-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215 (3), 403-10.
-
(1990)
J. Mol. Biol.
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
0027516090
-
A protein alignment scoring system sensitive at all evolutionary distances
-
Altschul, S.F. 1993. A protein alignment scoring system sensitive at all evolutionary distances. J. Mol. Evol. 36 (3), 290-300.
-
(1993)
J. Mol. Evol.
, vol.36
, Issue.3
, pp. 290-300
-
-
Altschul, S.F.1
-
3
-
-
0000964654
-
Stochastic scrabbles: A law of large numbers for sequence matching with scores
-
Arratia, R., Morris, P., and Waterman, M.S. 1988. Stochastic scrabbles: a law of large numbers for sequence matching with scores. J. Appl. Probab. 25, 106-19.
-
(1988)
J. Appl. Probab.
, vol.25
, pp. 106-119
-
-
Arratia, R.1
Morris, P.2
Waterman, M.S.3
-
4
-
-
0001619220
-
A phase transition for the score in matching random sequences allowing deletions
-
Arratia, R., and Waterman, M.S., 1994. A phase transition for the score in matching random sequences allowing deletions. Ann of Appl. Prob. 4, 200-25.
-
(1994)
Ann of Appl. Prob.
, vol.4
, pp. 200-225
-
-
Arratia, R.1
Waterman, M.S.2
-
5
-
-
0027483434
-
Empirical and structural models for insertions and deletions in the divergent evolution of proteins
-
Benner, S.A., Cohen, M.A., and Gonnet, G.H. 1993. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Mol. Biol. 229 (4), 1065-82.
-
(1993)
J. Mol. Biol.
, vol.229
, Issue.4
, pp. 1065-1082
-
-
Benner, S.A.1
Cohen, M.A.2
Gonnet, G.H.3
-
6
-
-
0022474446
-
Maximum likelihood alignment of DNA sequences
-
Bishop, M.J., and Thompson, E.A. 1986. Maximum likelihood alignment of DNA sequences. J. Mol. Biol. 190 (2), 159-65.
-
(1986)
J. Mol. Biol.
, vol.190
, Issue.2
, pp. 159-165
-
-
Bishop, M.J.1
Thompson, E.A.2
-
7
-
-
0013693065
-
Extensive simulations for longest common subsequences
-
Boutet de Monvel, J. 1999. Extensive simulations for longest common subsequences. Eur. Phys. J. B 7, 293-308.
-
(1999)
Eur. Phys. J. B
, vol.7
, pp. 293-308
-
-
Boutet De Monvel, J.1
-
9
-
-
0001678047
-
Longest common subsequences of two random sequences
-
Chvátal V., and Sankoff D. 1975. Longest common subsequences of two random sequences. J. Appl. Prob. 12, 306-315.
-
(1975)
J. Appl. Prob.
, vol.12
, pp. 306-315
-
-
Chvátal, V.1
Sankoff, D.2
-
10
-
-
0000741959
-
Static and dynamic properties of inhomogeneous elastic media on disordered substrate
-
Cule, D., and Hwa, T. 1998. Static and dynamic properties of inhomogeneous elastic media on disordered substrate. Phys. Rev. B. 57, 8235-8253.
-
(1998)
Phys. Rev. B.
, vol.57
, pp. 8235-8253
-
-
Cule, D.1
Hwa, T.2
-
11
-
-
4043160171
-
Directed polymers on a factorized disorder landscape
-
de los Rios P., and Zhang Y.C. 1998. Directed polymers on a factorized disorder landscape. Phys. Rev. Lett. 81, 1083-6.
-
(1998)
Phys. Rev. Lett.
, vol.81
, pp. 1083-1086
-
-
De Los Rios, P.A.1
Zhang, Y.C.2
-
12
-
-
0030658182
-
DNA sequence alignment and critical phenomena
-
Drasdo, D., Hwa, T., and Lässig, M. 1997. DNA sequence alignment and critical phenomena. Mat. Res. Soc. Symp. Proc. 263, 75-80.
-
(1997)
Mat. Res. Soc. Symp. Proc.
, vol.263
, pp. 75-80
-
-
Drasdo, D.1
Hwa, T.2
Lässig, M.3
-
13
-
-
0031608753
-
A statistical theory of sequence alignment with gaps
-
J. Glasgow et al. eds., AAAI Press, Menlo Park
-
Drasdo, D., Hwa, T., and Lässig, M. 1998. A statistical theory of sequence alignment with gaps. Proceeding of The Sixth International Conference on Intelligent Systems for Molecular Biology, J. Glasgow et al. eds., 52-58, AAAI Press, Menlo Park.
-
(1998)
Proceeding of the Sixth International Conference on Intelligent Systems for Molecular Biology
, pp. 52-58
-
-
Drasdo, D.1
Hwa, T.2
Lässig, M.3
-
15
-
-
0028806386
-
Characterization of two genes coding for a similar four-cysteine motif of the amino-terminal propeptide of a sea urchin fibrillar collagen
-
From MEDLINE; 96096722, cf. Exposito J.Y., Boute N., Deleage G., Garrone R. 1995. Characterization of two genes coding for a similar four-cysteine motif of the amino-terminal propeptide of a sea urchin fibrillar collagen. Eur. J. Biochem. 234:59-65.
-
(1995)
Eur. J. Biochem.
, vol.234
, pp. 59-65
-
-
Exposito, J.Y.1
Boute, N.2
Deleage, G.3
Garrone, R.4
-
16
-
-
0028325048
-
A Drosophila homologue of membrane-skeleton protein 4.1 is associated with septate junctions and is encoded by the coracle gene
-
From MEDLINE; 94215495, cf. Fehon R.G., Dawson I.A., Artavanis-Tsakonas S. 1994. A Drosophila homologue of membrane-skeleton protein 4.1 is associated with septate junctions and is encoded by the coracle gene. Development 120:545-557.
-
(1994)
Development
, vol.120
, pp. 545-557
-
-
Fehon, R.G.1
Dawson, I.A.2
Artavanis-Tsakonas, S.3
-
17
-
-
0000768885
-
Directed paths in a random potential
-
Fisher, D.S., and Huse, D.A. 1991. Directed paths in a random potential. Phys. Rev. B 43 (13), 10728-10742.
-
(1991)
Phys. Rev. B
, vol.43
, Issue.13
, pp. 10728-10742
-
-
Fisher, D.S.1
Huse, D.A.2
-
19
-
-
0001016480
-
Anomalous fluctuations of directed polymers in random media
-
Hwa, T., and Fisher, D.S. 1994. Anomalous fluctuations of directed polymers in random media. Phys. Rev. B 49, 3136-54.
-
(1994)
Phys. Rev. B
, vol.49
, pp. 3136-3154
-
-
Hwa, T.1
Fisher, D.S.2
-
20
-
-
0001359551
-
Similarity detection and localization
-
Hwa, T., and Lässig, M. 1996. Similarity detection and localization, Phys. Rev. Lett. 76, 2591-2595.
-
(1996)
Phys. Rev. Lett.
, vol.76
, pp. 2591-2595
-
-
Hwa, T.1
Lässig, M.2
-
21
-
-
0031654086
-
Optimal detection of sequence similarity by local alignment
-
S. Istrail, P. Pevzner, and M.S. Waterman eds, ACM Press, 1998
-
Hwa, T., and Lässig, M. 1998. Optimal Detection of Sequence Similarity by Local Alignment. Proceedings of the Second Annual International Conference on Computational Molecular Biology, S. Istrail, P. Pevzner, and M.S. Waterman eds, 109-116, ACM Press, 1998.
-
(1998)
Proceedings of the Second Annual International Conference on Computational Molecular Biology
, pp. 109-116
-
-
Hwa, T.1
Lässig, M.2
-
22
-
-
0001759425
-
Disordered induced depinning transition
-
Hwa, T., and Nattermann, T. 1995. Disordered induced depinning transition, Phys. Rev. B 51, 455-469.
-
(1995)
Phys. Rev. B
, vol.51
, pp. 455-469
-
-
Hwa, T.1
Nattermann, T.2
-
23
-
-
5544248074
-
Replica Bethe ansatz studies of two-dimensional interfaces with quenched random impurities
-
Kardar, M. 1987. Replica Bethe ansatz studies of two-dimensional interfaces with quenched random impurities. Nucl. Phys. B 290, 582-602.
-
(1987)
Nucl. Phys. B
, vol.290
, pp. 582-602
-
-
Kardar, M.1
-
24
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin, S., and Altschul, S.F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natn. Acad. Sci. U.S.A. 87 (6), 2264-8.
-
(1990)
Proc. Natn. Acad. Sci. U.S.A.
, vol.87
, Issue.6
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
25
-
-
0027175241
-
Applications and statistics for multiple high-scoring segments in molecular sequences
-
Karlin, S., and Altschul, S.F. 1993. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natn. Acad. Sci. U.S.A. 90 (12), 5873-7.
-
(1993)
Proc. Natn. Acad. Sci. U.S.A.
, vol.90
, Issue.12
, pp. 5873-5877
-
-
Karlin, S.1
Altschul, S.F.2
-
27
-
-
0029895539
-
Self-consistently optimized statistical mechanical energy functions for sequence structure alignment
-
Koretke, K.K., Lutheyschulten, Z., Wolynes, P.G. 1996. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment Prot. Sci. 5, 1043-1059.
-
(1996)
Prot. Sci.
, vol.5
, pp. 1043-1059
-
-
Koretke, K.K.1
Lutheyschulten, Z.2
Wolynes, P.G.3
-
29
-
-
0343130876
-
On growth, disorder, and field theory
-
Lässig, M. 1998. On growth, disorder, and field theory. J. Phys. C 10, 9905-9950.
-
(1998)
J. Phys. C
, vol.10
, pp. 9905-9950
-
-
Lässig, M.1
-
30
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman, S.B., and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (3), 443-53.
-
(1970)
J. Mol. Biol.
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
31
-
-
0032610409
-
Optimizing Smith-Waterman alignments
-
World Scientific
-
Olsen R., Hwa. T., and Lässig, M. 1999a. Optimizing Smith-Waterman alignments. Pacific Symp. on Biocomputing 4, 302-13. World Scientific.
-
(1999)
Pacific Symp. on Biocomputing
, vol.4
, pp. 302-313
-
-
Olsen, R.1
Hwa, T.2
Lässig, M.3
-
33
-
-
0030628825
-
Protein folding funnels: The nature of the transition state ensemble
-
and references therein
-
Onuchic, J.N., LutheySchulten, Z., Wolynes, P.G. 1997. Protein folding funnels: the nature of the transition state ensemble. Ann. Rev. Phys. Chem. 48, 545-600, and references therein.
-
(1997)
Ann. Rev. Phys. Chem.
, vol.48
, pp. 545-600
-
-
Onuchic, J.N.1
Lutheyschulten, Z.2
Wolynes, P.G.3
-
34
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W.R. 1991. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11 (3), 635-650.
-
(1991)
Genomics
, vol.11
, Issue.3
, pp. 635-650
-
-
Pearson, W.R.1
-
35
-
-
0003725141
-
-
Addison Wesley, Reading, Mass
-
Sankoff D., and Kruskal J. 1983. Time warps, string edits, and macromolecules: The theory and practice of sequence comparison. Addison Wesley, Reading, Mass.
-
(1983)
Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
-
-
Sankoff, D.1
Kruskal, J.2
-
36
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F., and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147, 195-7.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
37
-
-
0013674793
-
Long common subsequences and the proximity of two random strings
-
Steele, J.M. 1982. Long common subsequences and the proximity of two random strings. SIAM J. Appl. Math. 42, 731-7.
-
(1982)
SIAM J. Appl. Math.
, vol.42
, pp. 731-737
-
-
Steele, J.M.1
-
38
-
-
0001150838
-
An Efron-Stein inequality for nonsymmetric statistics
-
Steele, J.M. 1986. An Efron-Stein inequality for nonsymmetric statistics. Ann. Stat. 14, 753-758.
-
(1986)
Ann. Stat.
, vol.14
, pp. 753-758
-
-
Steele, J.M.1
-
39
-
-
0026079507
-
An evolutionary model for maximum likelihood alignment of DNA sequence
-
Thorne, J.L., Kishino, H., and Felsenstein, J. 1991. An evolutionary model for maximum likelihood alignment of DNA sequence J. Mol. Evol. 33 (2), 114-24
-
(1991)
J. Mol. Evol.
, vol.33
, Issue.2
, pp. 114-124
-
-
Thorne, J.L.1
Kishino, H.2
Felsenstein, J.3
-
40
-
-
0026528734
-
Inching toward reality: An improved likelihood model of sequence evolution
-
Thorne, J.L., Kishino, H., and Felsenstein, J. 1992. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34 (1), 3-16.
-
(1992)
J. Mol. Evol.
, vol.34
, Issue.1
, pp. 3-16
-
-
Thorne, J.L.1
Kishino, H.2
Felsenstein, J.3
-
41
-
-
0028047892
-
Sequence alignment and penalty choice. Review of concepts, case studies and implications
-
Vingron, M., and Waterman, M.S. 1994. Sequence alignment and penalty choice. Review of concepts, case studies and implications. J. Mol. Biol. 235 (1), 1-12.
-
(1994)
J. Mol. Biol.
, vol.235
, Issue.1
, pp. 1-12
-
-
Vingron, M.1
Waterman, M.S.2
-
42
-
-
0001209011
-
Statistics of kinetic pathways on biased rough energy landscapes with application to protein folding
-
Wang, J., Onuchic, J., Wolynes, P.G. 1996. Statistics of kinetic pathways on biased rough energy landscapes with application to protein folding. Phys. Rev. Lett. 76, 4861-4864.
-
(1996)
Phys. Rev. Lett.
, vol.76
, pp. 4861-4864
-
-
Wang, J.1
Onuchic, J.2
Wolynes, P.G.3
-
43
-
-
0006711632
-
Phase transitions in sequence matches and nucleic acid structure
-
Waterman, M.S., Gordon, L., and Arratia, R. 1987. Phase transitions in sequence matches and nucleic acid structure. Proc. Natl. Acad. Sci. U.S.A. 84 (5), 1239-43.
-
(1987)
Proc. Natl. Acad. Sci. U.S.A.
, vol.84
, Issue.5
, pp. 1239-1243
-
-
Waterman, M.S.1
Gordon, L.2
Arratia, R.3
-
45
-
-
0026736581
-
Parametric sequence comparisons
-
Waterman, M.S., Eggert, M., and Lander, E. 1992. Parametric sequence comparisons. Proc. Nat. Acad. Sci. U.S.A. 89 (13), 6090-3.
-
(1992)
Proc. Nat. Acad. Sci. U.S.A.
, vol.89
, Issue.13
, pp. 6090-6093
-
-
Waterman, M.S.1
Eggert, M.2
Lander, E.3
-
47
-
-
84972546031
-
Sequence comparison significance and poisson approximation
-
Watermann, M.S., and Vingron, M. Sequence comparison significance and Poisson approximation. Stat. Sci. 9, 367-381.
-
Stat. Sci.
, vol.9
, pp. 367-381
-
-
Watermann, M.S.1
Vingron, M.2
-
48
-
-
0029078793
-
Alignment of molecular sequences seen as random path analysis
-
Zhang, M.Q., and Marr, T.G. 1995. Alignment of molecular sequences seen as random path analysis. J. Theo. Biol. 174 (2), 119-29.
-
(1995)
J. Theo. Biol.
, vol.174
, Issue.2
, pp. 119-129
-
-
Zhang, M.Q.1
Marr, T.G.2
|