-
1
-
-
0028094986
-
The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments
-
Allison, L., and Wallace, C. S. (1994), 'The Posterior Probability Distribution of Alignments and Its Application to Parameter Estimation of Evolutionary Trees and to Optimization of Multiple Alignments,” Journal of Molecular Evolution, 39, 418-430.
-
(1994)
Journal of Molecular Evolution
, vol.39
, pp. 418-430
-
-
Allison, L.1
Wallace, C.S.2
-
2
-
-
0013567941
-
Minimum message length encoding evolutionary trees and multiple alignment
-
Allison, L., Wallace, C. S., and Yee, C. N. (1992), “Minimum Message Length Encoding Evolutionary Trees and Multiple Alignment,” Proceedings of 25th Hawaii International Conference on System Science, 1, 663-674.
-
(1992)
Proceedings of 25Th Hawaii International Conference on System Science
, vol.1
, pp. 663-674
-
-
Allison, L.1
Wallace, C.S.2
Yee, C.N.3
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, M., Myers, E. W., and Lipman, D. J. (1990), “Basic Local Alignment Search Tool,” Journal of Molecular Biology, 215, 403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, M.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
0028011075
-
Hidden markov models of biological primary sequence information
-
Baldi, P., Chauvin, Y., McClure, M., and Hunkapiller, T. (1994), “Hidden Markov Models of Biological Primary Sequence Information,” Proceedings of the National Academy of Science, 91, 1059-1063.
-
(1994)
Proceedings of the National Academy of Science
, vol.91
, pp. 1059-1063
-
-
Baldi, P.1
Chauvin, Y.2
McClure, M.3
Hunkapiller, T.4
-
5
-
-
0022474446
-
Maximum likelihood alignment of dna sequences
-
Bishop, M. J” and Thompson, E. A. (1986), “Maximum Likelihood Alignment of DNA Sequences,” Journal of Molecular Biology, 190, 159-165.
-
(1986)
Journal of Molecular Biology
, vol.190
, pp. 159-165
-
-
Bishop, M.1
Thompson, E.A.2
-
6
-
-
0001135785
-
Sampling and bayes inference in scientific modeling and robustness
-
Box, G. E. P. (1980), “Sampling and Bayes Inference in Scientific Modeling and Robustness,” Journal of the Royal Statistical Society, Ser. A, 143, 383-430.
-
(1980)
Journal of the Royal Statistical Society, Ser. A
, vol.143
, pp. 383-430
-
-
Box, G.1
-
7
-
-
0028221943
-
Mutation in the dna mismatch repair gene homologue hmlhl is associated with hereditary non-polyposis colon cancer
-
Bronner, C. E., Baker, S. M., Morrison, P. T., Warren, G., Smith, L. G., Lescoe, M. K., Kane, M., Earabino, C., Lipford, J., Lindblom, A., Tan-nergard, P., Bollag, R. J., Godwin, A. R., Ward, D. C., Nordenskj0ld, M., Fishel, R., Kolodner, R., and Liskay, R. M. (1994), “Mutation in the DNA Mismatch Repair Gene Homologue hMLHl Is Associated With Hereditary Non-Polyposis Colon Cancer,” Nature, 368, 258-261.
-
(1994)
Nature
, vol.368
, pp. 258-261
-
-
Bronner, C.E.1
Baker, S.M.2
Morrison, P.T.3
Warren, G.4
Smith, L.G.5
Lescoe, M.K.6
Kane, M.7
Earabino, C.8
Lipford, J.9
Lindblom, A.10
Tan-Nergard, P.11
Bollag, R.J.12
Godwin, A.R.13
Ward, D.C.14
Nordenskjold, M.15
Fishel, R.16
Kolodner, R.17
Liskay, R.M.18
-
8
-
-
0004053613
-
-
2nd ed.), New York: Saunders College Publishing
-
Campbell, M. K. (1995), Biochemistry (2nd ed.), New York: Saunders College Publishing.
-
(1995)
Biochemistry
-
-
Campbell, M.K.1
-
9
-
-
0024557590
-
Stochastic models for heterogeneous dna sequences
-
Churchill, G. A. (1989), “Stochastic Models for Heterogeneous DNA Sequences,” Bulletin of Mathematical Biology, 51, 79-94.
-
(1989)
Bulletin of Mathematical Biology
, vol.51
, pp. 79-94
-
-
Churchill, G.A.1
-
10
-
-
0029889611
-
Effective large-scale sequences similarity searches
-
Claverie, J. M. (1996), “Effective Large-Scale Sequences Similarity Searches,” Methods in Enzymology, 266, 212-227.
-
(1996)
Methods in Enzymology
, vol.266
, pp. 212-227
-
-
Claverie, J.M.1
-
12
-
-
0029174347
-
Multiple alignment using hidden markov models
-
Eddy, S. R. (1995), “Multiple Alignment Using Hidden Markov Models,” Intelligent Systems for Molecular Biology, 3, 114-120.
-
(1995)
Intelligent Systems for Molecular Biology
, vol.3
, pp. 114-120
-
-
Eddy, S.R.1
-
13
-
-
25444484077
-
Posterior predictive assessment of model fitness via realized discrepancies
-
Gelman, A., Meng, X. L., and Stern, H. (1996), “Posterior Predictive Assessment of Model Fitness via Realized Discrepancies” (with discussion), Statistica Sinica, 6, 733-796.
-
(1996)
Statistica Sinica
, vol.6
, pp. 733-796
-
-
Gelman, A.1
Meng, X.L.2
Stern, H.3
-
14
-
-
0027399170
-
Ancient conserved regions in new gene-sequences and the protein databases
-
Green, P., Lipman, D., Hillier, L., Waterston, R., States, D., and Claverie, I. M. (1993), “Ancient Conserved Regions in New Gene-Sequences and the Protein Databases,” Science, 259, 1711-1715.
-
(1993)
Science
, vol.259
, pp. 1711-1715
-
-
Green, P.1
Lipman, D.2
Hillier, L.3
Waterston, R.4
States, D.5
Claverie, I.M.6
-
15
-
-
0026410103
-
Automated assembly of protein blocks for database searching
-
Henikoff, S., and Henikoff, J. G. (1991), “Automated Assembly of Protein Blocks for Database Searching,” Nucleic Acids Research, 19, 6565-6572.
-
(1991)
Nucleic Acids Research
, vol.19
, pp. 6565-6572
-
-
Henikoff, S.1
Henikoff, J.G.2
-
16
-
-
0028825276
-
Automated construction and graphical presentation of protein blocks from unaligned sequences
-
Henikoff, S., Henikoff, J. G., Alford, W. J., and Pietrokovski, S. (1995), “Automated Construction and Graphical Presentation of Protein Blocks From Unaligned Sequences,” Gene, 163 (2), GC17-GC26.
-
(1995)
Gene
, vol.163
, Issue.2
, pp. GC17-GC26
-
-
Henikoff, S.1
Henikoff, J.G.2
Alford, W.J.3
Pietrokovski, S.4
-
17
-
-
0026718403
-
Chance and statistical significance in protein and dna sequence analysis
-
Karlin, S., and Brendel, V. (1992), “Chance and Statistical Significance in Protein and DNA Sequence Analysis,” Science, 257, 39-49.
-
(1992)
Science
, vol.257
, pp. 39-49
-
-
Karlin, S.1
Brendel, V.2
-
18
-
-
84950934893
-
Bayes factors
-
Kass, R. E., and Raftery, A. E. (1995), “Bayes Factors,” Journal of the American Statistical Association, 90, 377-395.
-
(1995)
Journal of the American Statistical Association
, vol.90
, pp. 377-395
-
-
Kass, R.E.1
Raftery, A.E.2
-
19
-
-
0028181441
-
Protein modeling using hidden markov models
-
Krogh, A., Brown, M., Mian, S., Sjolander, K., and Haussier, D. (1994), “Protein Modeling Using Hidden Markov Models,” Journal of Molecular Biology, 235, 1501-1531.
-
(1994)
Journal of Molecular Biology
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, S.3
Sjolander, K.4
Haussier, D.5
-
20
-
-
0027912333
-
Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment
-
Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., and Wootton, J. C. (1993), “Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment,” Science, 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
21
-
-
0025320805
-
An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
Lawrence, C. E., and Reilly, A. A. (1990), “An Expectation Maximization Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymer Sequences,” PROTEINS: Structure, Function, and Genetics, 7, 41-51.
-
(1990)
PROTEINS: Structure, Function, and Genetics
, vol.7
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
22
-
-
0006384020
-
Likelihood inferences for permuted data with application to gene regulation
-
Lawrence, C. E., and Reilly, A. A. (1992), “Likelihood Inferences for Permuted Data With Application to Gene Regulation,” Journal of the American Statistical Association, 91, 76-85.
-
(1992)
Journal of the American Statistical Association
, vol.91
, pp. 76-85
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
23
-
-
33744590886
-
Bayesian restoration of a hidden markov chain with applications to dna sequencing
-
unpublished manuscript submitted to
-
Lazareva, B., and Churchil, G. A. (1997), “Bayesian Restoration of a Hidden Markov Chain With Applications to DNA Sequencing,” unpublished manuscript submitted to Journal of the American Statistical Association.
-
(1997)
Journal of the American Statistical Association
-
-
Lazareva, B.1
Churchil, G.A.2
-
24
-
-
79951870792
-
The collapsed gibbs sampler in bayesian computations with applications to a gene regulation problem
-
Liu, J. S. (1994), “The Collapsed Gibbs Sampler in Bayesian Computations With Applications to a Gene Regulation Problem,” Journal of the American Statistical Association, 89, 958-966.
-
(1994)
Journal of the American Statistical Association
, vol.89
, pp. 958-966
-
-
Liu, J.S.1
-
25
-
-
84950424966
-
Bayesian models for multiple local sequence alignment and gibbs sampling strategies
-
Liu, J. S., Neuwald, A. F., and Lawrence, C. E. (1995), “Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies,” Journal of the American Statistical Association, 90, 1156-1170.
-
(1995)
Journal of the American Statistical Association
, vol.90
, pp. 1156-1170
-
-
Liu, J.S.1
Neuwald, A.F.2
Lawrence, C.E.3
-
26
-
-
0030017287
-
Hot property: Biologists who compute
-
Marshall, E. (1996), “Hot Property: Biologists Who Compute,” Science, 272, 1730-1732.
-
(1996)
Science
, vol.272
, pp. 1730-1732
-
-
Marshall, E.1
-
27
-
-
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,” Journal of Molecular Biology, 48, 443-453.
-
(1970)
Journal of Molecular Biology
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
28
-
-
0029144601
-
Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
-
Neuwald, A. F., Liu, J. S., and Lawrence, C. E. (1995), “Gibbs Motif Sampling: Detection of Bacterial Outer Membrane Protein Repeats,” Protein Science, 4, 1618-1632.
-
(1995)
Protein Science
, vol.4
, pp. 1618-1632
-
-
Neuwald, A.F.1
Liu, J.S.2
Lawrence, C.E.3
-
29
-
-
0030788541
-
Extracting protein alignment models from the sequence database
-
Neuwald, A. F., Liu, J. S., Lipman, D. J., and Lawrence, C. E. (1997), “Extracting Protein Alignment Models From the Sequence Database,” Nucleic Acid Research, 25(9), 1665-1677.
-
(1997)
Nucleic Acid Research
, vol.25
, Issue.9
, pp. 1665-1677
-
-
Neuwald, A.F.1
Liu, J.S.2
Lipman, D.J.3
Lawrence, C.E.4
-
30
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W. R., and Lipman, D. J. (1988), “Improved Tools for Biological Sequence Comparison,” Proceedings of the National Academy of Science, 85, 2444-2448.
-
(1988)
Proceedings of the National Academy of Science
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
31
-
-
33744578756
-
Extended homology prediction for motif structure by multiple sequence alignment
-
unpublished manuscript submitted to
-
Qu, K., and Lawrence, C. E. (1999), “Extended Homology Prediction for Motif Structure by Multiple Sequence Alignment,” unpublished manuscript submitted to Modeling and Scientific Computing.
-
(1999)
Modeling and Scientific Computing
-
-
Qu, K.1
Lawrence, C.E.2
-
32
-
-
0031863617
-
Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase
-
Qu, K., Martin, D. L., and Lawrence, C. E. (1998), “Motifs and Structural Fold of the Cofactor Binding Site of Human Glutamate Decarboxylase,” Protein Science, 7, 1092-1105.
-
(1998)
Protein Science
, vol.7
, pp. 1092-1105
-
-
Qu, K.1
Martin, D.L.2
Lawrence, C.E.3
-
33
-
-
0024610919
-
A tutorial on hidden markov models and selected applications in speech recognition
-
Rabiner, L. R. (1989), “A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition,” Proceedings of the IEEE, 77, 257-286.
-
(1989)
Proceedings of the IEEE
, vol.77
, pp. 257-286
-
-
Rabiner, L.R.1
-
34
-
-
0000439370
-
Bayesianly justifiable and relevant frequency calculations for the applied statistician
-
Rubin, D. B. (1984), “Bayesianly Justifiable and Relevant Frequency Calculations for the Applied Statistician,” The Annals of Statistics, 12, 1151-1172.
-
(1984)
The Annals of Statistics
, vol.12
, pp. 1151-1172
-
-
Rubin, D.B.1
-
35
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider, T. D., and Stephens, R. M. (1990), “Sequence Logos: A New Way To Display Consensus Sequences,” Nucleic Acids Research, 20, 6097-6100.
-
(1990)
Nucleic Acids Research
, vol.20
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
36
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T. F., and Waterman, M. S. (1981), “Identification of Common Molecular Subsequences,” Journal of Molecular Biology, 147, 195-197.
-
(1981)
Journal of Molecular Biology
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
37
-
-
0030925920
-
Pfam: A comprehensive database of protein domain families based on seed alignments
-
Sonnhammer, E. L. L., Eddy, S. R., and Durbin, R. (1997), “Pfam: A Comprehensive Database of Protein Domain Families Based on Seed Alignments,” Proteins, 28, 405-420.
-
(1997)
Proteins
, vol.28
, pp. 405-420
-
-
Sonnhammer, E.1
Eddy, S.R.2
Durbin, R.3
-
38
-
-
0030564702
-
Software matchmakers help make sense of sequences
-
Taubes, G. (1996), “Software Matchmakers Help Make Sense of Sequences,” Science, 273, 588-590.
-
(1996)
Science
, vol.273
, pp. 588-590
-
-
Taubes, G.1
-
39
-
-
0027968068
-
Clustal w: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice
-
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994), “CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position-Specific Gap Penalties, and Weight Matrix Choice,” Nucleic Acid Research, 22, 4673-4680.
-
(1994)
Nucleic Acid Research
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
40
-
-
0026079507
-
An evolutionary model for maximum likelihood alignment of dna sequences
-
Thome, J. L., Kishino, H., and Felsenstein, J. (1991), “An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences,” Journal of Molecular Evolution, 33, 114-124.
-
(1991)
Journal of Molecular Evolution
, vol.33
, pp. 114-124
-
-
Thome, J.L.1
Kishino, H.2
Felsenstein, J.3
-
41
-
-
0026528734
-
Inching toward reality: An improved likelihood model of sequence evolution
-
Thome, J. L., Kishino, H., and Felsenstein, J. (1992), “Inching Toward Reality: An Improved Likelihood Model of Sequence Evolution,” Journal of Molecular Evolution, 34, 3-16.
-
(1992)
Journal of Molecular Evolution
, vol.34
, pp. 3-16
-
-
Thome, J.L.1
Kishino, H.2
Felsenstein, J.3
-
44
-
-
0031874740
-
Bayesian adaptive sequence alignment algorithms
-
Zhu, J., Liu, J. S., and Lawrence, C. E. (1998), “Bayesian Adaptive Sequence Alignment Algorithms,” Bioinformics, 14, 25-39.
-
(1998)
Bioinformics
, vol.14
, pp. 25-39
-
-
Zhu, J.1
Liu, J.S.2
Lawrence, C.E.3
|