메뉴 건너뛰기




Volumn 5, Issue 10, 2009, Pages

Modeling structure-function relationships in synthetic DNA sequences using attribute grammars

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; COMPUTER AIDED DESIGN; DNA; FUNCTIONS; GENE EXPRESSION;

EID: 73349101023     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000529     Document Type: Article
Times cited : (27)

References (78)
  • 1
    • 0004120906 scopus 로고    scopus 로고
    • Cambridge, Mass, Harvard University Press. 186 p
    • Keller EF (2000) The century of the gene. Cambridge, Mass.: Harvard University Press. 186 p.
    • (2000) The century of the gene
    • Keller, E.F.1
  • 2
    • 0003898626 scopus 로고    scopus 로고
    • Cold Spring Harbor, N.Y, Cold Spring Harbor Laboratory Press. 174 p
    • Sturtevant AH (2001) A history of genetics. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press. 174 p.
    • (2001) A history of genetics
    • Sturtevant, A.H.1
  • 3
    • 9444240966 scopus 로고    scopus 로고
    • Timeline - George Beadle: From genes to proteins
    • Singer M, Berg P (2004) Timeline - George Beadle: from genes to proteins. Nat Rev Genet 5: 949-954.
    • (2004) Nat Rev Genet , vol.5 , pp. 949-954
    • Singer, M.1    Berg, P.2
  • 4
    • 33745435889 scopus 로고
    • A case history in biological research
    • Tatum EL (1959) A case history in biological research. Science 129: 1711-1715.
    • (1959) Science , vol.129 , pp. 1711-1715
    • Tatum, E.L.1
  • 8
    • 0037249630 scopus 로고    scopus 로고
    • Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
    • Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, et al. (2003) Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res 31: 216-218.
    • (2003) Nucleic Acids Res , vol.31 , pp. 216-218
    • Weng, S.1    Dong, Q.2    Balakrishnan, R.3    Christie, K.4    Costanzo, M.5
  • 12
    • 33646432245 scopus 로고    scopus 로고
    • Stochastic model of coliphage lambda regulatory network
    • Wang SY, Zhang YP, Qi OY (2006) Stochastic model of coliphage lambda regulatory network. Phys Rev E 73.
    • (2006) Phys Rev E , vol.73
    • Wang, S.Y.1    Zhang, Y.P.2    Qi, O.Y.3
  • 14
    • 0034644270 scopus 로고    scopus 로고
    • The segment polarity network is a robust developmental module
    • von Dassow G, Meir E, Munro EM, Odell GM (2000) The segment polarity network is a robust developmental module. Nature 406: 188-192.
    • (2000) Nature , vol.406 , pp. 188-192
    • von Dassow, G.1    Meir, E.2    Munro, E.M.3    Odell, G.M.4
  • 15
    • 33748311990 scopus 로고    scopus 로고
    • Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
    • Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, et al. (2006) Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 38: 1082-1087.
    • (2006) Nat Genet , vol.38 , pp. 1082-1087
    • Ramsey, S.A.1    Smith, J.J.2    Orrell, D.3    Marelli, M.4    Petersen, T.W.5
  • 16
    • 0035011208 scopus 로고    scopus 로고
    • The parts list of life
    • Bains W (2001) The parts list of life. Nat Biotechnol 19: 401-402.
    • (2001) Nat Biotechnol , vol.19 , pp. 401-402
    • Bains, W.1
  • 17
    • 7444233131 scopus 로고    scopus 로고
    • ORFeome cloning and systems biology: Standardized mass production of the parts from the parts-list
    • Brasch MA, Hartley JL, Vidal M (2004) ORFeome cloning and systems biology: Standardized mass production of the parts from the parts-list. Genome Res 14: 2001-2009.
    • (2004) Genome Res , vol.14 , pp. 2001-2009
    • Brasch, M.A.1    Hartley, J.L.2    Vidal, M.3
  • 18
    • 28244441875 scopus 로고    scopus 로고
    • Plant functional genomics: Beyond the parts list
    • Stewart CN (2005) Plant functional genomics: beyond the parts list. Trends Plant Sci 10: 561-562.
    • (2005) Trends Plant Sci , vol.10 , pp. 561-562
    • Stewart, C.N.1
  • 20
  • 21
    • 33846847440 scopus 로고    scopus 로고
    • Annotating the human proteome: Beyond establishing a parts list
    • Mueller M, Martens L, Apweiler R (2007) Annotating the human proteome: Beyond establishing a parts list. Biochim Biophys Acta 1774: 175-191.
    • (2007) Biochim Biophys Acta , vol.1774 , pp. 175-191
    • Mueller, M.1    Martens, L.2    Apweiler, R.3
  • 22
    • 54449097862 scopus 로고    scopus 로고
    • Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes
    • Rabani M, Kertesz M, Segal E (2008) Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A 105: 14885-14890.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14885-14890
    • Rabani, M.1    Kertesz, M.2    Segal, E.3
  • 24
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 25
    • 0037165942 scopus 로고    scopus 로고
    • Combinatorial synthesis of genetic networks
    • Guet CC, Elowitz MB, Hsing W, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296: 1466-1470.
    • (2002) Science , vol.296 , pp. 1466-1470
    • Guet, C.C.1    Elowitz, M.B.2    Hsing, W.3    Leibler, S.4
  • 26
    • 36249017917 scopus 로고    scopus 로고
    • Programming gene expression with combinatorial promoters
    • Cox RS, 3rd, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3: 145.
    • (2007) Mol Syst Biol , vol.3 , pp. 145
    • Cox 3rd, R.S.1    Surette, M.G.2    Elowitz, M.B.3
  • 27
    • 58149354385 scopus 로고    scopus 로고
    • Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    • Gertz J, Siggia ED, Cohen BA (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457: 215-218.
    • (2009) Nature , vol.457 , pp. 215-218
    • Gertz, J.1    Siggia, E.D.2    Cohen, B.A.3
  • 28
    • 34547925618 scopus 로고    scopus 로고
    • Combinatorial promoter design for engineering noisy gene expression
    • Murphy KF, Balazsi G, Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 104: 12726-12731.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 12726-12731
    • Murphy, K.F.1    Balazsi, G.2    Collins, J.J.3
  • 30
    • 0014932468 scopus 로고
    • Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast
    • Agarwal KL, Buchi H, Caruthers MH, Gupta N, Khorana HG, et al. (1970) Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast. Nature 227: 27-34.
    • (1970) Nature , vol.227 , pp. 27-34
    • Agarwal, K.L.1    Buchi, H.2    Caruthers, M.H.3    Gupta, N.4    Khorana, H.G.5
  • 32
    • 61549086812 scopus 로고    scopus 로고
    • Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course
    • Dymond JS, Scheifele LZ, Richardson S, Lee P, Chandrasegaran S, et al. (2009) Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course. Genetics 181: 13-21.
    • (2009) Genetics , vol.181 , pp. 13-21
    • Dymond, J.S.1    Scheifele, L.Z.2    Richardson, S.3    Lee, P.4    Chandrasegaran, S.5
  • 33
    • 28544433105 scopus 로고    scopus 로고
    • Chan LY, Kosuri S, Endy D (2005) Refactoring bacteriophage T7. Mol Syst Biol 1: 2005.0018.
    • Chan LY, Kosuri S, Endy D (2005) Refactoring bacteriophage T7. Mol Syst Biol 1: 2005.0018.
  • 35
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • Endy D (2005) Foundations for engineering biology. Nature 438: 449-453.
    • (2005) Nature , vol.438 , pp. 449-453
    • Endy, D.1
  • 37
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26: 787-793.
    • (2008) Nat Biotechnol , vol.26 , pp. 787-793
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 38
    • 46449120581 scopus 로고    scopus 로고
    • Virus attenuation by genome-scale changes in codon pair bias
    • Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, et al. (2008) Virus attenuation by genome-scale changes in codon pair bias. Science 320: 1784-1787.
    • (2008) Science , vol.320 , pp. 1784-1787
    • Coleman, J.R.1    Papamichail, D.2    Skiena, S.3    Futcher, B.4    Wimmer, E.5
  • 39
    • 33644841721 scopus 로고    scopus 로고
    • Protein linguistics - a grammar for modular protein assembly?
    • Gimona M (2006) Protein linguistics - a grammar for modular protein assembly? Nat Rev Mol Cell Biol 7: 68-73.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 68-73
    • Gimona, M.1
  • 40
    • 33745603223 scopus 로고    scopus 로고
    • Grammatical representations of macromolecular structure
    • Chiang D, Joshi AK, Searls DB (2006) Grammatical representations of macromolecular structure. J Comput Biol 13: 1077-1100.
    • (2006) J Comput Biol , vol.13 , pp. 1077-1100
    • Chiang, D.1    Joshi, A.K.2    Searls, D.B.3
  • 41
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31: 3423-3428.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 42
    • 0037079055 scopus 로고    scopus 로고
    • The language of genes
    • Searls DB (2002) The language of genes. Nature 420: 211-217.
    • (2002) Nature , vol.420 , pp. 211-217
    • Searls, D.B.1
  • 43
    • 0034046133 scopus 로고    scopus 로고
    • The language of RNA: A formal grammar that includes pseudoknots
    • Rivas E, Eddy SR (2000) The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics 16: 334-340.
    • (2000) Bioinformatics , vol.16 , pp. 334-340
    • Rivas, E.1    Eddy, S.R.2
  • 44
    • 0030821916 scopus 로고    scopus 로고
    • Linguistic approaches to biological sequences
    • Searls DB (1997) Linguistic approaches to biological sequences. Comput Appl Biosci 13: 333-344.
    • (1997) Comput Appl Biosci , vol.13 , pp. 333-344
    • Searls, D.B.1
  • 45
    • 0027944162 scopus 로고
    • Gene Structure Prediction by Linguistic Methods
    • Dong S, Searls DB (1994) Gene Structure Prediction by Linguistic Methods. Genomics 23: 540-551.
    • (1994) Genomics , vol.23 , pp. 540-551
    • Dong, S.1    Searls, D.B.2
  • 46
    • 0003108273 scopus 로고
    • The Linguistics of DNA
    • Searls DB (1992) The Linguistics of DNA. Am Sci 80: 579-591.
    • (1992) Am Sci , vol.80 , pp. 579-591
    • Searls, D.B.1
  • 47
    • 0029812203 scopus 로고    scopus 로고
    • A grammar describing 'biological binding operators' to model gene regulation
    • Bentolila S (1996) A grammar describing 'biological binding operators' to model gene regulation. Biochimie 78: 335-350.
    • (1996) Biochimie , vol.78 , pp. 335-350
    • Bentolila, S.1
  • 48
  • 50
    • 35748938455 scopus 로고    scopus 로고
    • A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
    • Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23: 2760-2767.
    • (2007) Bioinformatics , vol.23 , pp. 2760-2767
    • Cai, Y.1    Hartnett, B.2    Gustafsson, C.3    Peccoud, J.4
  • 51
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 52
    • 84976834682 scopus 로고
    • Attribute Grammar Paradigms - a High-Level Methodology in Language Implementation
    • Paakki J (1995) Attribute Grammar Paradigms - a High-Level Methodology in Language Implementation. Acm Computing Surveys 27: 196-255.
    • (1995) Acm Computing Surveys , vol.27 , pp. 196-255
    • Paakki, J.1
  • 53
    • 0001538613 scopus 로고
    • Semantics of context-free languages
    • Knuth DE (1968) Semantics of context-free languages. Mathematical Systems Theory 2: 127-145.
    • (1968) Mathematical Systems Theory , vol.2 , pp. 127-145
    • Knuth, D.E.1
  • 57
    • 0004089617 scopus 로고    scopus 로고
    • Cambridge, MA: Harvard University Press. 144 p
    • Lewontin RC (2000) The Triple Helix. Cambridge, MA: Harvard University Press. 144 p.
    • (2000) The Triple Helix
    • Lewontin, R.C.1
  • 59
    • 33750970021 scopus 로고    scopus 로고
    • Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network
    • Griffith M, Courtney T, Peccoud J, Sanders WH (2006) Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network. Bioinformatics 22: 2782-2789.
    • (2006) Bioinformatics , vol.22 , pp. 2782-2789
    • Griffith, M.1    Courtney, T.2    Peccoud, J.3    Sanders, W.H.4
  • 60
    • 2942514591 scopus 로고    scopus 로고
    • Biochemical Network Stochastic Simulator (BioNetS): Software for stochastic modeling of biochemical networks
    • Adalsteinsson D, McMillen D, Elston TC (2004) Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics 5: 24.
    • (2004) BMC Bioinformatics , vol.5 , pp. 24
    • Adalsteinsson, D.1    McMillen, D.2    Elston, T.C.3
  • 61
    • 57349087320 scopus 로고    scopus 로고
    • Removing left recursion from context-free grammars. 6th Applied Natural Language Processing Conference/1st Meeting of the North American Chapter of the Association for Computational Linguistics
    • Morgan Kaufmann. pp
    • Moore RC (2000) Removing left recursion from context-free grammars. 6th Applied Natural Language Processing Conference/1st Meeting of the North American Chapter of the Association for Computational Linguistics, Proceedings of the Conference and Proceedings of the Anlp-Naacl 2000 Student Research Workshop: Morgan Kaufmann. pp A249-A255.
    • (2000) Proceedings of the Conference and Proceedings of the Anlp-Naacl 2000 Student Research Workshop
    • Moore, R.C.1
  • 63
    • 0026544545 scopus 로고
    • The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo
    • Vellanoweth RL, Rabinowitz JC (1992) The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol Microbiol 6: 1105-1114.
    • (1992) Mol Microbiol , vol.6 , pp. 1105-1114
    • Vellanoweth, R.L.1    Rabinowitz, J.C.2
  • 64
    • 50549103571 scopus 로고    scopus 로고
    • Computational design of synthetic gene circuits with composable parts
    • Marchisio MA, 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
  • 65
    • 46249085749 scopus 로고    scopus 로고
    • Asmparts: Assembly of biological model parts
    • Rodrigo G, Carrera J, Jaramillo A (2007) Asmparts: assembly of biological model parts. Syst Synth Biol 1: 167-170.
    • (2007) Syst Synth Biol , vol.1 , pp. 167-170
    • Rodrigo, G.1    Carrera, J.2    Jaramillo, A.3
  • 67
    • 67650663955 scopus 로고    scopus 로고
    • Toward programming languages for synthetic biology
    • Pedersen M, Philipps A (2009) Toward programming languages for synthetic biology. J R Soc Interface 6: S437-450.
    • (2009) J R Soc Interface , vol.6
    • Pedersen, M.1    Philipps, A.2
  • 68
    • 0025166089 scopus 로고
    • Secondary Structure of the Ribosome Binding-Site Determines Translational Efficiency - a Quantitative-Analysis
    • Desmit MH, Vanduin J (1990) Secondary Structure of the Ribosome Binding-Site Determines Translational Efficiency - a Quantitative-Analysis. Proc Natl Acad Sci U S A 87: 7668-7672.
    • (1990) Proc Natl Acad Sci U S A , vol.87 , pp. 7668-7672
    • Desmit, M.H.1    Vanduin, J.2
  • 69
    • 0028036559 scopus 로고
    • Control of translation of messenger-RNA secondary structure in Escherichia coli - A quantitative analysis of literature data
    • Desmit MH, Vanduin J (1994) Control of translation of messenger-RNA secondary structure in Escherichia coli - A quantitative analysis of literature data. J Mol Biol 244: 144-150.
    • (1994) J Mol Biol , vol.244 , pp. 144-150
    • Desmit, M.H.1    Vanduin, J.2
  • 70
    • 64849114915 scopus 로고    scopus 로고
    • Coding-Sequence Determinants of Gene Expression in Escherichia coli
    • Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-Sequence Determinants of Gene Expression in Escherichia coli. Science 324: 255-258.
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 74
    • 73549084899 scopus 로고    scopus 로고
    • Bratko I (1986) Prolog programming for artificial intelligence. Wokingham, England; Reading, Mass.: Addison-Wesley. xvii, 423 p.
    • Bratko I (1986) Prolog programming for artificial intelligence. Wokingham, England; Reading, Mass.: Addison-Wesley. xvii, 423 p.
  • 75
    • 73549099260 scopus 로고    scopus 로고
    • Parr T (2007) The complete ANTLR reference guide. Lewisville, TX: Pragmatic. 361 p.
    • Parr T (2007) The complete ANTLR reference guide. Lewisville, TX: Pragmatic. 361 p.
  • 76
    • 66149143984 scopus 로고    scopus 로고
    • Measuring the activity of BioBrick promoters using an in vivo reference standard
    • Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, et al. (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 3: 4.
    • (2009) J Biol Eng , vol.3 , pp. 4
    • Kelly, J.R.1    Rubin, A.J.2    Davis, J.H.3    Ajo-Franklin, C.M.4    Cumbers, J.5
  • 77
    • 53549123008 scopus 로고    scopus 로고
    • Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
    • Raj A, van Oudenaarden A (2008) Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences. Cell 135: 216-226.
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    van Oudenaarden, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.