Systems Biology (Methods in Molecular Biology)

18. Lee W-P, Tzou W-S (2009) Computational
    methods for discovering gene networks from
    expression data. Brief Bioinform 10:408–423


19. Zahiri J, Bozorgmehr JH, Masoudi-Nejad A
    (2013) Computational prediction of pro-
    tein–protein interaction networks: algo-
    rithms and resources. Curr Genomics
    14:397–414


20. Matsuoka Y, Matsumae H, Katoh M et al
    (2013) A comprehensive map of the influenza
    A virus replication cycle. BMC Syst Biol 7:97


21. Wu G, Zhu L, Dent JE et al (2010) A com-
    prehensive molecular interaction map for
    rheumatoid arthritis. PLoS One 5:e10137


22. Caron E, Ghosh S, Matsuoka Y et al (2010) A
    comprehensive map of the mTOR signaling
    network. Mol Syst Biol 6:453


23. Calzone L, Gelay A, Zinovyev A et al (2008)
    A comprehensive modular map of molecular
    interactions in RB/E2F pathway. Mol Syst
    Biol 4:173


24. Oda K, Matsuoka Y, Funahashi A et al (2005)
    A comprehensive pathway map of epidermal
    growth factor receptor signaling. Mol Syst
    Biol 1:2005.0010


25. Ritz A, Poirel CL, Tegge AN et al (2016)
    Pathways on demand: automated reconstruc-
    tion of human signaling networks. Syst Biol
    Appl 2:16002


26. Supper J, Spangenberg L, Planatscher H et al
    (2009) BowTieBuilder: modeling signal
    transduction pathways. BMC Syst Biol 3:67


27. Gursoy A, Keskin O, Nussinov R (2008)
    Topological properties of protein interaction
    networks from a structural perspective. Bio-
    chem Soc Trans 36:1398–1403


28. Zhang Z, Zhang J (2009) A big world inside
    small-world networks. PLoS One 4:e5686


29. Jeong H, Mason SP, Baraba ́si A-L et al (2001)
    Lethality and centrality in protein networks.
    Nature 411:41–42


30. Kotlyar M, Fortney K, Jurisica I (2012)
    Network-based characterization of drug-
    regulated genes, drug targets, and toxicity.
    Methods 57:499–507


31. Mitra K, Carvunis A-R, Ramesh SK et al
    (2013) Integrative approaches for finding
    modular structure in biological networks.
    Nat Rev Genet 14:719–732


32. Wang J, Lu M, Qiu C et al (2010) TransmiR:
    a transcription factor-microRNA regulation
    database. Nucleic Acids Res 38:D119–D122


33. Oti M, Brunner HG (2007) The modular
    nature of genetic diseases. Clin Genet 71:1–11


34. Yeger-Lotem E, Sattath S, Kashtan N et al
    (2004) Network motifs in integrated cellular

networks of transcription–regulation and pro-

tein–protein interaction. Proc Natl Acad Sci U

S A 101:5934–5939

35. Tyson JJ, Nova ́k B (2010) Functional motifs
    in biochemical reaction networks. Annu Rev
    Phys Chem 61:219–240


36. Zhang Y, Xuan J, de Los Reyes BG et al
    (2008) Network motif-based identification
    of breast cancer susceptibility genes. Confer-
    ence proceedings: annual international con-
    ference of the IEEE engineering in medicine
    and biology society. IEEE engineering in
    medicine and biology society annual confer-
    ence, 2008, pp 5696–5699


37. Wang X, Gulbahce N, Yu H (2011) Network-
    based methods for human disease gene pre-
    diction. Brief Funct Genomics 10:280–293


38. Baraba ́si A-L, Oltvai ZN (2004) Network
    biology: understanding the cell’s functional
    organization. Nat Rev Genet 5:101–113


39. Guebel DV, Schmitz U, Wolkenhauer O et al
    (2012) Analysis of cell adhesion during early
    stages of colon cancer based on an extended
    multi-valued logic approach. Mol BioSyst
    8:1230–1242


40. Voit EO (2016) The inner workings of life:
    vignettes in systems biology. Cambridge Uni-
    versity Press, Cambridge, NY


41. Bezrucˇko BP, Smirnov DA (2010) Extracting
    knowledge from time series: an introduction
    to nonlinear empirical modeling. Springer,
    New York, NY


42. Vera J, Gonza ́lez-Alco ́n C, Marı ́n-Sanguino A
    et al (2010) Optimization of biochemical sys-
    tems through mathematical programming:
    methods and applications. Comput Oper Res
    37:1427–1438


43. Tyson JJ, Chen KC, Novak B (2003) Sniffers,
    buzzers, toggles and blinkers: dynamics of
    regulatory and signaling pathways in the cell.
    Curr Opin Cell Biol 15:221–231


44. Zi Z, Klipp E (2007) Constraint-based mod-
    eling and kinetic analysis of the smad depen-
    dent TGF-βsignaling pathway. PLoS One 2:
    e936


45. Raia V, Schilling M, Bo ̈hm M et al (2011)
    Dynamic mathematical modeling of IL13-
    induced signaling in Hodgkin and primary
    mediastinal B-cell lymphoma allows predic-
    tion of therapeutic targets. Cancer Res
    71:693–704


46. Vera J, Schmitz U, Lai X et al (2013) Kinetic
    modeling-based detection of genetic signa-
    tures that provide chemoresistance via the
    E2F1-p73/DNp73-miR-205 network. Can-
    cer Res 73:3511–3524

Integrative Workflow for Predicting Disease Signatures 273