DOI: 10.1371/journal.pone.0063754. FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences

FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences

10.1371/journal.pone.0063754

Crossref journal-article

Public Library of Science (PLoS)

PLoS ONE (340)

Bibliography

Minneci, F., Piovesan, D., Cozzetto, D., & Jones, D. T. (2013). FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences. PLoS ONE, 8(5), e63754.

Authors 4

Federico Minneci (first)
Damiano Piovesan (additional)
Domenico Cozzetto (additional)
David T. Jones (additional)

References 34 Referenced 42

10.1038/nature09792 / Nature / Initial impact of the sequencing of the human genome by ES Lander (2011)
10.1038/nature11247 / Nature / An integrated encyclopedia of DNA elements in the human genome by I Dunham (2012)
10.1038/nature07509 / Nature / Alternative isoform regulation in human tissue transcriptomes by ET Wang (2008)
10.1093/nar/gkr981 / Nucleic acids research / Reorganizing the protein space at the Universal Protein Resource (UniProt) by Consortium UniProt (2012)
10.1038/75556 / Nature genetics / Gene ontology: tool for the unification of biology. The Gene Ontology Consortium by M Ashburner (2000)
10.1016/j.sbi.2012.05.001 / Current opinion in structural biology / The use of evolutionary patterns in protein annotation by AD Wilkins (2012)
10.1186/gb-2009-10-2-206 / Genome biology / Sequence-based feature prediction and annotation of proteins by AS Juncker (2009)
10.1016/S0022-2836(02)00379-0 / Journal of molecular biology / Prediction of human protein function from post-translational modifications and localization features by LJ Jensen (2002)
10.1093/bioinformatics/btg036 / Bioinformatics / Prediction of human protein function according to Gene Ontology categories by LJ Jensen (2003)
10.1371/journal.pcbi.0030162 / PLoS computational biology / Inferring function using patterns of native disorder in proteins by A Lobley (2007)
10.1093/nar/gkn193 / Nucleic acids research / FFPred: an integrated feature-based function prediction server for vertebrate proteomes by AE Lobley (2008)
10.1002/pmic.201100607 / Proteomics / Combining many interaction networks to predict gene function and analyze gene lists by S Mostafavi (2012)
10.1093/nar/gkn803 / Nucleic acids research / The GOA database in 2009–an integrated Gene Ontology Annotation resource by D Barrell (2009)
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{'key': 'ref15', 'first-page': '39', 'article-title': 'Protein subcellular localization prediction with WOLF PSORT', 'volume': '3', 'author': 'P Horton', 'year': '2006', 'journal-title': 'Proceedings of the 4th Asia-Pacific Bioinformatics Conference'} / Proceedings of the 4th Asia-Pacific Bioinformatics Conference / Protein subcellular localization prediction with WOLF PSORT by P Horton (2006)
10.1038/nmeth.1701 / Nature methods / SignalP 4.0: discriminating signal peptides from transmembrane regions by TN Petersen (2011)
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Joachims T (1999) Making large scale SVM learning practical.
10.1007/s10994-007-5018-6 / Machine learning / A note on Platt’s probabilistic outputs for support vector machines by HT Lin (2007)
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Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, <etal>et al</etal>.. (2013) A large-scale evaluation of computational protein function prediction. Nat Meth advance online publication.
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10.1093/bioinformatics/btp122 / Bioinformatics / The use of gene ontology evidence codes in preventing classifier assessment bias by MF Rogers (2009)
10.1186/1471-2105-9-S5-S4 / BMC bioinformatics / Metrics for GO based protein semantic similarity: a systematic evaluation by C Pesquita (2008)
10.1093/nar/gkq427 / Nucleic acids research / Protein annotation and modelling servers at University College London by DW Buchan (2010)
10.1186/1471-2105-10-159 / BMC bioinformatics / Transmembrane protein topology prediction using support vector machines by T Nugent (2009)
10.1006/jmbi.1999.3091 / Journal of molecular biology / Protein secondary structure prediction based on position-specific scoring matrices by DT Jones (1999)
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10.1093/glycob/cwh151 / Glycobiology / Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites by K Julenius (2005)

Dates

Type	When
Created	12 years, 3 months ago (May 22, 2013, 6:40 p.m.)
Deposited	6 years, 10 months ago (Oct. 22, 2018, 6:39 p.m.)
Indexed	4 months, 1 week ago (April 29, 2025, 10:29 p.m.)
Issued	12 years, 3 months ago (May 22, 2013)
Published	12 years, 3 months ago (May 22, 2013)
Published Online	12 years, 3 months ago (May 22, 2013)

Funders 0

None

BibTeX

@article{Minneci_2013, title={FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0063754}, DOI={10.1371/journal.pone.0063754}, number={5}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Minneci, Federico and Piovesan, Damiano and Cozzetto, Domenico and Jones, David T.}, editor={Kurgan, Lukasz}, year={2013}, month=may, pages={e63754} }

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