Papers on Protein Networks

  List of papers in reverse chronological order:      (Updated 08/01/2005 05:33PM)
  1. Y. Liu et al. "Inferring protein-protein interactions through high-throughput interaction data from diverse organisms", Bioinformatics, 21(15):3279-3285, 2005.Link
  2. D. Barker and M. Pagel "Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes", PLoS Computational Biology, 1(1):e3, 2005.Link
  3. Sharan et al. "Conserved patterns of protein interaction in multiple species", PNAS vol. 102, February 8, 2005.Link
  4. Yamanishi et al. "Supervised enzyme network inference from the integration of genomic data and chemical information", ISMB, 2005.Link
  5. Nabieva et al. "Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps", ISMB, 2005.Link
  6. Hu et al. "Mining coherent dense subgraphs across massive biological networks for functional discovery", ISMB, 2005.Link
  7. Jothi et al. "Predicting protein-protein interaction by searching evolutionary tree automorphism space", ISMB, 2005.Link
  8. Borgwardt et al. "Protein function prediction via graph kernels", ISMB, 2005.Link
  9. A. Ben-Hur and W. S. Noble "Kernel methods for predicting protein-protein interactions", ISMB, 2005.Link
  10. A. Jaimovich et al. "Towards an integrated protein-protein interaction network", RECOMB, 2005.Link
  11. J. Scott et al. "Efficient algorithms for detecting signaling pathways in protein interaction networks", RECOMB, 2005.Link
  12. M. Middendorf et al. "Inferring network mechanisms: The Drosophila melanogaster protein interaction network", Proc. Natl. Acad. Sci. USA, 102(9):3192-3197, 2005.Link
  13. 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
  14. P. M. Bowers et al. "Use of logic relationships to decipher protein network organization", Science, 306:2246-2249, 2004.Link
  15. I. Lee et al. "A Probabilistic functional network of yeast genes", Science, 306:1555-1558, 2004.Link
  16. A. D. King et al. "Protein complex prediction via cost-based clustering", Bioinformatics, 20(17):3013-3020, 2004.Link
  17. S. Li et al. "A Map of the interactome network of the metazoan C. elegans", Science, 303:540-543, 2004.Link
  18. I. Pournara and L. Wernisch "Reconstruction of gene networks using Bayesian learning and manipulation experiments", Bioinformatics, 20(17):2934-2942, 2004.Link
  19. X. Zhou et al. "A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks", Bioinformatics, 20(17):2918-2927, 2004.Link
  20. P. Bork et al. "Protein interaction networks from yeast to human", Current Opinion in Structural Biology, 14(3):292-299, 2004.Link
  21. F. Sohler et al. "New methods for joint analysis of biological networks and expression data", Bioinformatics, 20(10):1517-1521, 2004.Link
  22. Y. Yamanishi et al. "Protein network inference from multiple genomic data: a supervised approach", Bioinformatics ISMB 2004 Supplement, 20(S1):i363-i370, 2004.Link
  23. K. Tsuda and W. S. Noble "Learning kernels from biological networks by maximizing entropy", Bioinformatics ISMB 2004 Supplement, 20(S1):i326-i333, 2004.Link
  24. C. A. Stanyon et al. "A Drosophila protein-interaction map centered on cell-cycle regulators", Genome Biology, 5(12):R96, 2004.Link
  25. S. Asthana et al. "Predicting protein complex membership using probabilistic network reliability", Genome Research, 14(6):1170-1175, 2004.Link
  26. I. Iossifov et al. "Probabilistic inference of molecular networks from noisy data sources", Bioinformatics, 20(8):1205-1213, 2004.Link
  27. P. M. Bowers et al. "Prolinks: a database of protein functional linkages derived from coevolution", Genome Biology, 5(5):R35, 2004.Link
  28. L. Giot et al. "A Protein interaction map of Drosophila melanogaster", Science, 302:1727-1736, 2003.Link
  29. R. Jansen et al. "A Bayesian networks approach for predicting protein-protein interactions from genomic data", Science, 302:449-453, 2003.Link
  30. C. von Mering et al. "STRING: a database of predicted functional associations between proteins", Nucleic Acids Research, 31(1):258-261, 2003.Link
  31. V. Spirin and L. A. Mirny "Protein complexes and functional modules in molecular networks", Proc. Natl. Acad. Sci. USA, 100:12123-12128, 2003.Link
  32. 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
  33. 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
  34. J. S. Bader "Greedily building protein networks with confidence", Bioinformatics, 19(15):1869-1874, 2003.Link
  35. M. A. Huynen et al. "Function prediction and protein networks", Current Opinion in Cell Biology, 15(2):191-198, 2003.Link
  36. E. Segal et al. "Discovering molecular pathways from protein interaction and gene expression data", Bioinformatics ISMB 2003 Supplement, 19(S1):i264-i272, 2003.Link
  37. 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
  38. 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
  39. J. P. Vert and M. Kanehisa "Extracting active pathways from gene expression data", Bioinformatics ECCB 2003 Supplement, 19(S2):ii238-ii244, 2003.Link
  40. J. R. Bock and D. A. Gough "Whole-proteome interaction mining", Bioinformatics, 19(1):125:134, 2003.Link
  41. 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
  42. J. C. Mellor et al. "Predictome: a database of putative functional links between proteins", Nucleic Acids Research, 30(1):306-309, 2002.Link
  43. C. von Mering et al. "Comparative assessment of large-scale data sets of protein-protein interactions", Nature, 417:399-403, 2002.Link
  44. V. Schachter "Bioinformatics of large-scale protein interaction networks", BioTechniques Computational Proteomics Supplement, 32:S16-S27, 2002.Link
  45. A.-C. Gavin et al. "Functional organization of the yeast proteome by systematic analysis of protein complexes", Nature, 415:141-147, 2002.Link
  46. S. S. Shen-Orr et al. "Network motifs in the transcriptional regulation network of Escherichia coli", Nature Genetics, 31:64-68, 2002.Link
  47. D. Hanisch et al. "Co-clustering of biological networks and gene expression data", Bioinformatics ISMB 2002 Supplement, 18(S1):S145-S154, 2002.Link
  48. S. M. Gomez and A. Rzhetsky "Towards the prediction of complete protein-protein interaction networks", Pacific Symposium on Biocomputing, 7:413-424, 2002.Link
  49. 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
  50. A. J. M. Walhout and M. Vidal "Protein interaction maps for model organisms", Nature Reviews Molecular Cell Biology, 2(1):55-62, 2001.Link
  51. P. Uetz et al. "A Comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae", Nature, 403:623-627, 2000.Link
  52. M. C. Gustin et al. "MAP Kinase Pathways in the Yeast Saccharomyces cerevisiae", Microbiol. Mol. Biol. Rev., 62:1264-1300, 1998.Link