메뉴 건너뛰기




Volumn 8, Issue 3, 2009, Pages 259-270

Retrieval efficiency of DNA-based databases of digital signals

Author keywords

DNA; DNA based digital signal processing; Hybridization; Modeling; Signal processing; Simulations

Indexed keywords

CLOSED FORM APPROXIMATIONS; DATABASE SIZE; DIGITAL DOMAIN; DIGITAL SIGNALS; DNA DATABASE; DNA HYBRIDIZATION; DNA MOLECULES; HYBRIDIZATION; HYBRIDIZATION EFFICIENCY; MATHEMATICAL FRAMEWORKS; MODELING; NUMERICAL SOLUTION; RETRIEVAL EFFICIENCY; SIMILARITY CRITERIA; SOURCE DISTRIBUTION;

EID: 75149156102     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2009.2026371     Document Type: Article
Times cited : (2)

References (52)
  • 1
    • 0028114541 scopus 로고
    • Molecular computation of solutions to combinatorial problems
    • Nov.
    • L. M. Adleman, "Molecular computation of solutions to combinatorial problems," Science, vol.266, no.11, pp. 1021-1024, Nov. 1994.
    • (1994) Science , vol.266 , Issue.11 , pp. 1021-1024
    • Adleman, L.M.1
  • 2
    • 0029054951 scopus 로고
    • Building an associative memory vastly larger than the brain
    • Apr.
    • E. B. Baum, "Building an associative memory vastly larger than the brain," Science, vol.268, no.5210, pp. 583-585, Apr. 1995.
    • (1995) Science , vol.268 , Issue.5210 , pp. 583-585
    • Baum, E.B.1
  • 4
    • 33745751103 scopus 로고    scopus 로고
    • Conformational addressing using the hairpin structure of single-strand DNA
    • L.Wang, K. Chen, and Y. S. Ong, Eds. Berlin, Germany: Springer-Verlag, Jun.
    • A. Kameda, M. Yamamoto, H. Uejima, M. Hagiya, K. Sakamoto, and A. Ohuchi, "Conformational addressing using the hairpin structure of single-strand DNA," in DNA Computing 9, vol.2943, L.Wang, K. Chen, and Y. S. Ong, Eds. Berlin, Germany: Springer-Verlag, Jun. 2004.
    • (2004) DNA Computing 9 , vol.2943
    • Kameda, A.1    Yamamoto, M.2    Uejima, H.3    Hagiya, M.4    Sakamoto, K.5    Ohuchi, A.6
  • 5
    • 24144441068 scopus 로고    scopus 로고
    • Hierarchical DNA memory based on nested PCR
    • (Lecture Notes in Computer Science vol. 2568) M.Hagiya and A. Ohuchi, Eds. New York: Springer-Verlag
    • S. Kashiwamura, M. Yamamoto, A. Kameda, T. Shiba, and A. Ohuchi, "Hierarchical DNA memory based on nested PCR," in DNA Computing 8 (Lecture Notes in Computer Science vol. 2568),M.Hagiya and A. Ohuchi, Eds. New York: Springer-Verlag, 2002, pp. 112-123.
    • (2002) DNA Computing 8 , pp. 112-123
    • Kashiwamura, S.1    Yamamoto, M.2    Kameda, A.3    Shiba, T.4    Ohuchi, A.5
  • 6
    • 84944877006 scopus 로고    scopus 로고
    • Experimental construction of very large scale DNA databases with associative search capability
    • Berlin, Germany: Springer-Verlag, Jan.
    • J. H. Reif, T. H. Labean, M. Pirrung, V. S. Rana, B. Guo, C. Kingsford, and G. S. Wickham, "Experimental construction of very large scale DNA databases with associative search capability," in Lecture Notes in Computer Science, vol.2340. Berlin, Germany: Springer-Verlag, Jan. 2002, pp. 231-247.
    • (2002) Lecture Notes in Computer Science , vol.2340 , pp. 231-247
    • Reif, J.H.1    Labean, T.H.2    Pirrung, M.3    Rana, V.S.4    Guo, B.5    Kingsford, C.6    Wickham, G.S.7
  • 7
    • 33749985208 scopus 로고    scopus 로고
    • Hairpin-DNA memory using molecular addressing
    • M. Takinoue and A. Suyama, "Hairpin-DNA memory using molecular addressing," Small, vol.2, no.11, pp. 1244-1247, 2006.
    • (2006) Small , vol.2 , Issue.11 , pp. 1244-1247
    • Takinoue, M.1    Suyama, A.2
  • 8
    • 33645508614 scopus 로고    scopus 로고
    • DNAcomputing approach to semantic knowledge representation
    • Y. Tsuboi, Z. Ibrahim, and O. Ono, "DNAcomputing approach to semantic knowledge representation," Int. J. Hybrid Intell. Syst., vol.2, no.1, pp. 1- 12, 2005.
    • (2005) Int. J. Hybrid Intell. Syst. , vol.2 , Issue.1 , pp. 1-12
    • Tsuboi, Y.1    Ibrahim, Z.2    Ono, O.3
  • 9
    • 23144457442 scopus 로고    scopus 로고
    • A DNA-based memory with in vitro learning and associative recall
    • Jun.
    • J. Chen, R. Deaton, and Y.-Z. Wang, "A DNA-based memory with in vitro learning and associative recall," Natural Comput., vol.4, no.2, pp. 83-101, Jun. 2005.
    • (2005) Natural Comput , vol.4 , Issue.2 , pp. 83-101
    • Chen, J.1    Deaton, R.2    Wang, Y.-Z.3
  • 11
    • 26844510903 scopus 로고    scopus 로고
    • On designing DNA databases for the storage and retrieval of digital signals
    • Berlin, Germany: Springer-Verlag, Jul.
    • S. A. Tsaftaris and A. K. Katsaggelos, "On designing DNA databases for the storage and retrieval of digital signals," in Lecture Notes in Computer Science, vol.3611. Berlin, Germany: Springer-Verlag, Jul. 2005, pp. 1192-1201.
    • (2005) Lecture Notes in Computer Science , vol.3611 , pp. 1192-1201
    • Tsaftaris, S.A.1    Katsaggelos, A.K.2
  • 13
    • 33947627061 scopus 로고    scopus 로고
    • DNA hybridization as a similarity criterion for querying digital signals stored in DNA databases
    • May
    • S. A. Tsaftaris, V. Hatzimanikatis, and A. K. Katsaggelos, "DNA hybridization as a similarity criterion for querying digital signals stored in DNA databases," in Proc. ICASSP 2006,May, vol.2, pp. II-1084-II-1087.
    • Proc. ICASSP 2006 , vol.2
    • Tsaftaris, S.A.1    Hatzimanikatis, V.2    Katsaggelos, A.K.3
  • 14
    • 64549154351 scopus 로고    scopus 로고
    • The not so digital future of digital signal processing
    • Mar.
    • S. A. Tsaftaris and A. K. Katsaggelos, "The not so digital future of digital signal processing," Proc. IEEE, vol.96, no.3, pp. 375-377, Mar. 2008.
    • (2008) Proc. IEEE , vol.96 , Issue.3 , pp. 375-377
    • Tsaftaris, S.A.1    Katsaggelos, A.K.2
  • 16
    • 75149152120 scopus 로고    scopus 로고
    • In silico estimation of annealing specificity of query searches in DNA databases
    • Dec.
    • S. A. Tsaftaris, V. Hatzimanikatis, and A. K. Katsaggelos, "In silico estimation of annealing specificity of query searches in DNA databases," J. Jpn. Soc. Simul. Technol.(JSST), vol.24, no.4, pp. 268-276, Dec. 2005.
    • (2005) J. Jpn. Soc. Simul. Technol.(JSST) , vol.24 , Issue.4 , pp. 268-276
    • Tsaftaris, S.A.1    Hatzimanikatis, V.2    Katsaggelos, A.K.3
  • 17
    • 35248838409 scopus 로고    scopus 로고
    • Stochastic local search algorithms for DNA word design
    • Berlin, Germany: Springer-Verlag
    • D. C. Tulpan, H. H. Hoos, and A. E. Condon, "Stochastic local search algorithms for DNA word design," in Lecture Notes in Computer Science, vol.2568. Berlin, Germany: Springer-Verlag, 2003, pp. 229-241.
    • (2003) Lecture Notes in Computer Science , vol.2568 , pp. 229-241
    • Tulpan, D.C.1    Hoos, H.H.2    Condon, A.E.3
  • 19
    • 77049102423 scopus 로고    scopus 로고
    • In search of optimal codes for DNAs computing
    • Berlin, Germany: Springer-Verlag
    • M. Garzon, V. Phan, S. Roy, and A. Neel, "In search of optimal codes for DNAs computing," in DNA Computing. Berlin, Germany: Springer- Verlag, 2006, pp. 143-156.
    • (2006) DNA Computing , pp. 143-156
    • Garzon, M.1    Phan, V.2    Roy, S.3    Neel, A.4
  • 20
    • 33745357804 scopus 로고    scopus 로고
    • Designed DNA molecules: Principles and applications of molecular nanotechnology
    • Jun.
    • A. Condon, "Designed DNA molecules: Principles and applications of molecular nanotechnology," Nature Rev. Genet., vol.7, no.7, pp. 565- 575, Jun. 2006.
    • (2006) Nature Rev. Genet. , vol.7 , Issue.7 , pp. 565-575
    • Condon, A.1
  • 22
    • 0036418698 scopus 로고    scopus 로고
    • Predicting out-of-sequence reassembly in DNA shuffling
    • Nov.
    • G. L. Moore and C. D. Maranas, "Predicting out-of-sequence reassembly in DNA shuffling," J. Theor. Biol., vol.219, no.1, pp. 9-17, Nov. 2002.
    • (2002) J. Theor. Biol. , vol.219 , Issue.1 , pp. 9-17
    • Moore, G.L.1    Maranas, C.D.2
  • 25
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Jul.
    • M. Zuker, "Mfold web server for nucleic acid folding and hybridization prediction," Nucleic Acids Res., vol.31, no.13, pp. 3406-3415, Jul. 2003.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 26
    • 45849154696 scopus 로고    scopus 로고
    • Statistical mechanics of base stacking and pairing in DNA melting
    • Nov.
    • V. Ivanov, Y. Zeng, and G. Zocchi, "Statistical mechanics of base stacking and pairing in DNA melting," Phys. Rev. E, Stat. Phys. Plasmas Fluids Relat., vol.70, no.5, pp. 051 907-1-051 907-6, Nov. 2004.
    • (2004) Phys. Rev. E, Stat. Phys. Plasmas Fluids Relat. , vol.70 , Issue.5 , pp. 0519071-0519076
    • Ivanov, V.1    Zeng, Y.2    Zocchi, G.3
  • 27
    • 3543063923 scopus 로고    scopus 로고
    • A statistical mechanical treatment of error in the annealing biostep of DNA computation
    • Orlando, FL, Jul. 13-17
    • J. A. Rose, R. J.Deaton, D. R. Franceschetti, M. Garzon, and S. E. Stevens, Jr., "A statistical mechanical treatment of error in the annealing biostep of DNA computation," in Proc. Genet. Evol. Comput. Conf., Orlando, FL, Jul. 13-17, 1999, vol.2, pp. 1829-1834.
    • (1999) Proc. Genet. Evol. Comput. Conf. , vol.2 , pp. 1829-1834
    • Rose, J.A.1    Deaton, R.J.2    Franceschetti, D.R.3    Garzon, M.4    Stevens Jr., S.E.5
  • 28
    • 0037401145 scopus 로고    scopus 로고
    • Modeling hybridization kinetics
    • May
    • J.-Y. Wang and K. Drlica, "Modeling hybridization kinetics," Math. Biosci., vol.183, no.1, pp. 37-47, May 2003.
    • (2003) Math. Biosci. , vol.183 , Issue.1 , pp. 37-47
    • Wang, J.-Y.1    Drlica, K.2
  • 29
    • 75149155393 scopus 로고    scopus 로고
    • A new codeword design algorithm for DNA based storage and retrieval of digital signals
    • presented at London, ON, Canada
    • S. A. Tsaftaris and A. K. Katsaggelos, "A new codeword design algorithm for DNA based storage and retrieval of digital signals," presented at the 11th Int.Meeting DNA-Based Comput. (DNA 11), London, ON, Canada, 2005.
    • (2005) The 11th Int.Meeting DNA-Based Comput. (DNA 11)
    • Tsaftaris, S.A.1    Katsaggelos, A.K.2
  • 30
    • 33847609597 scopus 로고    scopus 로고
    • Thermodynamic analysis of interacting nucleic acid strands
    • R. M. Dirks, J. S. Bois, J. M. Schaeffer, E. Winfree, and N. A. Pierce, "Thermodynamic analysis of interacting nucleic acid strands," SIAM Rev., vol.49, no.1, pp. 65-88, 2007.
    • (2007) SIAM Rev , vol.49 , Issue.1 , pp. 65-88
    • Dirks, R.M.1    Bois, J.S.2    Schaeffer, J.M.3    Winfree, E.4    Pierce, N.A.5
  • 31
    • 0032729689 scopus 로고    scopus 로고
    • Predicting oligonucleotide affinity to nucleic acid targets
    • Nov.
    • D. H. Mathews, M. E. Burkard, S. M. Freier, J. R.Wyatt, and D. H. Turner, "Predicting oligonucleotide affinity to nucleic acid targets," RNA, vol.5, no.11, pp. 1458-1469, Nov. 1999.
    • (1999) RNA , vol.5 , Issue.11 , pp. 1458-1469
    • Mathews, D.H.1    Burkard, M.E.2    Freier, S.M.3    Wyatt, J.R.4    Turner, D.H.5
  • 32
    • 57649214363 scopus 로고    scopus 로고
    • Biomolecular computation in virtual test tubes
    • Berlin, Germany: Springer-Verlag
    • M. Garzon and C. Oehmen, "Biomolecular computation in virtual test tubes," in DNA Computing. Berlin, Germany: Springer-Verlag, 2002, pp. 117-128.
    • (2002) DNA Computing , pp. 117-128
    • Garzon, M.1    Oehmen, C.2
  • 33
    • 13844321607 scopus 로고    scopus 로고
    • Virtual test tubes: For biomoleculebased computing
    • Dec.
    • M. Garzon, D. Blain, and A. Neel, "Virtual test tubes: For biomoleculebased computing," Natural Comput., vol.3, no.4, pp. 461-477, Dec. 2004.
    • (2004) Natural Comput , vol.3 , Issue.4 , pp. 461-477
    • Garzon, M.1    Blain, D.2    Neel, A.3
  • 34
    • 33947145127 scopus 로고    scopus 로고
    • Coupled equilibrium model of hybridization error for the DNA microarray and tag-antitag systems
    • Mar.
    • J. A. Rose,R. J.Deaton, M. Hagiya, and A. Suyama, "Coupled equilibrium model of hybridization error for the DNA microarray and tag-antitag systems," IEEE Trans. Nanobiosci., vol.6, no.1, pp. 18-27, Mar. 2007.
    • (2007) IEEE Trans. Nanobiosci. , vol.6 , Issue.1 , pp. 18-27
    • Rose, J.A.1    Deaton, R.J.2    Hagiya, M.3    Suyama, A.4
  • 35
    • 33845368662 scopus 로고    scopus 로고
    • Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions
    • Dec.
    • M. T. Horne, D. J. Fish, and A. S. Benight, "Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions," Biophys. J., vol.91, no.11, pp. 4133-4153, Dec. 2006.
    • (2006) Biophys. J. , vol.91 , Issue.11 , pp. 4133-4153
    • Horne, M.T.1    Fish, D.J.2    Benight, A.S.3
  • 36
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • Feb.
    • J. Santalucia, "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics," Proc. Nat. Acad. Sci. USA, vol.95, no.4, pp. 1460-1465, Feb. 1998.
    • (1998) Proc. Nat. Acad. Sci. USA , vol.95 , Issue.4 , pp. 1460-1465
    • Santalucia, J.1
  • 37
    • 65249086255 scopus 로고    scopus 로고
    • A unified Poland-Scheraga model of oligo-and polynucleotideDNAmelting: Salt effects and predictive power
    • D. Jost and R. Everaers, "A unified Poland-Scheraga model of oligo- and polynucleotideDNAmelting: Salt effects and predictive power," Biophys. J., vol.96, no.3, pp. 1056-1067, 2009.
    • (2009) Biophys. J. , vol.96 , Issue.3 , pp. 1056-1067
    • Jost, D.1    Everaers, R.2
  • 38
    • 84863752357 scopus 로고    scopus 로고
    • Retrieval accuracy of very large DNA-based databases of digital signals
    • Poznán, Polland, Sep. 3-7
    • S. A. Tsaftaris and A. K. Katsaggelos, "Retrieval accuracy of very large DNA-based databases of digital signals," in Proc. 2007 Eur. Signal Process. Conf., Poznán, Polland, Sep. 3-7, pp. 1561-1567.
    • Proc. 2007 Eur. Signal Process. Conf. , pp. 1561-1567
    • Tsaftaris, S.A.1    Katsaggelos, A.K.2
  • 39
    • 27744491204 scopus 로고    scopus 로고
    • Competitive hybridization kinetics reveals unexpected behavior patterns
    • Nov.
    • Y. Zhang, D. A. Hammer, and D. J. Graves, "Competitive hybridization kinetics reveals unexpected behavior patterns," Biophys. J., vol.89, no.5, pp. 2950-2959, Nov. 2005.
    • (2005) Biophys. J. , vol.89 , Issue.5 , pp. 2950-2959
    • Zhang, Y.1    Hammer, D.A.2    Graves, D.J.3
  • 40
    • 14744306436 scopus 로고
    • Simultaneous amplification and detection of specific DNA sequences
    • Apr.
    • R. Higuchi, G. Dollinger, P. S. Walsh, and R. Griffith, "Simultaneous amplification and detection of specific DNA sequences," Biotechnology, vol.10, no.4, pp. 413-417, Apr. 1992.
    • (1992) Biotechnology , vol.10 , Issue.4 , pp. 413-417
    • Higuchi, R.1    Dollinger, G.2    Walsh, P.S.3    Griffith, R.4
  • 41
    • 1642569566 scopus 로고    scopus 로고
    • Quantitative analysis of nucleic acids-The last fewyears of progress
    • Jan.
    • C. Ding and C. R. Cantor, "Quantitative analysis of nucleic acids-The last fewyears of progress," J. Biochem. Mol. Biol., vol.37, no.1, pp. 1-10, Jan. 2004.
    • (2004) J. Biochem. Mol. Biol. , vol.37 , Issue.1 , pp. 1-10
    • Ding, C.1    Cantor, C.R.2
  • 44
    • 0037215734 scopus 로고    scopus 로고
    • The importance of thermodynamic equilibrium for high throughput gene expression arrays
    • Jan.
    • G. Bhanot,Y. Louzoun, J. Zhu, and C.DeLisi, "The importance of thermodynamic equilibrium for high throughput gene expression arrays," Biophys. J., vol.84, no.1, pp. 124-135, Jan. 2003.
    • (2003) Biophys. J. , vol.84 , Issue.1 , pp. 124-135
    • Bhanot, G.1    Louzoun, Y.2    Zhu, J.3    Delisi, C.4
  • 45
    • 33646181184 scopus 로고    scopus 로고
    • A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants
    • Feb.
    • J. Bishop, S. Blair, and A. M. Chagovetz, "A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants," Biophys. J., vol.90, no.3, pp. 831-840, Feb. 2006.
    • (2006) Biophys. J. , vol.90 , Issue.3 , pp. 831-840
    • Bishop, J.1    Blair, S.2    Chagovetz, A.M.3
  • 46
    • 0037620483 scopus 로고    scopus 로고
    • Modeling of DNA hybridization kinetics for spatially resolved biochips
    • Jun.
    • D. Erickson, D. Li, and U. J. Krull, "Modeling of DNA hybridization kinetics for spatially resolved biochips," Anal. Biochem., vol.317, no.2, pp. 186-200, Jun. 2003.
    • (2003) Anal. Biochem. , vol.317 , Issue.2 , pp. 186-200
    • Erickson, D.1    Li, D.2    Krull, U.J.3
  • 47
    • 0345548600 scopus 로고    scopus 로고
    • Chipcheck-A program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays
    • Nov.
    • K. H. Siegmund, U. E. Steiner, and C. Richert, "Chipcheck-A program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays," J. Chem. Inf. Comput. Sci., vol.43, no.6, pp. 2153-2162, Nov. 2003.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , Issue.6 , pp. 2153-2162
    • Siegmund, K.H.1    Steiner, U.E.2    Richert, C.3
  • 48
    • 0025970049 scopus 로고
    • Theory of molecular machines. I. Channel capacity of molecular machines
    • T. D. Schneider, "Theory of molecular machines. I. Channel capacity of molecular machines," J. Theor. Biol., vol.148, no.1, pp. 83-123, 1991.
    • (1991) J. Theor. Biol. , vol.148 , Issue.1 , pp. 83-123
    • Schneider, T.D.1
  • 49
    • 34547343930 scopus 로고    scopus 로고
    • Efficiency and reliability of semantic retrieval in DNA-based memories
    • Berlin, Germany: Springer-Verlag
    • M. H. Garzon, K. Bobba, and A. Neel, "Efficiency and reliability of semantic retrieval in DNA-based memories," in DNA Computing. Berlin, Germany: Springer-Verlag, 2004, pp. 157-169.
    • (2004) DNA Computing , pp. 157-169
    • Garzon, M.H.1    Bobba, K.2    Neel, A.3
  • 50
    • 33744503151 scopus 로고    scopus 로고
    • Astatistical model for microarrays, optimal estimation algorithms, and limits of performance
    • Jun.
    • H.Vikalo, B.Hassibi, and A. Hassibi, "Astatistical model for microarrays, optimal estimation algorithms, and limits of performance," IEEE Trans. Signal Process., vol.54, no.6, pp. 2444-2455, Jun. 2006.
    • (2006) IEEE Trans. Signal Process. , vol.54 , Issue.6 , pp. 2444-2455
    • Vikalo, H.1    Hassibi, B.2    Hassibi, A.3
  • 51
    • 0242404586 scopus 로고    scopus 로고
    • Diffusion-reaction modelling of DNA hybridization kinetics on biochips
    • Nov.
    • K. Pappaert, P. Van Hummelen, J. Vanderhoeven, G. V. Baron, and G. Desmet, "Diffusion-reaction modelling of DNA hybridization kinetics on biochips," Chem. Eng. Sci., vol.58, no.21, pp. 4921-4930, Nov. 2003.
    • (2003) Chem. Eng. Sci. , vol.58 , Issue.21 , pp. 4921-4930
    • Pappaert, K.1    Van Hummelen, P.2    Vanderhoeven, J.3    Baron, G.V.4    Desmet, G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.