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Items: 1 to 20 of 100

1.

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.

3.

In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.

Chitale M, Khan IK, Kihara D.

BMC Bioinformatics. 2013;14 Suppl 3:S2. doi: 10.1186/1471-2105-14-S3-S2. Epub 2013 Feb 28.

4.

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.

5.

Protein function prediction using text-based features extracted from the biomedical literature: the CAFA challenge.

Wong A, Shatkay H.

BMC Bioinformatics. 2013;14 Suppl 3:S14. doi: 10.1186/1471-2105-14-S3-S14. Epub 2013 Feb 28.

6.

Protein function prediction by massive integration of evolutionary analyses and multiple data sources.

Cozzetto D, Buchan DW, Bryson K, Jones DT.

BMC Bioinformatics. 2013;14 Suppl 3:S1. doi: 10.1186/1471-2105-14-S3-S1. Epub 2013 Feb 28.

7.

Orthology prediction methods: a quality assessment using curated protein families.

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P.

Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011 Aug 19.

8.

The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches.

Khan IK, Wei Q, Chapman S, Kc DB, Kihara D.

Gigascience. 2015 Sep 14;4:43. doi: 10.1186/s13742-015-0083-4. eCollection 2015.

9.

Genome-Wide Protein Function Prediction through Multi-Instance Multi-Label Learning.

Wu JS, Huang SJ, Zhou ZH.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Sep-Oct;11(5):891-902. doi: 10.1109/TCBB.2014.2323058.

PMID:
26356861
10.

Computational prediction of protein-protein interactions.

Ehrenberger T, Cantley LC, Yaffe MB.

Methods Mol Biol. 2015;1278:57-75. doi: 10.1007/978-1-4939-2425-7_4.

11.

Ten years of predictions ... and counting.

Cozzetto D, Di Matteo A, Tramontano A.

FEBS J. 2005 Feb;272(4):881-2.

12.

Genome annotation assessment in Drosophila melanogaster.

Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE.

Genome Res. 2000 Apr;10(4):483-501.

13.

Large-scale protein annotation through gene ontology.

Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz L.

Genome Res. 2002 May;12(5):785-94.

14.

Genome-scale phylogenetic function annotation of large and diverse protein families.

Engelhardt BE, Jordan MI, Srouji JR, Brenner SE.

Genome Res. 2011 Nov;21(11):1969-80. doi: 10.1101/gr.104687.109. Epub 2011 Jul 22.

15.

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.

16.

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.

Yu C, Zavaljevski N, Desai V, Johnson S, Stevens FJ, Reifman J.

BMC Bioinformatics. 2008 Jan 25;9:52. doi: 10.1186/1471-2105-9-52.

17.

Analysis and prediction of functional sub-types from protein sequence alignments.

Hannenhalli SS, Russell RB.

J Mol Biol. 2000 Oct 13;303(1):61-76.

PMID:
11021970
18.

Negative example selection for protein function prediction: the NoGO database.

Youngs N, Penfold-Brown D, Bonneau R, Shasha D.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003644. doi: 10.1371/journal.pcbi.1003644. eCollection 2014 Jun.

19.
20.

N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence.

Maurer-Stroh S, Eisenhaber B, Eisenhaber F.

J Mol Biol. 2002 Apr 5;317(4):541-57.

PMID:
11955008

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