-
- 1
-
A. Ben-Hur and W.S. Noble.
Choosing negative examples for the prediction of protein-protein
interactions.
BMC Bioinformatics, 7(Suppl 1/S2), 2006.
- 2
-
A.P. Davierwala, J. Haynes, Z. Li, R.L. Brost, M.D. Robinson, L. Yu,
S. Mnaimneh, H. Ding, H. Zhu, Y. Chen, et al.
The synthetic genetic interaction spectrum of essential genes.
Nature Genet, 37:1147-1152, 2005.
- 3
-
M. Deng, T. Chen, and F. Sun.
An integrated probabilistic model for functional prediction of
proteins.
In Proc 7th Int Conf Comp Mol Biol, pages 95-103, 2003.
- 4
-
SR Eddy.
Profile hidden markov models.
Bioinformatics, 14(9):755-763, 1998.
- 5
-
R.D. Finn, J. Tate, J. Mistry, P.C. Coggill, J.S. Sammut, H.R. Hotz, G. Ceric,
K. Forslund, S.R. Eddy, E.L. Sonnhammer, and A. Bateman.
The Pfam protein families database.
Nucleic Acids Research, 36:D281-D288, 2008.
- 6
-
P. Gasch et al.
Genomic expression programs in the response of yeast cells to
environmental changes.
Mol.Biol.Cell, 11:4241-4257, 2000.
- 7
-
Y Guan, C.L. Myers, D.C. Hess, Z. Barutcuoglu, A. Caudy, and O.G. Troyanskaya.
Predicting gene function in a hierarchical context with an ensemble
of classifiers.
Genome Biology, 9:S2, 2008.
- 8
-
Y. Ho, A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar,
P. Taylor, K. Bennett, K. Boutilier, et al.
Systematic identification of protein complexes in Saccharomyces
cerevisiae by mass spectrometry.
Nature, 415:180-183, 2002.
- 9
-
G.R. Lanckriet, R. G. Gert, M. Deng, N. Cristianini, M. Jordan, and W.S. Noble.
Kernel-based data fusion and its application to protein function
prediction in yeast.
In Proceedings of the Pacific Symposium on Biocomputing, pages
300-311, 2004.
- 10
-
P. Pavlidis, J. Weston, J. Cai, and W.S. Noble.
Learning gene functional classification from multiple data.
J. Comput. Biol., 9:401-411, 2002.
- 11
-
P. Spellman et al.
Comprehensive identification of cell cycle-regulated genes of the
yeast Saccharomices cerevisiae by microarray hybridization.
Mol. Biol. Cell, 9:3273-3297, 1998.
- 12
-
C. Stark, B. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and M. Tyers.
BioGRID: a general repository for interaction datasets.
Nucleic Acids Res., 34:D535-D539, 2006.
- 13
-
P. Uetz, L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight,
D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, et al.
A comprehensive analysis of protein-protein interactions in
Saccharomyces cerevisiae.
Nature, 403:623-627, 2000.
- 14
-
G. Valentini and N. Cesa-Bianchi.
Hcgene: a software tool to support the hierarchical classification of
genes.
Bioinformatics, 24(5):729-731, 2008.
- 15
-
K. Verspoor, J. Cohn, S. Mnizewski, and C. Joslyn.
A categorization approach to automated ontological function
annotation.
Protein Science, 15:1544-1549, 2006.
- 16
-
C. von Mering, R. Krause, B. Snel, M. Cornell, S. Oliver, S. Fields, and
P. Bork.
Comparative assessment of large-scale data sets of protein-protein
interactions.
Nature, 417:399-403, 2002.