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Results: 1 to 20 of 72

1.

Training the next generation of quantitative biologists in the era of big data.

Pattin KA, Greene AC, Altman RB, Cohen KB, Wethington E, Görg C, Hunter LE, Muse SV, Radivojac P, Moore JH.

Pac Symp Biocomput. 2015;20:488-92.

PMID:
25592609
[PubMed - in process]
Free Article
2.

On the Split Personality of Penultimate Proline.

Glover MS, Shi L, Fuller DR, Arnold RJ, Radivojac P, Clemmer DE.

J Am Soc Mass Spectrom. 2014 Dec 12. [Epub ahead of print]

PMID:
25503299
[PubMed - as supplied by publisher]
3.

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential.

Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC.

Sci Rep. 2014 Nov 21;4:7155. doi: 10.1038/srep07155.

PMID:
25412673
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
25161254
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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]
6.

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 - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
24590444
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
24451234
[PubMed - in process]
Free PMC Article
9.

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

Clark WT, Radivojac P.

Pac Symp Biocomput. 2014:316-27.

PMID:
24297558
[PubMed - indexed for MEDLINE]
Free Article
10.

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
11.

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
12.

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]
Free PMC Article
13.

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
14.

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
15.

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
16.

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
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.

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
19.

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]
20.

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
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