TY - JOUR AU - Little, J. W. AU - Shepley, D. P. AU - Wert, D. W. PY - 1999 DA - 1999// TI - Robustness of a gene regulatory circuit JO - EMBO J VL - 18 UR - https://doi.org/10.1093/emboj/18.15.4299 DO - 10.1093/emboj/18.15.4299 ID - Little1999 ER - TY - JOUR AU - Yi, T. M. AU - Huang, Y. AU - Simon, M. I. AU - Doyle, J. PY - 2000 DA - 2000// TI - Robust perfect adaptation in bacterial chemotaxis through integral feedback control JO - Proc Natl Acad Sci U S A VL - 97 UR - https://doi.org/10.1073/pnas.97.9.4649 DO - 10.1073/pnas.97.9.4649 ID - Yi2000 ER - TY - JOUR AU - Ingolia, N. T. PY - 2004 DA - 2004// TI - Topology and robustness in the Drosophila segment polarity network JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020123 DO - 10.1371/journal.pbio.0020123 ID - Ingolia2004 ER - TY - JOUR AU - Klein, C. AU - Marino, A. AU - Sagot, M. F. AU - Vieira Milreu, P. AU - Brilli, M. PY - 2012 DA - 2012// TI - Structural and dynamical analysis of biological networks JO - Brief Funct Genomics VL - 11 UR - https://doi.org/10.1093/bfgp/els030 DO - 10.1093/bfgp/els030 ID - Klein2012 ER - TY - JOUR AU - Kitano, H. PY - 2004 DA - 2004// TI - Biological robustness JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1471 DO - 10.1038/nrg1471 ID - Kitano2004 ER - TY - JOUR AU - Kitano, H. PY - 2007 DA - 2007// TI - Towards a theory of biological robustness JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100179 DO - 10.1038/msb4100179 ID - Kitano2007 ER - TY - JOUR AU - Lev Bar-Or, R. AU - Maya, R. AU - Segel, L. A. AU - Alon, U. AU - Levine, A. J. AU - Oren, M. PY - 2000 DA - 2000// TI - Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study JO - Proc Natl Acad Sci U S A VL - 97 UR - https://doi.org/10.1073/pnas.210171597 DO - 10.1073/pnas.210171597 ID - Lev Bar-Or2000 ER - TY - JOUR AU - Morohashi, M. AU - Winn, A. E. AU - Borisuk, M. T. AU - Bolouri, H. AU - Doyle, J. AU - Kitano, H. PY - 2002 DA - 2002// TI - Robustness as a measure of plausibility in models of biochemical networks JO - J Theor Biol VL - 216 UR - https://doi.org/10.1006/jtbi.2002.2537 DO - 10.1006/jtbi.2002.2537 ID - Morohashi2002 ER - TY - JOUR AU - Kwon, Y. K. AU - Cho, K. H. PY - 2008 DA - 2008// TI - Coherent coupling of feedback loops: a design principle of cell signaling networks JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn337 DO - 10.1093/bioinformatics/btn337 ID - Kwon2008 ER - TY - JOUR AU - Kwon, Y. K. AU - Choi, S. S. AU - Cho, K. H. PY - 2007 DA - 2007// TI - Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-384 DO - 10.1186/1471-2105-8-384 ID - Kwon2007 ER - TY - JOUR AU - Kauffman, S. AU - Peterson, C. AU - Samuelsson, B. AU - Troein, C. PY - 2003 DA - 2003// TI - Random Boolean network models and the yeast transcriptional network JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.2036429100 DO - 10.1073/pnas.2036429100 ID - Kauffman2003 ER - TY - JOUR AU - Le, D. H. AU - Kwon, Y. K. PY - 2013 DA - 2013// TI - A coherent feedforward loop design principle to sustain robustness of biological networks JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt026 DO - 10.1093/bioinformatics/btt026 ID - Le2013 ER - TY - JOUR AU - Gonzalez, A. G. AU - Naldi, A. AU - Sanchez, L. AU - Thieffry, D. AU - Chaouiya, C. PY - 2006 DA - 2006// TI - GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks JO - BioSystems VL - 84 UR - https://doi.org/10.1016/j.biosystems.2005.10.003 DO - 10.1016/j.biosystems.2005.10.003 ID - Gonzalez2006 ER - TY - JOUR AU - Mussel, C. AU - Hopfensitz, M. AU - Kestler, H. A. PY - 2010 DA - 2010// TI - BoolNet--an R package for generation, reconstruction and analysis of Boolean networks JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq124 DO - 10.1093/bioinformatics/btq124 ID - Mussel2010 ER - TY - JOUR AU - Zheng, J. AU - Zhang, D. AU - Przytycki, P. F. AU - Zielinski, R. AU - Capala, J. AU - Przytycka, T. M. PY - 2010 DA - 2010// TI - SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp617 DO - 10.1093/bioinformatics/btp617 ID - Zheng2010 ER - TY - JOUR AU - Trinh, H. C. AU - Le, D. H. AU - Kwon, Y. K. PY - 2014 DA - 2014// TI - PANET: a GPU-based tool for fast parallel analysis of robustness dynamics and feed-forward/feedback loop structures in large-scale biological networks JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0103010 DO - 10.1371/journal.pone.0103010 ID - Trinh2014 ER - TY - JOUR AU - Bock, M. AU - Scharp, T. AU - Talnikar, C. AU - Klipp, E. PY - 2014 DA - 2014// TI - BooleSim: an interactive Boolean network simulator JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt568 DO - 10.1093/bioinformatics/btt568 ID - Bock2014 ER - TY - JOUR AU - Bhalla, U. S. AU - Ram, P. T. AU - Iyengar, R. PY - 2002 DA - 2002// TI - MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network JO - Science VL - 297 UR - https://doi.org/10.1126/science.1068873 DO - 10.1126/science.1068873 ID - Bhalla2002 ER - TY - JOUR AU - Ferrell, J. E. AU - Machleder, E. M. PY - 1998 DA - 1998// TI - The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes JO - Science VL - 280 UR - https://doi.org/10.1126/science.280.5365.895 DO - 10.1126/science.280.5365.895 ID - Ferrell1998 ER - TY - JOUR AU - Pomerening, J. R. AU - Sontag, E. D. AU - Ferrell, J. E. PY - 2003 DA - 2003// TI - Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2 JO - Nat Cell Biol VL - 5 UR - https://doi.org/10.1038/ncb954 DO - 10.1038/ncb954 ID - Pomerening2003 ER - TY - JOUR AU - Ciliberti, S. AU - Martin, O. C. AU - Wagner, A. PY - 2007 DA - 2007// TI - Robustness can evolve gradually in complex regulatory gene networks with varying topology JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030015 DO - 10.1371/journal.pcbi.0030015 ID - Ciliberti2007 ER - TY - JOUR AU - Huang, S. AU - Eichler, G. AU - Bar-Yam, Y. AU - Ingber, D. E. PY - 2005 DA - 2005// TI - Cell fates as high-dimensional attractor states of a complex gene regulatory network JO - Phys Rev Lett VL - 94 UR - https://doi.org/10.1103/PhysRevLett.94.128701 DO - 10.1103/PhysRevLett.94.128701 ID - Huang2005 ER - TY - JOUR AU - Kitano, H. PY - 2004 DA - 2004// TI - Cancer as a robust system: implications for anticancer therapy JO - Nat Rev Cancer VL - 4 UR - https://doi.org/10.1038/nrc1300 DO - 10.1038/nrc1300 ID - Kitano2004 ER - TY - JOUR AU - Li, F. AU - Long, T. AU - Lu, Y. AU - Ouyang, Q. AU - Tang, C. PY - 2004 DA - 2004// TI - The yeast cell-cycle network is robustly designed JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0305937101 DO - 10.1073/pnas.0305937101 ID - Li2004 ER - TY - JOUR AU - Kim, J. R. AU - Kim, J. AU - Kwon, Y. K. AU - Lee, H. Y. AU - Heslop-Harrison, P. AU - Cho, K. H. PY - 2011 DA - 2011// TI - Reduction of complex signaling networks to a representative kernel JO - Sci Signal VL - 4 UR - https://doi.org/10.1126/scisignal.2001390 DO - 10.1126/scisignal.2001390 ID - Kim2011 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. PY - 2000 DA - 2000// TI - KEGG: kyoto encyclopedia of genes and genomes JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.27 DO - 10.1093/nar/28.1.27 ID - Kanehisa2000 ER - TY - JOUR AU - Cui, Q. AU - Ma, Y. AU - Jaramillo, M. AU - Bari, H. AU - Awan, A. AU - Yang, S. AU - Zhang, S. AU - Liu, L. AU - Lu, M. AU - O’Connor-McCourt, M. AU - Purisima, E. O. AU - Wang, E. PY - 2007 DA - 2007// TI - A map of human cancer signaling JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100200 DO - 10.1038/msb4100200 ID - Cui2007 ER - TY - JOUR AU - Zhang, R. AU - Lin, Y. PY - 2009 DA - 2009// TI - DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn858 DO - 10.1093/nar/gkn858 ID - Zhang2009 ER - TY - JOUR AU - Amberger, J. AU - Bocchini, C. A. AU - Scott, A. F. AU - Hamosh, A. PY - 2009 DA - 2009// TI - McKusick’s Online Mendelian Inheritance in Man (OMIM) JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn665 DO - 10.1093/nar/gkn665 ID - Amberger2009 ER - TY - JOUR AU - Knox, C. AU - Law, V. AU - Jewison, T. AU - Liu, P. AU - Ly, S. AU - Frolkis, A. AU - Pon, A. AU - Banco, K. AU - Mak, C. AU - Neveu, V. AU - Djoumbou, Y. AU - Eisner, R. AU - Guo, A. C. AU - Wishart, D. S. PY - 2011 DA - 2011// TI - DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1126 DO - 10.1093/nar/gkq1126 ID - Knox2011 ER - TY - STD TI - Robert F. Discrete iterations: a metric study. Berlin: Springer Verlag; 1986. ID - ref31 ER - TY - JOUR AU - Thomas, R. AU - Thieffry, D. AU - Kaufman, M. PY - 1995 DA - 1995// TI - Dynamical behaviour of biological regulatory networks--I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state JO - Bull Math Biol VL - 57 UR - https://doi.org/10.1007/BF02460618 DO - 10.1007/BF02460618 ID - Thomas1995 ER - TY - JOUR AU - Kwon, Y. K. AU - Cho, K. H. PY - 2007 DA - 2007// TI - Boolean dynamics of biological networks with multiple coupled feedback loops JO - Biophys J VL - 92 UR - https://doi.org/10.1529/biophysj.106.097097 DO - 10.1529/biophysj.106.097097 ID - Kwon2007 ER - TY - JOUR AU - Bovolenta, L. A. AU - Acencio, M. L. AU - Lemke, N. PY - 2012 DA - 2012// TI - HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-405 DO - 10.1186/1471-2164-13-405 ID - Bovolenta2012 ER - TY - STD TI - Liu ZP, Wu C, Miao H, Wu H. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database (Oxford). 2015. doi:10.1093/database/bav095. Print 2015. ID - ref35 ER - TY - JOUR AU - Kwon, Y. K. AU - Cho, K. H. PY - 2008 DA - 2008// TI - Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn060 DO - 10.1093/bioinformatics/btn060 ID - Kwon2008 ER -