Papers on Protein Networks
List of papers in reverse chronological order:      (Updated 08/01/2005 05:33PM)
- Y. Liu et al. "Inferring protein-protein interactions through high-throughput interaction data from diverse organisms", Bioinformatics, 21(15):3279-3285, 2005.Link
- D. Barker and M. Pagel "Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes", PLoS Computational Biology, 1(1):e3, 2005.Link
- Sharan et al. "Conserved patterns of protein interaction in multiple species", PNAS vol. 102, February 8, 2005.Link
- Yamanishi et al. "Supervised enzyme network inference from the integration of genomic data and chemical information", ISMB, 2005.Link
- Nabieva et al. "Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps", ISMB, 2005.Link
- Hu et al. "Mining coherent dense subgraphs across massive biological networks for functional discovery", ISMB, 2005.Link
- Jothi et al. "Predicting protein-protein interaction by searching evolutionary tree automorphism space", ISMB, 2005.Link
- Borgwardt et al. "Protein function prediction via graph kernels", ISMB, 2005.Link
- A. Ben-Hur and W. S. Noble "Kernel methods for predicting protein-protein interactions", ISMB, 2005.Link
- A. Jaimovich et al. "Towards an integrated protein-protein interaction network", RECOMB, 2005.Link
- J. Scott et al. "Efficient algorithms for detecting signaling pathways in protein interaction networks", RECOMB, 2005.Link
- M. Middendorf et al. "Inferring network mechanisms: The Drosophila melanogaster protein interaction network", Proc. Natl. Acad. Sci. USA, 102(9):3192-3197, 2005.Link
- C. von Mering et al. "STRING: known and predicted protein-protein associations, integrated and transferred across organisms", Nucleic Acids Research, 33:D433-D437, 2005.Link
- P. M. Bowers et al. "Use of logic relationships to decipher protein network organization", Science, 306:2246-2249, 2004.Link
- I. Lee et al. "A Probabilistic functional network of yeast genes", Science, 306:1555-1558, 2004.Link
- A. D. King et al. "Protein complex prediction via cost-based clustering", Bioinformatics, 20(17):3013-3020, 2004.Link
- S. Li et al. "A Map of the interactome network of the metazoan C. elegans", Science, 303:540-543, 2004.Link
- I. Pournara and L. Wernisch "Reconstruction of gene networks using Bayesian learning and manipulation experiments", Bioinformatics, 20(17):2934-2942, 2004.Link
- X. Zhou et al. "A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks", Bioinformatics, 20(17):2918-2927, 2004.Link
- P. Bork et al. "Protein interaction networks from yeast to human", Current Opinion in Structural Biology, 14(3):292-299, 2004.Link
- F. Sohler et al. "New methods for joint analysis of biological networks and expression data", Bioinformatics, 20(10):1517-1521, 2004.Link
- Y. Yamanishi et al. "Protein network inference from multiple genomic data: a supervised approach", Bioinformatics ISMB 2004 Supplement, 20(S1):i363-i370, 2004.Link
- K. Tsuda and W. S. Noble "Learning kernels from biological networks by maximizing entropy", Bioinformatics ISMB 2004 Supplement, 20(S1):i326-i333, 2004.Link
- C. A. Stanyon et al. "A Drosophila protein-interaction map centered on cell-cycle regulators", Genome Biology, 5(12):R96, 2004.Link
- S. Asthana et al. "Predicting protein complex membership using probabilistic network reliability", Genome Research, 14(6):1170-1175, 2004.Link
- I. Iossifov et al. "Probabilistic inference of molecular networks from noisy data sources", Bioinformatics, 20(8):1205-1213, 2004.Link
- P. M. Bowers et al. "Prolinks: a database of protein functional linkages derived from coevolution", Genome Biology, 5(5):R35, 2004.Link
- L. Giot et al. "A Protein interaction map of Drosophila melanogaster", Science, 302:1727-1736, 2003.Link
- R. Jansen et al. "A Bayesian networks approach for predicting protein-protein interactions from genomic data", Science, 302:449-453, 2003.Link
- C. von Mering et al. "STRING: a database of predicted functional associations between proteins", Nucleic Acids Research, 31(1):258-261, 2003.Link
- V. Spirin and L. A. Mirny "Protein complexes and functional modules in molecular networks", Proc. Natl. Acad. Sci. USA, 100:12123-12128, 2003.Link
- S. Mangan and U. Alon "Structure and function of the feed-forward loop network motif", Proc. Natl. Acad. Sci. USA, 100:11980-11985, 2003.Link
- B. P. Kelley et al. "Conserved pathways within bacteria and yeast as revealed by global protein network alignment", Proc. Natl. Acad. Sci. USA, 100:11394-11399, 2003.Link
- J. S. Bader "Greedily building protein networks with confidence", Bioinformatics, 19(15):1869-1874, 2003.Link
- M. A. Huynen et al. "Function prediction and protein networks", Current Opinion in Cell Biology, 15(2):191-198, 2003.Link
- E. Segal et al. "Discovering molecular pathways from protein interaction and gene expression data", Bioinformatics ISMB 2003 Supplement, 19(S1):i264-i272, 2003.Link
- S. Letovsky and S. Kasif "Predicting protein function from protein-protein interaction data: a probabilistic approach", Bioinformatics ISMB 2003 Supplement, 19(S1):i197-i204, 2003.Link
- G. D. Bader and C. W. V. Hogue "An automated method for finding molecular complexes in large protein interaction networks", BMC Bioinformatics, 4(2), 2003.Link
- J. P. Vert and M. Kanehisa "Extracting active pathways from gene expression data", Bioinformatics ECCB 2003 Supplement, 19(S2):ii238-ii244, 2003.Link
- J. R. Bock and D. A. Gough "Whole-proteome interaction mining", Bioinformatics, 19(1):125:134, 2003.Link
- A. M. Edwards et al. "Bridging structural biology and genomics: assessing protein interaction data with known complexes", Trends in Genetics, 18(10):529:536, 2002.Link
- J. C. Mellor et al. "Predictome: a database of putative functional links between proteins", Nucleic Acids Research, 30(1):306-309, 2002.Link
- C. von Mering et al. "Comparative assessment of large-scale data sets of protein-protein interactions", Nature, 417:399-403, 2002.Link
- V. Schachter "Bioinformatics of large-scale protein interaction networks", BioTechniques Computational Proteomics Supplement, 32:S16-S27, 2002.Link
- A.-C. Gavin et al. "Functional organization of the yeast proteome by systematic analysis of protein complexes", Nature, 415:141-147, 2002.Link
- S. S. Shen-Orr et al. "Network motifs in the transcriptional regulation network of Escherichia coli", Nature Genetics, 31:64-68, 2002.Link
- D. Hanisch et al. "Co-clustering of biological networks and gene expression data", Bioinformatics ISMB 2002 Supplement, 18(S1):S145-S154, 2002.Link
- S. M. Gomez and A. Rzhetsky "Towards the prediction of complete protein-protein interaction networks", Pacific Symposium on Biocomputing, 7:413-424, 2002.Link
- L. R. Matthews et al. "Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or Interologs", Geneme Research, 11(12):2120-2126, 2001.Link
- A. J. M. Walhout and M. Vidal "Protein interaction maps for model organisms", Nature Reviews Molecular Cell Biology, 2(1):55-62, 2001.Link
- P. Uetz et al. "A Comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae", Nature, 403:623-627, 2000.Link
- M. C. Gustin et al. "MAP Kinase Pathways in the Yeast Saccharomyces cerevisiae", Microbiol. Mol. Biol. Rev., 62:1264-1300, 1998.Link