[1] | Bacchus W, Aubel D, Fussenegger M (2013) Biomedically relevant circuit-design strategies in mammalian synthetic biology. Mol Syst Biol 9: 691. doi: 10.1038/msb.2013.48. pmid:24061539
|
[2] | Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA (2010) Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu Rev Biophys 39: 515–537. doi: 10.1146/annurev.biophys.050708.133652. pmid:20192780
|
[3] | Weber W, Fussenegger M (2011) Emerging biomedical applications of synthetic biology. Nature Reviews Genetics 13: 21–35. doi: 10.1038/nrg3094. pmid:22124480
|
[4] | Bray D (1995) Protein molecules as computational elements in living cells. Nature 376: 307–312. pmid:7630396 doi: 10.1038/376307a0
|
[5] | Amos Martyn (2004) Cellular Computing. Oxford University Press, USA.
|
[6] | Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491: 249–253. doi: 10.1038/nature11516. pmid:23041931
|
[7] | Slusarczyk AL, Lin A, Weiss R (2012) Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 13: 406–420. doi: 10.1038/nrg3227. pmid:22596318
|
[8] | Voigt CA (2006) Genetic parts to program bacteria. Curr Opin Biotechnol 17: 548–557. pmid:16978856 doi: 10.1016/j.copbio.2006.09.001
|
[9] | Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339–342. pmid:10659857 doi: 10.1038/35002131
|
[10] | Dari A, Kia B, Wang X, Bulsara AR, Ditto W (2011) Noise-aided computation within a synthetic gene network through morphable and robust logic gates. Phys Rev E Stat Nonlin Soft Matter Phys 83: 041909. pmid:21599203 doi: 10.1103/physreve.83.041909
|
[11] | Kramer BP, Fischer C, Fussenegger M (2004) BioLogic gates enable logical transcription control in mammalian cells. Biotechnol Bioeng 87: 478–484. pmid:15286985 doi: 10.1002/bit.20142
|
[12] | Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 25: 795–801. pmid:17515909 doi: 10.1038/nbt1307
|
[13] | Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335–338. pmid:10659856 doi: 10.1038/35002125
|
[14] | Greber D, Fussenegger M (2010) An engineered mammalian band-pass network. Nucleic Acids Res 38: e174. doi: 10.1093/nar/gkq671. pmid:20693530
|
[15] | Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y (2011) Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333: 1307–1311. doi: 10.1126/science.1205527. pmid:21885784
|
[16] | Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D (2013) Amplifying genetic logic gates. Science 340: 599–603. doi: 10.1126/science.1232758. pmid:23539178
|
[17] | Benenson Y (2012) Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 13: 455–468. doi: 10.1038/nrg3197. pmid:22688678
|
[18] | Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10: 410–422. doi: 10.1038/nrm2698. pmid:19461664
|
[19] | Kwok R (2010) Five hard truths for synthetic biology. Nature 463: 288–290. doi: 10.1038/463288a. pmid:20090726
|
[20] | Glass L, Kauffman SA (1973) The logical analysis of continuous, non-linear biochemical control networks. J Theor Biol 39: 103–129. pmid:4741704 doi: 10.1016/0022-5193(73)90208-7
|
[21] | Kauffman S (1974) The large scale structure and dynamics of gene control circuits: an ensemble approach. J Theor Biol 44: 167–190. pmid:4595774 doi: 10.1016/s0022-5193(74)80037-8
|
[22] | McAdams HH, Shapiro L (1995) Circuit simulation of genetic networks. Science 269: 650–656. pmid:7624793 doi: 10.1126/science.7624793
|
[23] | McAdams HH, Arkin A (2000) Towards a circuit engineering discipline. Curr Biol 10: R318–R320. pmid:10801411 doi: 10.1016/s0960-9822(00)00440-1
|
[24] | Hasty J, McMillen D, Collins JJ (2002) Engineered gene circuits. Nature 420: 224–230. pmid:12432407 doi: 10.1038/nature01257
|
[25] | Guet CC, Elowitz MB, Hsing W, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296: 1466–1470. pmid:12029133 doi: 10.1126/science.1067407
|
[26] | Rollié S, Mangold M, Sundmacher K (2012) Designing biological systems: systems engineering meets synthetic biology. Chemical Engineering Science 69: 1–29. doi: 10.1016/j.ces.2011.10.068
|
[27] | Macia J, Posas F, Sole RV (2012) Distributed computation: the new wave of synthetic biology devices. Trends Biotechnol 30: 342–349. doi: 10.1016/j.tibtech.2012.03.006. pmid:22516742
|
[28] | Vilanova C, Porcar M (2014) iGEM 2.0—refoundations for engineering biology. Nat Biotechnol 32: 420–424. doi: 10.1038/nbt.2899. pmid:24811510
|
[29] | Brenner K, You L, Arnold FH (2008) Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 26: 483–489. doi: 10.1016/j.tibtech.2008.05.004. pmid:18675483
|
[30] | Chuang JS (2012) Engineering multicellular traits in synthetic microbial populations. Curr Opin Chem Biol 16: 370–378. doi: 10.1016/j.cbpa.2012.04.002. pmid:22591687
|
[31] | Regot S, Macia J, Conde N, Furukawa K, Kjellen J, Peeters T, Hohmann S, de Nadal E, Posas F, Sole R (2011) Distributed biological computation with multicellular engineered networks. Nature 469: 207–211. doi: 10.1038/nature09679. pmid:21150900
|
[32] | Tamsir A, Tabor JJ, Voigt CA (2011) Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 469: 212–215. doi: 10.1038/nature09565. pmid:21150903
|
[33] | Kholodenko BN (2009) Spatially distributed cell signalling. FEBS letters 583: 4006–4012. doi: 10.1016/j.febslet.2009.09.045. pmid:19800332
|
[34] | Abelson H, Allen D, Coore D, Hanson C, Homsy G, Knight TF Jr, Nagpal R, Rauch E, Sussman GJ, Weiss R (2000) Amorphous computing. Communications of the ACM 43: 74–82. doi: 10.1145/332833.332842
|
[35] | Kinkhabwala A, Bastiaens PI (2010) Spatial aspects of intracellular information processing. Curr Opin Genet Dev 20: 31–40. doi: 10.1016/j.gde.2009.12.006. pmid:20096560
|
[36] | Haken, Hermann (1979) Pattern formation and pattern recognitionG??an attempt at a synthesis. Springer.
|
[37] | Haken, Hermann (2004) Synergetics: Introduction and advanced topics. Springer.
|
[38] | Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434: 1130–1134. pmid:15858574 doi: 10.1038/nature03461
|
[39] | Solé RV, Delgado J (1996) Universal computation in fluid neural networks. Complexity 2: 49–56. doi: 10.1002/(sici)1099-0526(199611/12)2:2<49::aid-cplx13>3.0.co;2-t
|
[40] | Bonabeau E, Sobkowski A, Theraulaz G, Deneubourg JL (1997) Adaptive Task Allocation Inspired by a Model of Division of Labor in Social Insects. BCEC 36–45.
|
[41] | Enderton, Herbert and Enderton, Herbert B. (2001) A mathematical introduction to logic. Access Online via Elsevier.
|
[42] | Karnaugh M (1953) The map method for synthesis of combinational logic circuits. American Institute of Electrical Engineers, Part I: Communication and Electronics, Transactions of the 72: 593–599.
|
[43] | McCluskey, Edward J. (1965) Introduction to the theory of switching circuits. McGraw-Hill New York.
|
[44] | Bender, Edward A. and Williamson, S Gill (2012) A short course in discrete mathematics. DoverPublications. com.
|
[45] | Grilly C, Stricker J, Pang WL, Bennett MR, Hasty J (2007) A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae. Mol Syst Biol 3: 127. pmid:17667949 doi: 10.1038/msb4100168
|
[46] | Gaber R, Lebar T, Majerle A, Ster B, Dobnikar A, Bencina M, Jerala R (2014) Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat Chem Biol 10: 203–208. doi: 10.1038/nchembio.1433. pmid:24413461
|
[47] | Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD (2009) A synthetic genetic edge detection program. Cell 137: 1272–1281. doi: 10.1016/j.cell.2009.04.048. pmid:19563759
|
[48] | Ellis T, Wang X, Collins JJ (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 27: 465–471. doi: 10.1038/nbt.1536. pmid:19377462
|
[49] | Asthana A, Lee KH, Kim KO, Kim DM, Kim DP (2012) Rapid and cost-effective fabrication of selectively permeable calcium-alginate microfluidic device using modified embedded template method. Biomicrofluidics 6: 012821. doi: 10.1063/1.3672189
|
[50] | Choi NW, Cabodi M, Held B, Gleghorn JP, Bonassar LJ, Stroock AD (2007) Microfluidic scaffolds for tissue engineering. Nature materials 6: 908–915. pmid:17906630 doi: 10.1038/nmat2022
|
[51] | Thorsen T, Maerkl SJ, Quake SR (2002) Microfluidic large-scale integration. Science 298: 580–584. pmid:12351675 doi: 10.1126/science.1076996
|
[52] | Luo D, Pullela SR, Marquez M, Cheng Z (2007) Cell encapsules with tunable transport and mechanical properties. Biomicrofluidics 1: 034102. doi: 10.1063/1.2757156
|
[53] | Williams JC, Holecko MM II, Massia SP, Rousche P, Kipke DR (2005) Multi-site incorporation of bioactive matrices into MEMS-based neural probes. Journal of neural engineering 2: L23. pmid:16317225 doi: 10.1088/1741-2560/2/4/l03
|
[54] | Ricoult SG, Goldman JS, Stellwagen D, Juncker D, Kennedy TE (2012) Generation of microisland cultures using microcontact printing to pattern protein substrates. Journal of neuroscience methods 208: 10–17. doi: 10.1016/j.jneumeth.2012.04.016. pmid:22561087
|
[55] | Feng XJ, Hooshangi S, Chen D, Li G, Weiss R, Rabitz H (2004) Optimizing genetic circuits by global sensitivity analysis. Biophys J 87: 2195–2202. pmid:15454422 doi: 10.1529/biophysj.104.044131
|
[56] | Weiss R, Basu S, Hooshangi S, Kalmbach A, Karig D, Mehreja R, Netravali I (2003) Genetic circuit building blocks for cellular computation, communications, and signal processing. Natural Computing 2: 47–84.
|