Computational Methods in Systems Biology

(Ann) #1
Abduction Based Drug Target Discovery Using Boolean Control Network 73


  1. Marquis, P.: Extending abduction from propositional to first-order logic. In: Jor-
    rand, P., Kelemen, J. (eds.) FAIR 1991. LNCS, vol. 535, pp. 141–155. Springer,
    Heidelberg (1991). doi:10.1007/3-540-54507-7 12

  2. Murrugarra, D., Veliz-Cuba, A., Aguilar, B., Laubenbacher, R.: Identification of
    control targets in boolean molecular network models via computational algebra.
    BMC Syst. Biol. 10 (1), 94 (2016)

  3. Narod, S.A., Foulkes, W.D.: BRCA1 and BRCA2: 1994 and beyond. Nat. Rev. —
    Cancer 4 (9), 665–676 (2004)

  4. Peirce, C.S.: On the natural classification of arguments. Proc. Am. Acad. Arts Sci.
    7 , 261–287 (1867)

  5. Perfetto, L., Briganti, L., Calderone, A., Perpetuini, A.C., Iannuccelli, M., Lan-
    gone, F., Licata, L., Marinkovic, M., Mattioni, A., Pavlidou, T., Peluso, D., Petrilli,
    L.L., Pirro, S., Posca, D., Santonico, E., Silvestri, A., Spada, F., Castagnoli, L.,
    Cesareni, G.: SIGNOR: a database of causal relationships between biological enti-
    ties. Nucl. Acids Res. 44 (D1), D548–D554 (2016)

  6. Phillips, P.C.: Epistasis - the essential role of gene interactions in the structure
    and evolution of genetic systems. Nat. Rev. Genetics 9 (11), 855–867 (2008)

  7. Pizzuti, C.: Computing prime implicants by integer programming. In: Proceedings
    Eighth IEEE International Conference on Tools with Artificial Intelligence, pp.
    332–336. IEEE Computer Society Press (1996)

  8. Quine, W.V.: On cores and prime implicants of truth functions. Am. Math. Mon.
    66 (9), 755–760 (1959)

  9. Spiliotaki, M., Mavroudis, D., Kapranou, K., Markomanolaki, H., Kallergi, G.,
    Koinis, F., Kalbakis, K., Georgoulias, V., Agelaki, S.: Evaluation of proliferation
    and apoptosis markers in circulating tumor cells of women with early breast cancer
    who are candidates for tumor dormancy. Breast Cancer Res. 16 (6), 485 (2014)

  10. Strimbu, K., Tavel, J.A.: What are biomarkers? Curr. Opin. HIV AIDS 5 (6), 463–
    466 (2011)

  11. Vidal, M.: A unifying view of 21st century systems biology. FEBS Lett. 583 (24),
    3891–3894 (2009)

  12. Vidal, M., Cusick, M.E., Barab ́asi, A.-L.: Interactome networks and human disease.
    Cell 144 (6), 986–998 (2011)

  13. Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S., Diaz, L.A., Kinzler,
    K.W.: Cancer genome landscapes. Science 339 (6127), 1546–1558 (2013)

  14. Von der Heyde, S., Bender, C., Henjes, F., Sonntag, J., Korf, U., Beissbarth, T.:
    Boolean ErbB network reconstructions and perturbation simulations reveal indi-
    vidual drug response in different breast cancer cell lines. BMC Syst. Biol. 8 (1), 75
    (2014)

  15. Wang, X., Fu, A.Q., McNerney, M.E., White, K.P.: Widespread genetic epistasis
    among cancer genes. Nat. Commun. 5 , 4828 (2014)

  16. Zanudo, J.G.T., Albert, R.: Cell fate reprogramming by control of intracellular
    network dynamics. PLoS Comput. Biol. 11 (4), e1004193 (2015)

  17. Zhong, Q., Simonis, N., Li, Q.-R., Charloteaux, B., Heuze, F., Klitgord, N., Tam,
    S., Haiyuan, Y., Venkatesan, K., Mou, D., Swearingen, V., Yildirim, M.A., Yan, H.,
    Dricot, A., Szeto, D., Lin, C., Hao, T., Fan, C., Milstein, S., Dupuy, D., Brasseur,
    R., Hill, D.E., Cusick, M.E., Vidal, M.: Edgetic perturbation models of human
    inherited disorders. Mol. Syst. Biol. 5 (321), 321 (2009)

Free download pdf