메뉴 건너뛰기




Volumn 3, Issue 1, 2008, Pages

A stitch in time: Efficient computation of genomic DNA melting bubbles

Author keywords

[No Author keywords available]

Indexed keywords


EID: 53149153562     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-3-10     Document Type: Article
Times cited : (5)

References (46)
  • 3
    • 0018504604 scopus 로고
    • Melting curves, denaturation maps, and genetic map of φX174: Their relationships and applications
    • 10.1002/bip.1979.360180808 159080
    • Tong BY Battersby SJ Melting curves, denaturation maps, and genetic map of φX174: Their relationships and applications Biopolymers 1979, 18:1917-1936. 10.1002/bip.1979.360180808 159080
    • (1979) Biopolymers , vol.18 , pp. 1917-1936
    • Tong, B.Y.1    Battersby, S.J.2
  • 4
    • 0021532338 scopus 로고
    • Stability distribution in the phage λ-DNA double helix: A correlation between physical and genetic structure
    • 6242869
    • Wada A Suyama A Stability distribution in the phage λ-DNA double helix: A correlation between physical and genetic structure J Biomol Struct Dyn 1984, 2(3):573-591. 6242869
    • (1984) J Biomol Struct Dyn , vol.2 , Issue.3 , pp. 573-591
    • Wada, A.1    Suyama, A.2
  • 5
    • 0027317073 scopus 로고
    • Stability, structure and complexity of yeast chromosome III
    • 310056 8414978 10.1093/nar/21.18.4239
    • King GJ Stability, structure and complexity of yeast chromosome III Nucl Acids Res 1993, 21(18):4239-4245. 310056 8414978 10.1093/nar/21.18.4239
    • (1993) Nucl Acids Res , vol.21 , Issue.18 , pp. 4239-4245
    • King, G.J.1
  • 6
    • 0031759433 scopus 로고    scopus 로고
    • Comparison of experimental to MELTSIM calculated DNA melting of the (A+T) rich Dictyostelium discoideum genome: Denaturation maps distinguish exons from introns
    • 9833671
    • Marx KA Assil IQ Bizzaro JW Blake RD Comparison of experimental to MELTSIM calculated DNA melting of the (A+T) rich Dictyostelium discoideum genome: Denaturation maps distinguish exons from introns J Biomol Struct Dyn 1998, 16:329-39. 9833671
    • (1998) J Biomol Struct Dyn , vol.16 , pp. 329-339
    • Marx, K.A.1    Assil, I.Q.2    Bizzaro, J.W.3    Blake, R.D.4
  • 7
    • 0034687143 scopus 로고    scopus 로고
    • Genes and the physics of the DNA double-helix
    • Yeramian E Genes and the physics of the DNA double-helix Gene 2000, 255:139-150. 10.1016/S0378-1119(00)00301-2 11024275
    • (2000) Gene , vol.255 , pp. 139-150
    • Yeramian, E.1
  • 8
    • 0034687101 scopus 로고    scopus 로고
    • The physics of DNA and the annotation of the Plasmodium falciparum genome
    • 10.1016/S0378-1119(00)00300-0 11024276
    • Yeramian E The physics of DNA and the annotation of the Plasmodium falciparum genome Gene 2000, 255:151-168. 10.1016/S0378-1119(00)00300-0 11024276
    • (2000) Gene , vol.255 , pp. 151-168
    • Yeramian, E.1
  • 9
    • 0043092354 scopus 로고    scopus 로고
    • GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences
    • 169033 12824434 10.1093/nar/gkg627
    • Yeramian E Jones L GeneFizz: A web tool to compare genetic (coding/ non-coding) and physical (helix/coil) segmentations of DNA sequences Nucleic Acids Res 2003, 31:3843-3849. 169033 12824434 10.1093/nar/gkg627
    • (2003) Nucleic Acids Res , vol.31 , pp. 3843-3849
    • Yeramian, E.1    Jones, L.2
  • 10
    • 0036171256 scopus 로고    scopus 로고
    • Physics-based gene identification: Proof of concept for plasmodium falciparum
    • 10.1093/bioinformatics/18.1.190 11836228
    • Yeramian E Bonnefoy S Langsley G Physics-based gene identification: proof of concept for plasmodium falciparum Bioinformatics 2002, 18:190-193. 10.1093/bioinformatics/18.1.190 11836228
    • (2002) Bioinformatics , vol.18 , pp. 190-193
    • Yeramian, E.1    Bonnefoy, S.2    Langsley, G.3
  • 11
    • 27144450646 scopus 로고    scopus 로고
    • Exons, Introns, and DNA Thermodynamics
    • 10.1103/PhysRevLett.94.178101 15904337
    • Carlon E Malki ML Blossey R Exons, Introns, and DNA Thermodynamics Physical Review Letters 2005, 94(17):178101. 10.1103/ PhysRevLett.94.178101 15904337
    • (2005) Physical Review Letters , vol.94 , Issue.17 , pp. 178101
    • Carlon, E.1    Malki, M.L.2    Blossey, R.3
  • 14
    • 28844464259 scopus 로고    scopus 로고
    • Can One Predict DNA Transcription Start Sites by Studying Bubbles?
    • 10.1103/PhysRevLett.95.218104 16384189
    • van Erp TS Cuesta-Lopez S Hagmann JG Peyrard M Can One Predict DNA Transcription Start Sites by Studying Bubbles? Physical Review Letters 2005, 95(21):218104. 10.1103/PhysRevLett.95.218104 16384189
    • (2005) Physical Review Letters , vol.95 , Issue.21 , pp. 218104
    • van Erp, T.S.1    Cuesta-Lopez, S.2    Hagmann, J.G.3    Peyrard, M.4
  • 15
    • 33746894748 scopus 로고    scopus 로고
    • Comment on "Can One Predict DNA Transcription Start Sites by Studying Bubbles?"
    • 10.1103/PhysRevLett.97.059801 17026148
    • Benham CJ Singh RRP Comment on "Can One Predict DNA Transcription Start Sites by Studying Bubbles?" Physical Review Letters 2006, 97(5):059801. 10.1103/PhysRevLett.97.059801 17026148
    • (2006) Physical Review Letters , vol.97 , Issue.5 , pp. 059801
    • Benham, C.J.1    Singh, R.R.P.2
  • 17
    • 33745205353 scopus 로고    scopus 로고
    • Comment on "can one predict DNA transcription start sites by studying bubbles?"
    • 10.1103/PhysRevLett.96.239801 16803416
    • Choi CH Usheva A Kalosakas G Rasmussen KØ Bishop AR Comment on "can one predict DNA transcription start sites by studying bubbles?" Physical Review Letters 2006, 96(23):239801. 10.1103/ PhysRevLett.96.239801 16803416
    • (2006) Physical Review Letters , vol.96 , Issue.23 , pp. 239801
    • Choi, C.H.1    Usheva, A.2    Kalosakas, G.3    Rasmussen, KØ.4    Bishop, A.R.5
  • 19
    • 0038050462 scopus 로고    scopus 로고
    • Bubble dynamics in double-stranded DNA
    • 10.1103/PhysRevLett.90.138101 12689326
    • Altan-Bonnet G Libchaber A Krichevsky O Bubble dynamics in double-stranded DNA Phys Rev Lett 2003, 90(1-4):138101. 10.1103/ PhysRevLett.90.138101 12689326
    • (2003) Phys Rev Lett , vol.90 , Issue.1-4 , pp. 138101
    • Altan-Bonnet, G.1    Libchaber, A.2    Krichevsky, O.3
  • 20
    • 34147109694 scopus 로고    scopus 로고
    • Breathing dynamics in heteropolymer DNA
    • 1831711 17237209 10.1529/biophysj.106.095935
    • Ambjörnsson T Banik SK Krichevsky O Metzler R Breathing dynamics in heteropolymer DNA Biophys J 2007, 92(8):2674-2684. 1831711 17237209 10.1529/biophysj.106.095935
    • (2007) Biophys J , vol.92 , Issue.8 , pp. 2674-2684
    • Ambjörnsson, T.1    Banik, S.K.2    Krichevsky, O.3    Metzler, R.4
  • 21
    • 0027400474 scopus 로고
    • Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci
    • 46224 8385354 10.1073/pnas.90.7.2999
    • Benham C Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci Proc Natl Acad Sci USA 1993, 90(7):2999-3003. 46224 8385354 10.1073/pnas.90.7.2999
    • (1993) Proc Natl Acad Sci USA , vol.90 , Issue.7 , pp. 2999-3003
    • Benham, C.1
  • 22
    • 4444337094 scopus 로고    scopus 로고
    • Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters
    • 509266 15289476 10.1101/gr.2080004
    • Wang H Noordewier M Benham C Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters Genome Res 2004, 14(8):1575-84. 509266 15289476 10.1101/ gr.2080004
    • (2004) Genome Res , vol.14 , Issue.8 , pp. 1575-1584
    • Wang, H.1    Noordewier, M.2    Benham, C.3
  • 23
    • 55449111943 scopus 로고    scopus 로고
    • Susceptibility to superhelically driven DNA duplex destabilization: A highly conserved property of yeast replication origins
    • 1183513 16103908 10.1371/journal.pcbi.0010007
    • Ak P Benham CJ Susceptibility to superhelically driven DNA duplex destabilization: A highly conserved property of yeast replication origins PLoS Computational Biology 2005, 1:e7. 1183513 16103908 10.1371/ journal.pcbi.0010007
    • (2005) PLoS Computational Biology , vol.1
    • Ak, P.1    Benham, C.J.2
  • 24
    • 0029965473 scopus 로고    scopus 로고
    • Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions
    • 10.1006/jmbi.1996.0035 8568887
    • Benham CJ Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions Journal of Molecular Biology 1996, 255:425-434. 10.1006/jmbi.1996.0035 8568887
    • (1996) Journal of Molecular Biology , vol.255 , pp. 425-434
    • Benham, C.J.1
  • 25
    • 33644877443 scopus 로고    scopus 로고
    • SIDDBASE: A database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes
    • Database 1347370 16381890 10.1093/nar/gkj007
    • Wang H Kaloper M Benham C SIDDBASE: A database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes Nucleic Acids Res 2006, 34(Database):D373-8. 1347370 16381890 10.1093/nar/gkj007
    • (2006) Nucleic Acids Res , vol.34
    • Wang, H.1    Kaloper, M.2    Benham, C.3
  • 27
    • 53149108372 scopus 로고    scopus 로고
    • Merging the physical properties of DNA with genomic annotations in Ensembl
    • Master's thesis University of Oslo, Institute of Informatics
    • Jerstad GI Merging the physical properties of DNA with genomic annotations in Ensembl Master's thesis University of Oslo, Institute of Informatics 2006
    • (2006)
    • Jerstad, G.I.1
  • 28
    • 0016266885 scopus 로고
    • Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations
    • 10.1002/bip.1974.360130916 4415504
    • Poland D Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations Biopolymers 1974, 13:1859-1871 10.1002/bip.1974.360130916 4415504
    • (1974) Biopolymers , vol.13 , pp. 1859-1871
    • Poland, D.1
  • 29
    • 27944507827 scopus 로고    scopus 로고
    • Partly melted DNA conformations obtained with a probability peak finding method
    • 16089780
    • Tøstesen E Partly melted DNA conformations obtained with a probability peak finding method Phys Rev E Stat Nonlin Soft Matter Phys 2005, 71(6 Pt 1):061922 16089780
    • (2005) Phys Rev E Stat Nonlin Soft Matter Phys , vol.71 , Issue.6 PART 1 , pp. 061922
    • Tøstesen, E.1
  • 30
    • 0242551290 scopus 로고    scopus 로고
    • Speed-up of DNA melting algorithm with complete nearest neighbor properties
    • 10.1002/bip.10495 14579309
    • Tøstesen E Liu F Jenssen TK Hovig E Speed-up of DNA melting algorithm with complete nearest neighbor properties Biopolymers 2003, 70:364-376 10.1002/bip.10495 14579309
    • (2003) Biopolymers , vol.70 , pp. 364-376
    • Tøstesen, E.1    Liu, F.2    Jenssen, T.K.3    Hovig, E.4
  • 31
    • 23144455034 scopus 로고    scopus 로고
    • Stitchprofiles.uio.no: Analysis of partly melted DNA conformations using stitch profiles
    • 1160185 15980539 10.1093/nar/gki424
    • Tøstesen E Jerstad GI Hovig E Stitchprofiles.uio.no: Analysis of partly melted DNA conformations using stitch profiles Nucleic Acids Res 2005, 33:w573-w576 1160185 15980539 10.1093/nar/gki424
    • (2005) Nucleic Acids Res , vol.33
    • Tøstesen, E.1    Jerstad, G.I.2    Hovig, E.3
  • 32
    • 0017587485 scopus 로고
    • Theory of DNA melting curves
    • 10.1002/bip.1977.360161209 597576
    • Fixman M Freire JJ Theory of DNA melting curves Biopolymers 1977, 16:2693-2704 10.1002/bip.1977.360161209 597576
    • (1977) Biopolymers , vol.16 , pp. 2693-2704
    • Fixman, M.1    Freire, J.J.2
  • 33
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • 10.1038/nsb0197-10
    • Dill KA Chan HS From Levinthal to pathways to funnels Nat Struct Mol Biol 1997, 4:10-19 10.1038/nsb0197-10
    • (1997) Nat Struct Mol Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 34
    • 0032552138 scopus 로고    scopus 로고
    • Archetypal energy landscapes
    • 10.1038/29487
    • Wales DJ Miller MA Walsh TR Archetypal energy landscapes Nature 1998, 394:758-760 10.1038/29487
    • (1998) Nature , vol.394 , pp. 758-760
    • Wales, D.J.1    Miller, M.A.2    Walsh, T.R.3
  • 35
    • 4544346660 scopus 로고    scopus 로고
    • Robustness of cellular functions
    • 10.1016/j.cell.2004.09.008 15369668
    • Stelling J Sauer U Szallasi Z Doyle FJ III Doyle J Robustness of cellular functions Cell 2004, 118:675-685 10.1016/j.cell.2004.09.008 15369668
    • (2004) Cell , vol.118 , pp. 675-685
    • Stelling, J.1    Sauer, U.2    Szallasi, Z.3    Doyle III, F.J.4    Doyle, J.5
  • 36
    • 0000629179 scopus 로고
    • Diffusion in hierarchies
    • 10.1103/PhysRevA.38.4261 9900879
    • Hoffmann KH Sibani P Diffusion in hierarchies Phys Rev A 1988, 38(8):4261-4270 10.1103/PhysRevA.38.4261 9900879
    • (1988) Phys Rev A , vol.38 , Issue.8 , pp. 4261-4270
    • Hoffmann, K.H.1    Sibani, P.2
  • 37
    • 0000208631 scopus 로고
    • Broken ergodicity and the geometry of rugged landscapes
    • 10.1103/PhysRevE.51.5228
    • Stein DL Newman CM Broken ergodicity and the geometry of rugged landscapes Phys Rev E 1995, 51(6):5228-5238 10.1103/PhysRevE.51.5228
    • (1995) Phys Rev E , vol.51 , Issue.6 , pp. 5228-5238
    • Stein, D.L.1    Newman, C.M.2
  • 40
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for double-stranded nucleic acids
    • 1304344 15240459 10.1529/biophysj.103.020743
    • Dimitrov RA Zuker M Prediction of hybridization and melting for double-stranded nucleic acids Biophys J 2004, 87:215-226 1304344 15240459 10.1529/biophysj.103.020743
    • (2004) Biophys J , vol.87 , pp. 215-226
    • Dimitrov, R.A.1    Zuker, M.2
  • 41
    • 0025066882 scopus 로고
    • An optimal formulation of the matrix method in statistical mechanics of one-dimensional interacting units: Efficient iterative algorithmic procedures
    • 10.1002/bip.360300502
    • Yeramian E Schaeffer F Caudron B Claverie P Buc H An optimal formulation of the matrix method in statistical mechanics of one-dimensional interacting units: Efficient iterative algorithmic procedures Biopolymers 1990, 30:481-497 10.1002/bip.360300502
    • (1990) Biopolymers , vol.30 , pp. 481-497
    • Yeramian, E.1    Schaeffer, F.2    Caudron, B.3    Claverie, P.4    Buc, H.5
  • 42
    • 0032527828 scopus 로고    scopus 로고
    • Thermal stability of DNA
    • 147704 9649614 10.1093/nar/26.14.3323
    • Blake RD Delcourt SG Thermal stability of DNA Nucleic Acids Res 1998, 26:3323-3332 147704 9649614 10.1093/nar/26.14.3323
    • (1998) Nucleic Acids Res , vol.26 , pp. 3323-3332
    • Blake, R.D.1    Delcourt, S.G.2
  • 43
    • 2542485691 scopus 로고    scopus 로고
    • Reparametrizing the loop entropy weights: Effect on DNA melting curves
    • 10.1103/PhysRevE.68.061911
    • Blossey R Carlon E Reparametrizing the loop entropy weights: Effect on DNA melting curves Phys Rev E 2003, 68(6):061911 10.1103/ PhysRevE.68.061911
    • (2003) Phys Rev E , vol.68 , Issue.6 , pp. 061911
    • Blossey, R.1    Carlon, E.2
  • 45
    • 53149136382 scopus 로고    scopus 로고
    • ftp://ftp.aip.org/epaps/phys_rev_e/E-PLEEE8-71-148506/lambdastitch.htm
    • Stitch Profiles of Bacteriophage Lambda DNA ftp://ftp.aip.org/epaps/ phys_rev_e/E-PLEEE8-71-148506/lambdastitch.htm
    • Stitch Profiles of Bacteriophage Lambda DNA
  • 46
    • 3142725514 scopus 로고    scopus 로고
    • The analysis of stress-induced duplex destabilization in long genomic DNA sequences
    • 10.1089/cmb.2004.11.519 15579230
    • Benham C Bi C The analysis of stress-induced duplex destabilization in long genomic DNA sequences J Comput Biol 2004, 11(4):519-43 10.1089/ cmb.2004.11.519 15579230
    • (2004) J Comput Biol , vol.11 , Issue.4 , pp. 519-543
    • Benham, C.1    Bi, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.