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Volumn 813, Issue , 2012, Pages 3-21

In silico implementation of synthetic gene networks

Author keywords

Automation; DNA assembly; Formal language; Gene circuits; Part composability; Standard Biological Parts; Visual design

Indexed keywords

PROTEIN;

EID: 82355171270     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-412-4_1     Document Type: Article
Times cited : (9)

References (98)
  • 1
    • 0004001955 scopus 로고
    • SPICE (simulation program with integrated circuit emphasis
    • University of California, Berkley
    • Nagel, L. W., and Pederson, D. O. (1973). SPICE (Simulation Program with Integrated Circuit Emphasis). Memorandum No. ERLM382 , University of California, Berkley.
    • (1973) Memorandum No. ERLM382
    • Nagel, L.W.1    Pederson, D.O.2
  • 2
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • DOI 10.1038/nature04342, PII N04342
    • Endy, D. (2005) Foundations for engineering biology, Nature 438 , 449-453. (Pubitemid 41742010)
    • (2005) Nature , vol.438 , Issue.7067 , pp. 449-453
    • Endy, D.1
  • 4
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
    • Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H. (2003) CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO 1 , 159-162.
    • (2003) BIOSILICO , vol.1 , pp. 159-162
    • Funahashi, A.1    Tanimura, N.2    Morohashi, M.3    Kitano, H.4
  • 8
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software Environment for integrated models of biomolecular interaction networks
    • DOI 10.1101/gr.1239303
    • Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res 13 , 2498-2504. (Pubitemid 37428274)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 10
    • 0242380634 scopus 로고    scopus 로고
    • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
    • DOI 10.1093/nar/gkg461
    • Kurata, H., Matoba, N., and Shimizu, N. (2003) CADLIVE for constructing a large-scale biochemical network based on a simulationdirected notation and its application to yeast cell cycle, Nucleic Acids Res 31 , 4071-4084. (Pubitemid 37442287)
    • (2003) Nucleic Acids Research , vol.31 , Issue.14 , pp. 4071-4084
    • Kurata, H.1    Matoba, N.2    Shimizu, N.3
  • 11
    • 17844397967 scopus 로고    scopus 로고
    • CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
    • DOI 10.1101/gr.3463705
    • Kurata, H., Masaki, K., Sumida, Y., and Iwasaki, R. (2005) CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models, Genome Res 15 , 590-600. (Pubitemid 41057822)
    • (2005) Genome Research , vol.15 , Issue.4 , pp. 590-600
    • Kurata, H.1    Masaki, K.2    Sumida, Y.3    Iwasaki, R.4
  • 12
    • 0035478586 scopus 로고    scopus 로고
    • The Virtual Cell: A software environment for computational cell biology
    • DOI 10.1016/S0167-7799(01)01740-1, PII S0167779901017401
    • Loew, L. M., and Schaff, J. C. (2001) The Virtual Cell: a software environment for computational cell biology, Trends Biotechnol 19 , 401-406. (Pubitemid 32925033)
    • (2001) Trends in Biotechnology , vol.19 , Issue.10 , pp. 401-406
    • Loew, L.M.1    Schaff, J.C.2
  • 14
    • 17644385076 scopus 로고    scopus 로고
    • Computational representation of developmental genetic regulatory networks
    • DOI 10.1016/j.ydbio.2005.04.023, PII S0012160605002575
    • Longabaugh, W. J. R., Davidson, E. H., and Bolouri, H. (2005) Computational representation of developmental genetic regulatory networks, Dev Biol 283 , 1-16. (Pubitemid 40828838)
    • (2005) Developmental Biology , vol.283 , Issue.1 , pp. 1-16
    • Longabaugh, W.J.R.1    Davidson, E.H.2    Bolouri, H.3
  • 16
    • 51449095986 scopus 로고    scopus 로고
    • Genetic design: Rising above the sequence
    • Goler, J. A., Bramlett, B. W., and Peccoud, J. (2008) Genetic design: rising above the sequence, Trends Biotechnol 26 , 538-544.
    • (2008) Trends Biotechnol , vol.26 , pp. 538-544
    • Goler, J.A.1    Bramlett, B.W.2    Peccoud, J.3
  • 17
    • 41149157016 scopus 로고    scopus 로고
    • TABASCO: A single molecule, base-pair resolved gene expression simulator
    • Kosuri, S., Kelly, J., and Endy, D. (2007) TABASCO: A single molecule, base-pair resolved gene expression simulator, BMC Bioinformatics 8 :480.
    • (2007) BMC Bioinformatics , vol.8 , pp. 480
    • Kosuri, S.1    Kelly, J.2    Endy, D.3
  • 18
    • 28544451327 scopus 로고    scopus 로고
    • Adventures in synthetic biology. Appeared in Foundations for engineering biology p449
    • Endy, D., Deese, I., and the, M. I. T. S. B. W. G. (2005). Adventures in synthetic biology. Appeared in Foundations for engineering biology p449, Nature , 438 , 449-453.
    • (2005) Nature , vol.438 , pp. 449-453
    • Endy, D.1    Deese, I.2    W, G.M.I.T.S.B.3
  • 19
    • 50549103571 scopus 로고    scopus 로고
    • Computational design of synthetic gene circuits with composable parts
    • Marchisio, M. A., and Stelling, J. (2008) Computational design of synthetic gene circuits with composable parts, Bioinformatics 24 , 1903-1910.
    • (2008) Bioinformatics , vol.24 , pp. 1903-1910
    • Marchisio, M.A.1    Stelling, J.2
  • 21
    • 34548778155 scopus 로고    scopus 로고
    • Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins
    • DOI 10.1038/nrg2172, PII NRG2172
    • Serganov, A., and Patel, D. J. (2007) Ribozymes, riboswitches and beyond: regulation of gene expression without proteins, Nat Rev Genet 8 , 776-790. (Pubitemid 47429208)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.10 , pp. 776-790
    • Serganov, A.1    Patel, D.J.2
  • 23
    • 0037715313 scopus 로고    scopus 로고
    • Modular modeling of cellular systems with ProMoT/Diva
    • DOI 10.1093/bioinformatics/btg128
    • Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., and Gilles, E. D. (2003) Modular modeling of cellular systems with ProMoT/Diva, Bioinformatics 19 , 1169-1176. (Pubitemid 36790021)
    • (2003) Bioinformatics , vol.19 , Issue.9 , pp. 1169-1176
    • Ginkel, M.1    Kremling, A.2    Nutsch, T.3    Rehner, R.4    Gilles, E.D.5
  • 25
    • 46249085749 scopus 로고    scopus 로고
    • Asmparts: Assembly of biological model parts
    • Rodrigo, G., Carrera, J., and Jaramillo, A. (2008) Asmparts: assembly of biological model parts, Syst Synth Biol 1 , 167-170.
    • (2008) Syst Synth Biol , vol.1 , pp. 167-170
    • Rodrigo, G.1    Carrera, J.2    Jaramillo, A.3
  • 26
    • 77951969603 scopus 로고    scopus 로고
    • Standard virtual biological parts: A repository of modular modeling components for synthetic biology
    • Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., and Wipat, A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology, Bioinformatics 26 , 925-931.
    • Bioinformatics , vol.26 , pp. 925-931
    • Cooling, M.T.1    Rouilly, V.2    Misirli, G.3    Lawson, J.4    Yu, T.5    Hallinan, J.6    Wipat, A.7
  • 27
  • 30
    • 71849095864 scopus 로고    scopus 로고
    • TinkerCell: Modular CAD tool for synthetic biology
    • Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009) TinkerCell: modular CAD tool for synthetic biology, J Biol Eng 3 :19.
    • (2009) J Biol Eng , vol.3 , pp. 19
    • Chandran, D.1    Bergmann, F.T.2    Sauro, H.M.3
  • 33
    • 77955033157 scopus 로고    scopus 로고
    • SynBioSS designer: A web-based tool for the automated generation of kinetic models for synthetic biological constructs
    • Weeding, E., Houle, J., and Kaznessis, Y. N. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs, Brief Bioinform 11 , 394-402.
    • Brief Bioinform , vol.11 , pp. 394-402
    • Weeding, E.1    Houle, J.2    Kaznessis, Y.N.3
  • 34
    • 33645465102 scopus 로고    scopus 로고
    • Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
    • Salis, H., Sotiropoulos, V., and Kaznessis, Y. N. (2006) Multiscale Hy3S: hybrid stochastic simulation for supercomputers, BMC Bioinformatics 7 :93.
    • (2006) BMC Bioinformatics , vol.7 , pp. 93
    • Salis, H.1    Sotiropoulos, V.2    Kaznessis, Y.N.3
  • 35
    • 10244219918 scopus 로고    scopus 로고
    • BioNetGen: Software for rule-based modeling of signal transduction based on the interactions of molecular domains
    • DOI 10.1093/bioinformatics/bth378
    • Blinov, M. L., Faeder, J. R., Goldstein, B., and Hlavacek, W. S. (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains, Bioinformatics 20 , 3289-3291. (Pubitemid 39619231)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3289-3291
    • Blinov, M.L.1    Faeder, J.R.2    Goldstein, B.3    Hlavacek, W.S.4
  • 36
    • 65649154507 scopus 로고    scopus 로고
    • Rule-based modeling of biochemical systems with BioNetGen
    • Faeder, J. R., Blinov, M. L., and Hlavacek, W. S. (2009) Rule-based modeling of biochemical systems with BioNetGen, Methods Mol Biol 500 , 113-167.
    • (2009) Methods Mol Biol , vol.500 , pp. 113-167
    • Faeder, J.R.1    Blinov, M.L.2    Hlavacek, W.S.3
  • 38
    • 0034961694 scopus 로고    scopus 로고
    • STOCHSIM: Modelling of stochastic biomolecular processes
    • Novere, N. L., and Shimizu, T. S. (2001) STOCHSIM: modelling of stochastic biomolecular processes, Bioinformatics 17 , 575-576. (Pubitemid 32600510)
    • (2001) Bioinformatics , vol.17 , Issue.6 , pp. 575-576
    • Le Novere, N.1    Shimizu, T.S.2
  • 40
  • 41
    • 0035235039 scopus 로고    scopus 로고
    • Representation and simulation of biochemical processes using the pi-calculus process algebra
    • Regev, A., Silverman, W., and Shapiro, E. (2001) Representation and simulation of biochemical processes using the pi-calculus process algebra, Pac Symp Biocomput , 459-470.
    • (2001) Pac Symp Biocomput , pp. 459-470
    • Regev, A.1    Silverman, W.2    Shapiro, E.3
  • 42
    • 43049179364 scopus 로고    scopus 로고
    • Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
    • DOI 10.1016/j.entcs.2007.12.008, PII S1571066108000285
    • Ciocchetta, F., and Hillston, J. (2008) Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks, Electronic Notes in Theoretical Computational Science 194 , 103-117. (Pubitemid 351173025)
    • (2008) Electronic Notes in Theoretical Computer Science , vol.194 , Issue.3 , pp. 103-117
    • Ciocchetta, F.1    Hillston, J.2
  • 43
    • 67650663955 scopus 로고    scopus 로고
    • Towards programming languages for genetic engineering of living cells
    • Pedersen, M., and Phillips, A. (2009) Towards programming languages for genetic engineering of living cells, J R Soc Interface 6 Suppl 4 , S437-S450.
    • (2009) J R Soc Interface , vol.6 , Issue.SUPPL. 4
    • Pedersen, M.1    Phillips, A.2
  • 44
    • 35748938455 scopus 로고    scopus 로고
    • A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
    • DOI 10.1093/bioinformatics/btm446
    • Cai, Y., Hartnett, B., Gustafsson, C., and Peccoud, J. (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts, Bioinformatics 23 , 2760-2767. (Pubitemid 350048342)
    • (2007) Bioinformatics , vol.23 , Issue.20 , pp. 2760-2767
    • Cai, Y.1    Hartnett, B.2    Gustafsson, C.3    Peccoud, J.4
  • 46
    • 75649131791 scopus 로고    scopus 로고
    • A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks
    • Monteiro, P. T., Dumas, E., Besson, B., Mateescu, R., Page, M., Freitas, A. T., and de Jong, H. (2009) A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks, BMC Bioinformatics 10 :450.
    • (2009) BMC Bioinformatics , vol.10 , pp. 450
    • Monteiro, P.T.1    Dumas, E.2    Besson, B.3    Mateescu, R.4    Page, M.5    Freitas, A.T.6    De Jong, H.7
  • 47
    • 49549114493 scopus 로고    scopus 로고
    • Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
    • Saez-Rodriguez, J., Gayer, S., Ginkel, M., and Gilles, E. D. (2008) Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules, Bioinformatics 24 , 213-219.
    • (2008) Bioinformatics , vol.24 , pp. 213-219
    • Saez-Rodriguez, J.1    Gayer, S.2    Ginkel, M.3    Gilles, E.D.4
  • 48
    • 33645677022 scopus 로고    scopus 로고
    • Infrastructure for engineered emergence on sensor/actuator networks
    • Beal, J., and Bachrach, J. (2006) Infrastructure for Engineered Emergence on Sensor/Actuator Networks, IEEE Intelligent Systems 21 (2) , 10-19.
    • (2006) IEEE Intelligent Systems , vol.21 , Issue.2 , pp. 10-19
    • Beal, J.1    Bachrach, J.2
  • 49
    • 64549144670 scopus 로고    scopus 로고
    • Programming with models: Modularity and abstraction provide powerful capabilities for systems biology
    • Mallavarapu, A., Thomson, M., Ullian, B., and Gunawardena, J. (2009) Programming with models: modularity and abstraction provide powerful capabilities for systems biology, J R Soc Interface 6 , 257-270.
    • (2009) J R Soc Interface , vol.6 , pp. 257-270
    • Mallavarapu, A.1    Thomson, M.2    Ullian, B.3    Gunawardena, J.4
  • 50
    • 34548747486 scopus 로고    scopus 로고
    • Robustness analysis and tuning of synthetic gene networks
    • DOI 10.1093/bioinformatics/btm362
    • Batt, Gg., Yordanov, B., Weiss, R., and Belta, C. (2007) Robustness analysis and tuning of synthetic gene networks, Bioinformatics 23 , 2415-2422. (Pubitemid 47423839)
    • (2007) Bioinformatics , vol.23 , Issue.18 , pp. 2415-2422
    • Batt, G.1    Yordanov, B.2    Weiss, R.3    Belta, C.4
  • 53
    • 34547861255 scopus 로고    scopus 로고
    • Genetdes: Automatic design of transcriptional networks
    • DOI 10.1093/bioinformatics/btm237
    • Rodrigo, G., Carrera, J., and Jaramillo, A. (2007) Genetdes: automatic design of transcriptional networks, Bioinformatics 23 , 1857-1858. (Pubitemid 47250327)
    • (2007) Bioinformatics , vol.23 , Issue.14 , pp. 1857-1858
    • Rodrigo, G.1    Carrera, J.2    Jaramillo, A.3
  • 54
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., Gelatt, C. D., and Vecchi, M. P. (1983) Optimization by Simulated Annealing, Science 220 , 671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 55
    • 46249108209 scopus 로고    scopus 로고
    • Computational design of digital and memory biological devices
    • Rodrigo, G., and Jaramillo, A. (2007) Computational design of digital and memory biological devices, Syst Synth Biol 1 , 183-195.
    • (2007) Syst Synth Biol , vol.1 , pp. 183-195
    • Rodrigo, G.1    Jaramillo, A.2
  • 56
    • 42549159572 scopus 로고    scopus 로고
    • OptCircuit: An optimization based method for computational design of genetic circuits
    • Dasika, M. S., and Maranas, C. D. (2008) OptCircuit: an optimization based method for computational design of genetic circuits, BMC Syst Biol 2 :24.
    • (2008) BMC Syst Biol , vol.2 , pp. 24
    • Dasika, M.S.1    Maranas, C.D.2
  • 57
    • 79952476417 scopus 로고    scopus 로고
    • Automatic design of digital synthetic gene circuits
    • Marchisio, M. A., and Stelling, Jr. (2011) Automatic Design of Digital Synthetic Gene Circuits, PLoS Comput Biol 7 , e1001083.
    • (2011) PLoS Comput Biol , vol.7
    • Marchisio, M.A.1    Stelling, J.2
  • 61
    • 19644370646 scopus 로고    scopus 로고
    • GeMS: An advanced software package for designing synthetic genes
    • DOI 10.1093/nar/gki614
    • Jayaraj, S., Reid, R., and Santi, D. V. (2005) GeMS: an advanced software package for designing synthetic genes, Nucleic Acids Res 33 , 3011-3016. (Pubitemid 41511238)
    • (2005) Nucleic Acids Research , vol.33 , Issue.9 , pp. 3011-3016
    • Jayaraj, S.1    Reid, R.2    Santi, D.V.3
  • 62
    • 0037095730 scopus 로고    scopus 로고
    • DNAWorks: An automated method for designing oligonucleotides for PCR-based gene synthesis
    • Hoover, D. M., and Lubkowski, J. (2002) DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis, Nucleic Acids Res 30 (10) :e43.
    • (2002) Nucleic Acids Res , vol.30 , Issue.10
    • Hoover, D.M.1    Lubkowski, J.2
  • 63
    • 3242888495 scopus 로고    scopus 로고
    • Gene2Oligo: Oligonucleotide design for in vitro gene synthesis
    • DOI 10.1093/nar/gkh401
    • Rouillard, J.-M., Lee, W., Truan, G., Gao, X., Zhou, X., and Gulari, E. (2004) Gene2Oligo: oligonucleotide design for in vitro gene synthesis, Nucleic Acids Res 32 , W176-W180. (Pubitemid 38997324)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB. SERV. ISS.
    • Rouillard, J.-M.1    Lee, W.2    Truan, G.3    Gao, X.4    Zhou, X.5    Gulari, E.6
  • 64
    • 33747816812 scopus 로고    scopus 로고
    • Zinc Finger Tools: Custom DNA-binding domains for transcription factors and nucleases
    • DOI 10.1093/nar/gkl209
    • Mandell, J. G., and Barbas, C. F. (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases, Nucleic Acids Res 34 , W516-W523. (Pubitemid 44529824)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Mandell, J.G.1    Barbas III, C.F.2
  • 65
    • 0042622239 scopus 로고    scopus 로고
    • NEBcutter: A program to cleave DNA with restriction enzymes
    • DOI 10.1093/nar/gkg526
    • Vincze, T., Posfai, J., and Roberts, R. J. (2003) NEBcutter: A program to cleave DNA with restriction enzymes, Nucleic Acids Res 31 , 3688-3691. (Pubitemid 37442224)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3688-3691
    • Vincze, T.1    Posfai, J.2    Roberts, R.J.3
  • 67
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: Software for nucleic acid folding and hybridization
    • Markham, N. R., and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization, Methods Mol Biol 453 , 3-31.
    • (2008) Methods Mol Biol , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 68
    • 23144440350 scopus 로고    scopus 로고
    • DINAMelt web server for nucleic acid melting prediction
    • DOI 10.1093/nar/gki591
    • Markham, N. R., and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction, Nucleic Acids Res 33 , W577-W581. (Pubitemid 44529988)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Markham, N.R.1    Zuker, M.2
  • 70
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • DOI 10.1093/nar/gkg599
    • Hofacker, I. L. (2003) Vienna RNA secondary structure server, Nucleic Acids Res 31 , 3429-3431. (Pubitemid 37442172)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3429-3431
    • Hofacker, I.L.1
  • 71
    • 77951796655 scopus 로고    scopus 로고
    • RNA FRABASE 2.0: An advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
    • Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E. K., Blazewicz, J., and Adamiak, R. W. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics 11 :231.
    • BMC Bioinformatics , vol.11 , pp. 231
    • Popenda, M.1    Szachniuk, M.2    Blazewicz, M.3    Wasik, S.4    Burke, E.K.5    Blazewicz, J.6    Adamiak, R.W.7
  • 72
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of CASP III targets using ROSETTA
    • DOI 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
    • Simons, K. T., Bonneau, R., Ruczinski, I., and Baker, D. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins Suppl 3 , 171-176. (Pubitemid 29463528)
    • (1999) Proteins: Structure, Function and Genetics , vol.37 , Issue.SUPPL. 3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 73
    • 0242369082 scopus 로고    scopus 로고
    • RAPTOR: Optimal protein threading by linear programming
    • Xu, J., Li, M., Kim, D., and Xu, Y. (2003) RAPTOR: optimal protein threading by linear programming, J Bioinform Comput Biol 1 , 95-117.
    • (2003) J Bioinform Comput Biol , vol.1 , pp. 95-117
    • Xu, J.1    Li, M.2    Kim, D.3    Xu, Y.4
  • 74
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • DOI 10.1093/nar/gki408
    • Soeding, J., Biegert, A., and Lupas, A. N. (2005) The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res 33 , W244-W248. (Pubitemid 44529917)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 76
    • 14144256681 scopus 로고    scopus 로고
    • Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
    • DOI 10.1016/j.jmb.2004.12.019
    • Pokala, N., and Handel, T. M. (2005) Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity, J Mol Biol 347 , 203-227. (Pubitemid 40283639)
    • (2005) Journal of Molecular Biology , vol.347 , Issue.1 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 77
    • 77649187057 scopus 로고    scopus 로고
    • PROTDES: CHARMM toolbox for computational protein design
    • Suarez, M., Tortosa, P., and Jaramillo, A. (2008) PROTDES: CHARMM toolbox for computational protein design, Syst Synth Biol 2 , 105-113.
    • (2008) Syst Synth Biol , vol.2 , pp. 105-113
    • Suarez, M.1    Tortosa, P.2    Jaramillo, A.3
  • 78
    • 33744471931 scopus 로고    scopus 로고
    • Enhanced automated function prediction using distantly related sequences and contextual association by PFP
    • DOI 10.1110/ps.062153506
    • Hawkins, T., Luban, S., and Kihara, D. (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP, Protein Sci 15 , 1550-1556. (Pubitemid 43800030)
    • (2006) Protein Science , vol.15 , Issue.6 , pp. 1550-1556
    • Hawkins, T.1    Luban, S.2    Kihara, D.3
  • 79
    • 59849089151 scopus 로고    scopus 로고
    • PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
    • Hawkins, T., Chitale, M., Luban, S., and Kihara, D. (2009) PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data, Proteins 74 , 566-582.
    • (2009) Proteins , vol.74 , pp. 566-582
    • Hawkins, T.1    Chitale, M.2    Luban, S.3    Kihara, D.4
  • 80
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • Kelley, L. A., and Sternberg, M. J. E. (2009) Protein structure prediction on the Web: a case study using the Phyre server, Nat Protoc 4 , 363-371.
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 81
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • Roy, A., Kucukural, A., and Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction, Nat Protoc 5 , 725-738.
    • Nat Protoc , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 84
    • 34147192127 scopus 로고    scopus 로고
    • Biskit - A software platform for structural bioinformatics
    • DOI 10.1093/bioinformatics/btl655
    • Gruenberg, R., Nilges, M., and Leckner, J. (2007) Biskit-a software platform for structural bioinformatics, Bioinformatics 23 , 769-770. (Pubitemid 46554731)
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 769-770
    • Grunberg, R.1    Nilges, M.2    Leckner, J.3
  • 85
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • DOI 10.1038/nbt1413, PII NBT1413
    • Canton, B., Labno, A., and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices, Nat Biotechnol 26 , 787-793. (Pubitemid 351961452)
    • (2008) Nature Biotechnology , vol.26 , Issue.7 , pp. 787-793
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 86
    • 4344703213 scopus 로고    scopus 로고
    • BioLogic gates enable logical transcription control in mammalian cells
    • DOI 10.1002/bit.20142
    • Kramer, B. P., Fischer, C., and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells, Biotechnol Bioeng 87 , 478-484. (Pubitemid 39150049)
    • (2004) Biotechnology and Bioengineering , vol.87 , Issue.4 , pp. 478-484
    • Kramer, B.P.1    Fischer, C.2    Fussenegger, M.3
  • 90
    • 41349118107 scopus 로고    scopus 로고
    • Complex riboswitches
    • DOI 10.1126/science.1152621
    • Breaker, R. R. (2008) Complex riboswitches, Science 319 , 1795-1797. (Pubitemid 351451558)
    • (2008) Science , vol.319 , Issue.5871 , pp. 1795-1797
    • Breaker, R.R.1
  • 91
    • 54249113318 scopus 로고    scopus 로고
    • Higher-order cellular information processing with synthetic RNA devices
    • Win, M. N., and Smolke, C. D. (2008) Higher-order cellular information processing with synthetic RNA devices, Science 322 , 456-460.
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 92
    • 21444457242 scopus 로고    scopus 로고
    • Programmable ligand-controlled riboregulators of eukaryotic gene expression
    • DOI 10.1038/nbt1069
    • Bayer, T. S., and Smolke, C. D. (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression, Nat Biotechnol 23 , 337-343. (Pubitemid 41094422)
    • (2005) Nature Biotechnology , vol.23 , Issue.3 , pp. 337-343
    • Bayer, T.S.1    Smolke, C.D.2
  • 93
    • 62649171253 scopus 로고    scopus 로고
    • Frameworks for programming biological function through RNA parts and devices
    • Win, M. N., Liang, J. C., and Smolke, C. D. (2009) Frameworks for programming biological function through RNA parts and devices, Chem Biol 16 , 298-310.
    • (2009) Chem Biol , vol.16 , pp. 298-310
    • Win, M.N.1    Liang, J.C.2    Smolke, C.D.3
  • 95
    • 77952473769 scopus 로고    scopus 로고
    • Strategies for protein synthetic biology
    • Gruenberg, R., and Serrano, L. (2010) Strategies for protein synthetic biology, Nucleic Acids Res 38 , 2663-2675.
    • (2010) Nucleic Acids Res , vol.38 , pp. 2663-2675
    • Gruenberg, R.1    Serrano, L.2


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