Querying Large Biological Network Datasets.
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[1] Kenji Satou,et al. Finding conserved and non-conserved reactions using a metabolic pathway alignment algorithm. , 2006, Genome informatics. International Conference on Genome Informatics.
[2] Tamer Kahveci,et al. Functional similarities of reaction sets in metabolic pathways , 2010, BCB '10.
[3] Nitin Bhardwaj,et al. Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators , 2010, Science Signaling.
[4] Dennis Shasha,et al. GraphGrep: A fast and universal method for querying graphs , 2002, Object recognition supported by user interaction for service robots.
[5] An-Ping Zeng,et al. The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks , 2003, Bioinform..
[6] Eugene L. Lawler,et al. A Note on the Complexity of the Chromatic Number Problem , 1976, Inf. Process. Lett..
[7] Ambuj K. Singh,et al. Closure-Tree: An Index Structure for Graph Queries , 2006, 22nd International Conference on Data Engineering (ICDE'06).
[8] Tamer Kahveci,et al. Inferring gene functions from metabolic reactions , 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).
[9] Roded Sharan,et al. QNet: A Tool for Querying Protein Interaction Networks , 2007, RECOMB.
[10] D. Fell,et al. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.
[11] Mara L. Hartsperger,et al. HiNO: An Approach for Inferring Hierarchical Organization from Regulatory Networks , 2010, PloS one.
[12] Thomas Zichner,et al. Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection , 2008, Algorithmica.
[13] Sanjay Jain,et al. Low degree metabolites explain essential reactions and enhance modularity in biological networks , 2005, BMC Bioinformatics.
[14] Jignesh M. Patel,et al. SAGA: a subgraph matching tool for biological graphs , 2007, Bioinform..
[15] David S. Johnson,et al. Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .
[16] M. Gerstein,et al. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. , 2002, Genes & development.
[17] S. Schuster,et al. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. , 2009, Genome research.
[18] Ron Y. Pinter,et al. Alignment of metabolic pathways , 2005, Bioinform..
[19] M. Gerstein,et al. Genomic analysis of the hierarchical structure of regulatory networks , 2006, Proceedings of the National Academy of Sciences.
[20] Michael Q. Zhang,et al. TRED: a transcriptional regulatory element database, new entries and other development , 2007, Nucleic Acids Res..
[21] A. Barabasi,et al. Lethality and centrality in protein networks , 2001, Nature.
[22] Roded Sharan,et al. PathBLAST: a tool for alignment of protein interaction networks , 2004, Nucleic Acids Res..
[23] Robert W. Harrison,et al. MetNetAligner: a web service tool for metabolic network alignments , 2009, Bioinform..
[24] Ning Sun,et al. Bayesian error analysis model for reconstructing transcriptional regulatory networks. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[25] H. Kuhn. The Hungarian method for the assignment problem , 1955 .
[26] M. Gerstein,et al. Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels , 2010, Proceedings of the National Academy of Sciences.
[27] D. Green,et al. Mechanisms of p53-dependent apoptosis. , 2001, Biochemical Society transactions.
[28] Alexander Bockmayr,et al. Analysis of Metabolic Subnetworks by Flux Cone Projection , 2011, Algorithms for Molecular Biology.
[29] Bonnie Berger,et al. IsoRankN: spectral methods for global alignment of multiple protein networks , 2009, Bioinform..
[30] L. Aravind,et al. Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. , 2006, Journal of molecular biology.
[31] M. Gerstein,et al. Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.
[32] Bonnie Berger,et al. Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology , 2007, RECOMB.
[33] Y. Yarden,et al. Untangling the ErbB signalling network , 2001, Nature Reviews Molecular Cell Biology.
[34] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[35] C. Francke,et al. Reconstructing the metabolic network of a bacterium from its genome. , 2005, Trends in microbiology.
[36] Roded Sharan,et al. QPath: a method for querying pathways in a protein-protein interaction network , 2006, BMC Bioinformatics.
[37] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[38] Jörg Raisch,et al. Subnetwork analysis reveals dynamic features of complex (bio)chemical networks , 2007, Proceedings of the National Academy of Sciences.
[39] Bonnie Berger,et al. Local Optimization for Global Alignment of Protein Interaction Networks , 2010, Pacific Symposium on Biocomputing.
[40] Kenji Satou,et al. Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology. , 2005, Genome informatics. International Conference on Genome Informatics.
[41] Terrance G. Cooper,et al. Complilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae , 1995 .
[42] M Madan Babu,et al. Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. , 2006, Journal of molecular biology.
[43] Joshua A. Grochow,et al. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture , 2009, Molecular systems biology.
[44] Tamer Kahveci,et al. HIDEN: Hierarchical decomposition of regulatory networks , 2012, BMC Bioinformatics.
[45] Bernhard O. Palsson,et al. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions , 2010, BMC Bioinformatics.
[46] E O Voit,et al. Optimization in integrated biochemical systems , 1992, Biotechnology and bioengineering.
[47] S. Teichmann,et al. Gene regulatory network growth by duplication , 2004, Nature Genetics.
[48] Sanjay Ranka,et al. Identifying differentially regulated genes , 2011, 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).
[49] D. Latchman. Transcription factors: an overview. , 1997, The international journal of biochemistry & cell biology.
[50] Yan Lin,et al. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes , 2008, Nucleic Acids Res..
[51] M. Krasnow,et al. Cellular and Genetic Analysis of Wound Healing in Drosophila Larvae , 2004, PLoS biology.
[52] Tamer Kahveci,et al. Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring , 2012, J. Bioinform. Comput. Biol..
[53] E. Banks,et al. NetGrep: fast network schema searches in interactomes , 2008, Genome Biology.
[54] Nicola J. Rinaldi,et al. Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.
[55] Nicolò Riggi,et al. The Biology of Ewing sarcoma. , 2007, Cancer letters.
[56] Robin Sibson,et al. SLINK: An Optimally Efficient Algorithm for the Single-Link Cluster Method , 1973, Comput. J..
[57] Dennis Shasha,et al. NetMatch : a Cytoscape plugin for searching biological networks , 2006 .
[58] Bernhard O. Palsson,et al. Expa: a Program for Calculating Extreme Pathways in Biochemical Reaction Networks , 2005, Bioinform..
[59] Hideo Matsuda,et al. A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy , 2000, ISMB.
[60] H. Lane,et al. ERBB receptors and cancer: the complexity of targeted inhibitors , 2005, Nature Reviews Cancer.
[61] S. Schuster,et al. Metabolic network structure determines key aspects of functionality and regulation , 2002, Nature.
[62] Roded Sharan,et al. Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm , 2010, J. Bioinform. Comput. Biol..
[63] Tamer Kahveci,et al. Topology aware coloring of gene regulatory networks , 2011, BCB '11.
[64] R. Bellman. Dynamic programming. , 1957, Science.
[65] E. Davidson,et al. Gene regulatory networks for development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[66] Roded Sharan,et al. Torque: topology-free querying of protein interaction networks , 2009, Nucleic Acids Res..