012;13 Suppl 16:S4. doi: 10.1186/1471-2105-13-S16-S4. Epub 2012 Nov 5. Review.

PMID:
23176300
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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]
14.

Post-translational modifications induce significant yet not extreme changes to protein structure.

Xin F, Radivojac P.

Bioinformatics. 2012 Nov 15;28(22):2905-13. doi: 10.1093/bioinformatics/bts541. Epub 2012 Sep 4.

PMID:
22947645
[PubMed - indexed for MEDLINE]
Free Article
15.

Allosteric post-translational modification codes.

Nussinov R, Tsai CJ, Xin F, Radivojac P.

Trends Biochem Sci. 2012 Oct;37(10):447-55. doi: 10.1016/j.tibs.2012.07.001. Epub 2012 Aug 8. Review.

PMID:
22884395
[PubMed - indexed for MEDLINE]
16.

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors.

Kosti I, Radivojac P, Mandel-Gutfreund Y.

PLoS Comput Biol. 2012;8(7):e1002603. doi: 10.1371/journal.pcbi.1002603. Epub 2012 Jul 26.

PMID:
22844237
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Protein identification problem from a Bayesian point of view.

Li YF, Arnold RJ, Radivojac P, Tang H.

Stat Interface. 2012 Jan 1;5(1):21-37.

PMID:
24761189
[PubMed]
Free PMC Article
18.

Investigation of VUV Photodissociation Propensities Using Peptide Libraries.

Liu X, Li YF, Bohrer BC, Arnold RJ, Radivojac P, Tang H, Reilly JP.

Int J Mass Spectrom. 2011 Dec 1;308(2-3):142-154.

PMID:
22125417
[PubMed]
Free PMC Article
19.

Prediction of functional regulatory SNPs in monogenic and complex disease.

Zhao Y, Clark WT, Mort M, Cooper DN, Radivojac P, Mooney SD.

Hum Mutat. 2011 Oct;32(10):1183-90. doi: 10.1002/humu.21559. Epub 2011 Sep 9.

PMID:
21796725
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Computational methods for identification of functional residues in protein structures.

Xin F, Radivojac P.

Curr Protein Pept Sci. 2011 Sep;12(6):456-69. Review.

PMID:
21787297
[PubMed - indexed for MEDLINE]

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