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Publications from the GeneFun project
Protein families and subfamilies (WP1)
Reliability scores for functional annotations (WP2)
- del Pozo and Valencia 2005
Manuscript
Domain Architecture (WP3)
- Multi--domain proteins in the three kingdoms of life - Orphan
domains and other unassigned regions. Diana Ekman, Åsa K. Björklund,
Johannes Frey-Skött and Arne Elofsson 2005
J. Mol. Biol in press
Structure-based prediction of function and interactions (WP4)
- Letunic, I., Copley, R., Schmidt, S., Ciccarelli, F.d., Doerks, T.,
Schultz, J., Ponting, C.P. and Bork, P. (2004) Nucl.Ac.Res.32, D142-D144
SMART 4.0: towards genomic data integration
- von Mering, C., Jensen, L.J., Hooper, S.D., Krupp, M., Fogliereni, M.,
Snel, B. Jouffre, N., Huynen, M.A., and Bork, P. (2005), Nucl. Acid Res.
33, D433-D437
STRING: Known and predicted protein-protein associations, integrated and
transferred across species
Meta-server, Context-based function prediction (WP5)
- Doerks, T., von Mering, C., and Bork, P. (2004) Nucl.Ac.Res. 32,
6321-6326
Function prediction for hypotical bacterial proteins using genomic context
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Meta-server, Integrated function prediction (WP6)
- Hermjakob, H. et al. (38 authors) (2004) Nature Biotech. 22, 177-183
The HUPO PSI Molecular Interaction Format: a community
standard for the representation of protein interaction data
Experimental validation of function predictions (WP7)
Other relevant publications
- Bork, P.*, Jensen, L.J.*, von Mering, C.*, Ramani, A.K.*, Lee, I.* and
Marcotte, E.M.* (2004) Curr.Opin.Struct.Biol., 14, 292-299
Protein interaction networks from yeast to man
- Doerks, T., von Mering, C., Andrade, M.A., Lathe, W. and Bork, P. (2004)
Trends Genet. 30, 126-131
Predicting the target processes of transcription regulators
- Jensen, L.J. and Bork, P. (2004) Drug Discovery Today (TARGETS) 3, 51-56
Quality analysis and integration of large scale molecular data sets
- Jensen, L.J., Lagarde, J., von Mering, C. and Bork, P. (2004) Nucl.
Ac.Res. 32, W445-W448
ArrayProspector: A Web resource of functional associations inferred from
microarray expression data
- Korbel, J., von Mering. C., Jensen, L.J. and Bork, P., (2004) Nature
Biotech 22, 911-917
Conservation of bidirectionally transcribed genes in prokaryotes predicts
gene regulation
- Perez, A.J., Perez-Iratxeta, C., Thode, G., Bork, P. and Andrade, M.
(2004) Bioinformatics 20, 2084-2091
Gene annotation from scientific literature using mappings
between keywords
- Sarik, J., Lensen, L.J., Ouzounova, R., Rojas, I. and Bork, P. (2004)
Proceedings of the 42nd Annual meeting of the Association of Computationl
Linguistics, 192-199.
Extracting regulatory gene expression networks from Pubmed
- Korbel, J.O., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaszanowski,
S., Hooper, S., Andrade, M.A., and Bork, P. (2005) PLoS Biology, in press
Systematic association of genes to phenotypes by genome and literature mining
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