CMSC 858L: Relevant Papers

  1. Zhu, Gerstein, Snyder. Getting connected: analysis and principles of biological networks , Genes Dev 21:1010-1024, 2007.
  2. Shoemaker and Panchenko. Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases , PLoS Comp. Biol. 3(3):e42, 2007.
  3. Li et al. A Map of the Interactome Network of the Metazoan C. elegans, Science 303(5657):540-543, 2004.
  4. Giot et al. A Protein Interaction Map of Drosophila melanogaster, 302(5651):1727-1736, 2003.
  5. Bauer and Kuster. Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes, Eur J Biochem 270(4):570-578, 2003.
  6. Hartwell, Hopfield, Leibler, Murray. From molecular to modular cell biology, Nature 402(6761), 1999.
  7. Yu et al. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network, Science, 2008.
  8. Sharan, Ulitsky, Shamir. Network-based prediction of protein function, Mol. Syst. Biol. 3, 2007.
  9. Vazquez, Flammini, Maritan, Vespignani. Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 21:697-700, 2003.
  10. Nabieva, Jim, Agarwal, Chazelle, Singh. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21(Suppl 1):i302-10, 2005.
  11. Newman. Modularity and community structure in networks, Proc. Natl. Acad Sci USA 103:8577-8582, 2006.
  12. Navlakha, White, Nagarajan, Pop, Kingsford. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. RECOMB 2009.
  13. Navlakha, Schatz, Kingsford. Revealing Biological Modules via Graph Summarization. J Comp. Biol. 16(2), 2009.
  14. Newman, Girvan. Finding and evaluating community structure in networks Phys. Rev. E, 69, 2004.
  15. Spirin and Mirny. Protein complexes and functional modules in molecular networks. Proc. Natl Acad. Sci. USA 100:12123-12128, 2003.
  16. Karaoz, Murali, Letovsky, Zheng, Ding, Cantor, Kasif. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc. Natl Acad. Sci. USA 101:2888-2893, 2004.
  17. Bader and Hogue. An automated method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 4, 2003.
  18. MCL - a cluster algorithm for graphs
  19. Kelley, Sharan, Karp, Sittler, Root, Stockwell, Ideker. Conserved pathways within bacteria and yeast as revealed by global protein network alignment, Proc. Natl. Acad. Sci. USA 100:11394-11399, 2003.
  20. Bandyopadhyay, Sharan, Ideker. Systematic identification of functional orthologs based on protein network comparison, Genome Res. 16:428-435, 2006.
  21. Scott, Ideker, Karp, Sharan. Efficient algorithms for detecting signaling pathways in protein interaction networks, RECOMB 2005.
  22. Flannick, Novak, Srinivasan, McAdams, Batzoglou. Graemlin: General and Robust Alignment of Multiple Large Interaction Networks, Genome Res, 16:1169-1181, 2006.
  23. Sharan and Ideker. Modeling cellular machinery through biological network comparison, Nat. Biotechnol. 24(4):427-433, 2006.
  24. Dost, Shlomi, Gupta, Ruppin, Bafna, Sharan. QNet: A tool for querying protein interaction networks, RECOMB 2007.
  25. Pinter, Rokhlenko, Yeger-Lotem, Ziv-Ukelson. Alignment of metabolic pathways. Bioinformatics 21(16):3401-3408, 2005.
  26. Banks, Nabieva, Peterson, Singh. NetGrep: fast network schema searches in interactomes Genome Biol. 9:R138, 2008.
  27. Milo, Shen-Orr, Itzkovitz, Kashtan, Chklovskii, Alon. Network motifs: simple building blocks of complex networks. Science 298:824-827, 2002.
  28. Grochow and Kellis. Network motif discovery using subgraph enumeration and symmetry-breaking. RECOMB 2007.
  29. Luscombe, Madan Babu, Yu, Snyder, Teichmann, Gerstein. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308-312, 2004.
  30. Sporns, Tononi, Kötter. The Human Connectome: A Structural Description of the Human Brain, PLoS Comp. Biol. 1(4):e42, 2005.
  31. Kiebel, Daunizeau, Friston. A Hierarchy of Time-Scales and the Brain, PLoS Comp. Biol. 4:e1000209, 2008.
  32. Kingsford, Chazelle, Singh. Solving and analyzing side-chain positioning problems using linear and integer programming Bioinformatics 21:1028-1036, 2004.
  33. Chazelle, Kingsford, Singh. A semidefinite programming approach to side-chain positioning with new rounding strategies INFORMS J Comput. 16:380-392, 2004.
  34. Nagarajan and Kingsford. Uncovering Genomic Reassortments Among Influenza Strains by Enumerating Maximal Bicliques. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 2008.
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