메뉴 건너뛰기




Volumn 28, Issue 12, 2012, Pages

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY; THEORETICAL MODEL;

EID: 84863506443     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts212     Document Type: Article
Times cited : (39)

References (31)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology
    • Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet., 25, 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 2
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • Bader, J.S. et al. (2004) Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol., 22, 78-85.
    • (2004) Nat Biotechnol , vol.22 , pp. 78-85
    • Bader, J.S.1
  • 3
    • 36849004088 scopus 로고    scopus 로고
    • Pathfinder: mining signal transduction pathway segments from protein-protein interaction networks
    • Bebek, G. and Yang, J. (2007) Pathfinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics, 8, 335.
    • (2007) BMC Bioinformatics , vol.8 , pp. 335
    • Bebek, G.1    Yang, J.2
  • 4
    • 33745620176 scopus 로고    scopus 로고
    • Integrated Assessment and Prediction of Transcription Factor Binding
    • Beyer, A. et al. (2006) Integrated Assessment and Prediction of Transcription Factor Binding. PLoS Comput Biol., 2, e70.
    • (2006) PLoS Comput Biol. , vol.2
    • Beyer, A.1
  • 5
    • 67650572770 scopus 로고    scopus 로고
    • The protein phosphatase 2a functions in the spindle position checkpoint by regulating the checkpoint kinase kin4
    • Chan, L. and Amon, A. (2009) The protein phosphatase 2a functions in the spindle position checkpoint by regulating the checkpoint kinase kin4. Genes Dev., 23, 1639-1649.
    • (2009) Genes Dev. , vol.23 , pp. 1639-1649
    • Chan, L.1    Amon, A.2
  • 7
    • 38849147181 scopus 로고    scopus 로고
    • Large scale statistical inference of signaling pathways from rnai and microarray data
    • Froehlich, H. et al. (2007) Large scale statistical inference of signaling pathways from rnai and microarray data. BMC Bioinformatics, 8, 386.
    • (2007) BMC Bioinformatics , vol.8 , pp. 386
    • Froehlich, H.1
  • 8
    • 78651271301 scopus 로고    scopus 로고
    • Fast top-k simple shortest paths discovery in graphs
    • Gao, J. et al. (2010) Fast top-k simple shortest paths discovery in graphs. In CIKM, pp. 509-518.
    • (2010) CIKM , pp. 509-518
    • Gao, J.1
  • 9
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • Hahn, M.W. and Kern, A.D. (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol., 22, 803.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 803
    • Hahn, M.W.1    Kern, A.D.2
  • 10
    • 3042848952 scopus 로고    scopus 로고
    • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    • Han, J.D.J., et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93.
    • (2004) Nature , vol.430 , pp. 88-93
    • Han, J.D.J.1
  • 11
    • 0041848443 scopus 로고    scopus 로고
    • Topic-sensitive pagerank: A context-sensitive ranking algorithm for web search
    • Haveliwala, T.H. (2003) Topic-sensitive pagerank: A context-sensitive ranking algorithm for web search. IEEE Transactions on Knowledge and Data Engineering, 15, 784-796.
    • (2003) IEEE Transactions on Knowledge and Data Engineering , vol.15 , pp. 784-796
    • Haveliwala, T.H.1
  • 12
    • 36448972779 scopus 로고    scopus 로고
    • Finding the k shortest simple paths: A new algorithm and its implementation
    • Hershberger, J. et al. (2007) Finding the k shortest simple paths: A new algorithm and its implementation. TALG, 3, 45.
    • (2007) TALG , vol.3 , pp. 45
    • Hershberger, J.1
  • 13
    • 0034616930 scopus 로고    scopus 로고
    • Functional discovery via a compendium of expression profiles
    • Hughes, T.R. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
    • (2000) Cell , vol.102 , pp. 109-126
    • Hughes, T.R.1
  • 14
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H. et al. (2001) Lethality and centrality in protein networks. Nature, 411, 41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1
  • 15
    • 43149087837 scopus 로고    scopus 로고
    • Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast
    • Jin, G. et al. (2007) Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS One, 2, e1207.
    • (2007) PLoS One , vol.2
    • Jin, G.1
  • 16
    • 79957792202 scopus 로고    scopus 로고
    • A continuous query system for dynamic route planning
    • Malviya, N. et al. (2011) A continuous query system for dynamic route planning. In ICDE, pp. 792-803.
    • (2011) ICDE , pp. 792-803
    • Malviya, N.1
  • 17
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein- protein interactions
    • Mering, C.V. et al. (2002) Comparative assessment of large-scale data sets of protein- protein interactions. Nature, 417, 399-404.
    • (2002) Nature , vol.417 , pp. 399-404
    • Mering, C.V.1
  • 18
    • 66249092826 scopus 로고    scopus 로고
    • Information flow analysis of interactome networks
    • Missiuro, P.V. et al. (2009) Information flow analysis of interactome networks. PLoS Comput Biol, 5, e1000350.
    • (2009) PLoS Comput Biol , vol.5
    • Missiuro, P.V.1
  • 19
    • 33745957596 scopus 로고    scopus 로고
    • Inferring protein-protein interactions using interaction network topologies
    • Paccanaro, A. et al. (2005) Inferring protein-protein interactions using interaction network topologies. In IJCNN, 1, 161-166.
    • (2005) IJCNN , vol.1 , pp. 161-166
    • Paccanaro, A.1
  • 20
    • 33646819227 scopus 로고    scopus 로고
    • Protein phosphatase 2a protects centromeric sister chromatid cohesion during meiosis i
    • Riedel, C. et al. (2006) Protein phosphatase 2a protects centromeric sister chromatid cohesion during meiosis i. Nature, 441, 53-61.
    • (2006) Nature , vol.441 , pp. 53-61
    • Riedel, C.1
  • 21
    • 33645983211 scopus 로고    scopus 로고
    • Efficient algorithms for detecting signaling pathways in protein interaction networks
    • Scott, J. et al. (2006) Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput. Biol., 13, 133-144.
    • (2006) J Comput. Biol. , vol.13 , pp. 133-144
    • Scott, J.1
  • 22
    • 33644873184 scopus 로고    scopus 로고
    • Biogrid: a general repository for interaction datasets
    • Stark, C. et al. (2006) Biogrid: a general repository for interaction datasets. Nucl. Acids Res., 34(Suppl_1), D535-539.
    • (2006) Nucl. Acids Res. , vol.34 , Issue.SUPPL. 1
    • Stark, C.1
  • 23
    • 69849111694 scopus 로고    scopus 로고
    • ITM probe: analyzing information flow in protein networks
    • Stojmirovíc, A. and Yu, Y. (2009) ITM probe: analyzing information flow in protein networks. Bioinformatics, 25, 2447.
    • (2009) Bioinformatics , vol.25 , pp. 2447
    • Stojmirovíc, A.1    Yu, Y.2
  • 24
    • 77958501842 scopus 로고    scopus 로고
    • Robust and accurate data enrichment statistics via distribution function of sum of weights
    • Stojmirovíc, A. and Yu, Y. (2010) Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics, 26, 2752.
    • (2010) Bioinformatics , vol.26 , pp. 2752
    • Stojmirovíc, A.1    Yu, Y.2
  • 25
    • 84874106110 scopus 로고    scopus 로고
    • Information flow in interaction networks II: channels, path lengths and potentials
    • 0901. 0287 (v3)
    • Stojmirovíc, A. and Yu, Y. (2011) Information flow in interaction networks II: channels, path lengths and potentials. ArXiv e-prints, (0901.0287 (v3)).
    • (2011) ArXiv e-prints
    • Stojmirovíc, A.1    Yu, Y.2
  • 26
    • 42949096140 scopus 로고    scopus 로고
    • eQED: an efficient method for interpreting eqtl associations using protein networks
    • Suthram, S. et al. (2008) eQED: an efficient method for interpreting eqtl associations using protein networks. Mol. Syst. Biol., 4, 162.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 162
    • Suthram, S.1
  • 27
    • 33747880011 scopus 로고    scopus 로고
    • An integrative approach for causal gene identification and gene regulatory pathway inference
    • Tu, Z. et al. (2006) An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics, 22, 489-496.
    • (2006) Bioinformatics , vol.22 , pp. 489-496
    • Tu, Z.1
  • 28
    • 59149106558 scopus 로고    scopus 로고
    • A factor graph nested effects model to identify networks from genetic perturbations
    • Vaske, C.J. et al. (2009) A factor graph nested effects model to identify networks from genetic perturbations. PLoS Comput Biol, 5, e1000274.
    • (2009) PLoS Comput Biol , vol.5
    • Vaske, C.J.1
  • 29
    • 73249127005 scopus 로고    scopus 로고
    • Spectral affinity in protein networks
    • Voevodski, K. et al. (2009) Spectral affinity in protein networks. BMC Syst. Biol., 3, 112.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 112
    • Voevodski, K.1
  • 30
    • 0035846951 scopus 로고    scopus 로고
    • Carboxymethylation of the pp2a catalytic subunit insaccharomyces cerevisiae is required for efficient interaction with the b-type subunits cdc55p and rts1p
    • Wei, H. et al. (2001) Carboxymethylation of the pp2a catalytic subunit insaccharomyces cerevisiae is required for efficient interaction with the b-type subunits cdc55p and rts1p. J. Biol. Chem., 276, 1570-1577.
    • (2001) J. Biol. Chem. , vol.276 , pp. 1570-1577
    • Wei, H.1
  • 31
    • 0000663732 scopus 로고
    • Finding the k shortest loopless paths in a network
    • Yen, J.Y. (1971) Finding the k shortest loopless paths in a network. Management Science, 17, 712-716.
    • (1971) Management Science , vol.17 , pp. 712-716
    • Yen, J.Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.