-
3
-
-
0018504604
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
26
-
-
34249723701
-
The human genomic melting map
-
1868775 17511513 10.1371/journal.pcbi.0030093
-
Liu F Tøstesen E Sundet JK Jenssen TK Bock C Jerstad GI Thilly WG Hovig E The human genomic melting map PLoS Computational Biology 2007, 3(5):e93 1868775 17511513 10.1371/journal.pcbi.0030093
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.5
-
-
Liu, F.1
Tøstesen, E.2
Sundet, J.K.3
Jenssen, T.K.4
Bock, C.5
Jerstad, G.I.6
Thilly, W.G.7
Hovig, E.8
-
27
-
-
53149108372
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
36
-
-
0000629179
-
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
-
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
-
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
-
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
-
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
-
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
-
-
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
-
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
|