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Volumn 13, Issue 2, 2016, Pages 301-314

BLARS: An Algorithm to Infer Gene Regulatory Networks

Author keywords

DREAM challenge; Gene regulatory network; regression; reverse engineering algorithms

Indexed keywords

BIOLOGY; ESCHERICHIA COLI; GENE EXPRESSION; GENES; INFERENCE ENGINES; REGRESSION ANALYSIS; REVERSE ENGINEERING; TRANSCRIPTION;

EID: 84963831376     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2015.2450740     Document Type: Article
Times cited : (24)

References (39)
  • 1
    • 84870305264 scopus 로고    scopus 로고
    • Wisdom of crowds for robust gene network inference
    • D. Marbach, C. Costello James, R. Küffner, et al. "Wisdom of crowds for robust gene network inference, " Nature Methods, vol. 9, no. 8, pp. 796-804, 2012.
    • (2012) Nature Methods , vol.9 , Issue.8 , pp. 796-804
    • Marbach, D.1    Costello James, C.2    Küffner, R.3
  • 2
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Jan.
    • J. Faith Jeremiah, B. Hayete, T. Thaden Joshua, et al. "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles, " PLoS Biol., vol. 5, no. 1, p. e8, Jan. 2007.
    • (2007) PLoS Biol. , vol.5 , Issue.1 , pp. e8
    • Faith Jeremiah, J.1    Hayete, B.2    Thaden Joshua, T.3
  • 3
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • Jan.
    • A. Margolin, I. Nemenman, K. Basso, et al. "ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context, " BMC Bioinformatics, vol. 7, p. S7, Jan. 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. S7
    • Margolin, A.1    Nemenman, I.2    Basso, K.3
  • 4
    • 84869882656 scopus 로고    scopus 로고
    • TIGRESS: Trustful inference of gene REgulation using stability selection
    • A.-C. Haury, F. Mordelet, P. Vera-Licona, and J.-P. Vert, "TIGRESS: Trustful inference of gene REgulation using stability selection, " BMC Syst. Biol., vol. 6, no. 1, p. 145, 2012.
    • (2012) BMC Syst. Biol. , vol.6 , Issue.1 , pp. 145
    • Haury, A.-C.1    Mordelet, F.2    Vera-Licona, P.3    Vert, J.-P.4
  • 5
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Jan.
    • N. Friedman, M. Linial, I. Nachman, and D. Pe'er, "Using Bayesian networks to analyze expression data, " J. Comput. Biol., vol. 7, no. 3/4, pp. 601-20, Jan. 2000.
    • (2000) J. Comput. Biol. , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'Er, D.4
  • 6
    • 0033258311 scopus 로고    scopus 로고
    • Unsupervised knowledge discovery in medical databases using relevance networks
    • Jan.
    • J. Butte Atul and I. S. Kohane, "Unsupervised knowledge discovery in medical databases using relevance networks, " in Proc. AMIA Symp., Jan. 1999, pp. 711-715.
    • (1999) Proc. AMIA Symp. , pp. 711-715
    • Butte Atul, J.1    Kohane, I.S.2
  • 7
    • 77958570788 scopus 로고    scopus 로고
    • Inferring regulatory networks from expression data using Tree-based methods
    • Jan.
    • Van Anh Huynh-Thu, A. Irrthum, L. Wehenkel, and P. Geurts, "Inferring regulatory networks from expression data using Tree-based methods, " PloS One, vol. 5, no. 9, pp. 1-10, Jan. 2010.
    • (2010) PloS One , vol.5 , Issue.9 , pp. 1-10
    • Van Anh Huynh-Thu, A.1    Irrthum, A.2    Wehenkel, L.3    Geurts, P.4
  • 10
    • 84963841018 scopus 로고    scopus 로고
    • Data available to download [Online]
    • DREAM5. (2010). DREAM5 challenge website. Data available to download [Online]. Available: http://wiki.c2b2.columbia.edu/ dream/index.php?title=D5c4
    • (2010) DREAM5 Challenge Website
    • DREAM51
  • 13
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene Co-expression network analysis
    • B. Zhang and S. Horvath, "A general framework for weighted gene Co-expression network analysis, " Statistical Appl. Genetics Molecular Biol., vol. 4, no. 1, pp. 1-45, 2005.
    • (2005) Statistical Appl. Genetics Molecular Biol. , vol.4 , Issue.1 , pp. 1-45
    • Zhang, B.1    Horvath, S.2
  • 14
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Jan.
    • P. Langfelder and S. Horvath, "WGCNA: An R package for weighted correlation network analysis, " BMC Bioinformat., vol. 9, no. 1, p. 559, Jan. 2008.
    • (2008) BMC Bioinformat. , vol.9 , Issue.1 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 15
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
    • Jan.
    • A. J. Butte and I. S. Kohane, "Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements, " in Proc. Pacific Symp. Biocomput., Jan. 2000, pp. 418-429.
    • (2000) Proc. Pacific Symp. Biocomput. , pp. 418-429
    • Butte, A.J.1    Kohane, I.S.2
  • 16
    • 12344259602 scopus 로고    scopus 로고
    • Advances to Bayesian network inference for generating causal networks from observational biological data
    • Dec.
    • J. Yu, V. Anne Smith, P. W. Paul, J. H. Alexander, and D. J. Erich, "Advances to Bayesian network inference for generating causal networks from observational biological data, " Bioinformatics, vol. 20, no. 18, pp. 3594-603, Dec. 2004.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3594-3603
    • Yu, J.1    Anne Smith, V.2    Paul, P.W.3    Alexander, J.H.4    Erich, D.J.5
  • 17
    • 0004188848 scopus 로고    scopus 로고
    • Wiley Series in Telecommunications and Signal Processing. New York, NY, USA: Wiley
    • M. C. Thomas and A. T. Joy, Elements of Information Theory (Wiley Series in Telecommunications and Signal Processing. New York, NY, USA: Wiley 2006.
    • (2006) Elements of Information Theory
    • Thomas, M.C.1    Joy, A.T.2
  • 19
    • 32544457104 scopus 로고    scopus 로고
    • Least absolute regression network analysis of the murine osteoblast differentiation network
    • Feb.
    • E P V. Someren, B L T. Vaes, W T. Steegenga, et al. "Least absolute regression network analysis of the murine osteoblast differentiation network, " Bioinformatics, vol. 22, no.4, pp. 477-84, Feb. 2006.
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 477-484
    • Someren, E.P.V.1    Vaes, B.L.T.2    Steegenga, W.T.3
  • 20
    • 84869390828 scopus 로고    scopus 로고
    • ADANET: Inferring gene regulatory networks using ensemble classifiers
    • New York, NY, USA
    • J. Slawek and T. Arodź, "ADANET: Inferring gene regulatory networks using ensemble classifiers, " in Proc. ACM Conf. Bioinformat., Comput. Biol. Biomed., New York, NY, USA, 2012, pp. 434-441.
    • (2012) Proc. ACM Conf. Bioinformat., Comput. Biol. Biomed. , pp. 434-441
    • Slawek, J.1    Arodź, T.2
  • 21
    • 84871752758 scopus 로고    scopus 로고
    • NARROMI: A noise and redundancy reduction technique improves accuracy of gene regulatory network inference
    • Jan.
    • X. Zhang, K. Liu, Z.-P. Liu, et al. "NARROMI: A noise and redundancy reduction technique improves accuracy of gene regulatory network inference, " Bioinformatics, vol. 29, no. 1, pp. 106-13, Jan. 2013.
    • (2013) Bioinformatics , vol.29 , Issue.1 , pp. 106-113
    • Zhang, X.1    Liu, K.2    Liu, Z.-P.3
  • 23
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • Oct.
    • G. Karlebach and R. Shamir, "Modelling and analysis of gene regulatory networks, " Nature Rev. Molecular Cell Biol., vol. 9, no. 10, pp. 770-80, Oct. 2008.
    • (2008) Nature Rev. Molecular Cell Biol. , vol.9 , Issue.10 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 24
    • 84899971737 scopus 로고    scopus 로고
    • Fast Bayesian inference for gene regulatory networks using ScanBMA
    • Apr.
    • C. Y. William, E. R. Adrian, and Y. Y. Ka, "Fast Bayesian inference for gene regulatory networks using ScanBMA, " BMC Syst. Biol., vol. 8, no. 1, p. 47, Apr. 2014.
    • (2014) BMC Syst. Biol. , vol.8 , Issue.1 , pp. 47
    • William, C.Y.1    Adrian, E.R.2    Ka, Y.Y.3
  • 25
    • 33645307955 scopus 로고    scopus 로고
    • Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
    • Apr.
    • M. Bansal, G. Della Gatta, and D. di Bernardo, "Inference of gene regulatory networks and compound mode of action from time course gene expression profiles, " Bioinformatics, vol. 22, no. 7, pp. 815-822, Apr. 2006.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 815-822
    • Bansal, M.1    Della Gatta, G.2    Di Bernardo, D.3
  • 26
    • 84929612020 scopus 로고    scopus 로고
    • Combining tree-based and dynamical systems for the inference of gene regulatory networks
    • V. A. Huynh-Thu and G. Sanguinetti, "Combining tree-based and dynamical systems for the inference of gene regulatory networks, " Bioinformatics, vol. 31, no. 10, pp. 1614-1622, 2015.
    • (2015) Bioinformatics , vol.31 , Issue.10 , pp. 1614-1622
    • Huynh-Thu, V.A.1    Sanguinetti, G.2
  • 27
    • 14844286390 scopus 로고    scopus 로고
    • Reverse-engineering transcription control networks
    • Mar.
    • S. G. Timothy and J. F. Jeremiah, "Reverse-engineering transcription control networks, " Phys. Life Rev., vol. 2, no. 1, pp. 65-88, Mar. 2005.
    • (2005) Phys. Life Rev. , vol.2 , Issue.1 , pp. 65-88
    • Timothy, S.G.1    Jeremiah, J.F.2
  • 28
    • 67649826220 scopus 로고    scopus 로고
    • From DNA sequence to transcriptional behaviour: A quantitative approach
    • Jul.
    • E. Segal and J. Widom, "From DNA sequence to transcriptional behaviour: A quantitative approach, " Nature Rev. Genetics, vol. 10, no. 7, pp. 443-56, Jul. 2009.
    • (2009) Nature Rev. Genetics , vol.10 , Issue.7 , pp. 443-456
    • Segal, E.1    Widom, J.2
  • 36
    • 79961200389 scopus 로고    scopus 로고
    • GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods
    • T. Schaffter, D. Marbach, and D. Floreano, "GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods, " Bioinformatics, vol. 27, no. 16, pp. 2263-2270, 2011.
    • (2011) Bioinformatics , vol.27 , Issue.16 , pp. 2263-2270
    • Schaffter, T.1    Marbach, D.2    Floreano, D.3
  • 38
    • 84887084951 scopus 로고    scopus 로고
    • Network-based stratification of tumor mutations
    • Nov.
    • M. Hofree, P. S. John, H. Carter, A. Gross, and T. Ideker, "Network-based stratification of tumor mutations, " Nature Methods, vol. 10, no. 11, pp. 1108-15, Nov. 2013.
    • (2013) Nature Methods , vol.10 , Issue.11 , pp. 1108-1115
    • Hofree, M.1    John, P.S.2    Carter, H.3    Gross, A.4    Ideker, T.5
  • 39
    • 52249116064 scopus 로고    scopus 로고
    • Necessary and sufficient conditions for dynamical structure structure reconstruction of LTI networks
    • Aug.
    • J. Gonccalves and S. Warnick, "Necessary and sufficient conditions for dynamical structure structure reconstruction of LTI networks, " IEEE Trans. Automat. Control, vol. 53, no. 7, pp. 1670-1674, Aug. 2008.
    • (2008) IEEE Trans. Automat. Control , vol.53 , Issue.7 , pp. 1670-1674
    • Gonccalves, J.1    Warnick, S.2


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