Likelihood Inference for Permuted Data with Application to Gene Regulation

References

• Aitkin , M. and Rubin , D. B. 1985 . “Estimation and Hypothesis Testing in Finite Mixture Models,” . Journal of the Royal Statistical Society , 47 : 67 – 75 . Ser. B
   Google Scholar
• Bacon , D. J. and Anderson , W. F. 1986 . “Multiple Sequence Alignment,” . Journal of Molecular Biology , 191 : 153 – 161 .
   PubMed Web of Science ®Google Scholar
• Baldi , P. , Chauvin , Y. , Hunkapiller , T. and McClure , M. 1994 . “Hidden Markov Models of Biological Primary Sequence Information,” . Proceedings of the National Academy of Sciences , 91 : 1059 – 1063 .
   PubMed Web of Science ®Google Scholar
• Berg , O. G. and von Hipple , P. H. 1988 . “Selection of DNA Binding Sites by Regulatory Proteins II: The Binding Specificity of Cyclic AMP Receptor Protein to Recognition Sites,” . Journal of Molecular Biology , 200 : 709 – 723 .
   PubMed Web of Science ®Google Scholar
• Bishop , Y. M. M. , Fienberg , S. E. and Holland , P. W. 1975 . Discrete Multivariate Analysis: Theory and Practice , 270 – 273 . Cambridge , MA : MIT Press .
   Google Scholar
• Boguski , M. S. , Hardison , R. C. , Schwartz , S. and Miller , W. 1992 . “Analysis of Conserved Domains and Sequence Motifs in Cellular Regulatory Proteins and Locus Control Regions Using New Software Tools for Multiple Alignment and Visualization,” . New Biology , 4 : 247 – 260 .
   Google Scholar
• Cardon , L. R. and Stormo , G. D. 1992 . “Expectation Maximization Algorithm for Identifying Protein Binding Sites With Variable Lengths From Unaligned DNA Fragments,” . Journal of Molecular Biology , 223 : 159 – 170 .
   PubMed Web of Science ®Google Scholar
• Cover , T. M. and Thomas , J. A. 1991 . Elements of Information Theory , New York : John Wiley .
   Google Scholar
• deCrombrugghe , B. D. , Busby , S. and Buc , H. 1984 . “Cyclic AMP Receptor Protein—Role in Transcription Activation,” . Science , TLA : 831 – 838 .
   Google Scholar
• Dempster , A. P. , Laird , N. M. and Rubin , D. B. 1977 . “Maximum Likelihood From Incomplete Data Via the EM Algorithm,” . Journal of the Royal Statistical Society , 39 : 1 – 38 . Ser. B
   Google Scholar
• Frank , J. , Rademacher , M. , Wagenknecht , T. and Verschoor , A. 1988 . “Studying Ribosome Structure by Electron Microscopy and Computer-Image Processing,” . Methods in Enzymology , 164 : 3 – 35 .
   Google Scholar
• Hertz , G. Z. , Hartzell , G. W. III and Stormo , G. D. 1990 . “Identification of Consensus Patterns in Unaligned DNA Sequences Known to be Functionally Related,” . Computer Applications in the Biosciences , 6 : 81 – 92 .
   PubMedGoogle Scholar
• Karlin , S. , Ost , F. and Blaisdell , B. E. 1989 . “Some Statistical Aspects of Primary Structure of Nucleotide Sequences,” . In Mathematical Methods for DNA Sequences , Edited by: Waterman , M. S. 133 – 157 . Boca Raton , FL : CRC Press .
   Google Scholar
• Krogh , A. , Brown , M. , Mian , S. , Sjolander , K. and Haussler , D. 1994 . “Protein Modeling Using Hidden Markov Models,” . Journal of Molecular Biology , 235 : 1501 – 1531 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Lawrence , C. E. , Altschul , S. F. , Boguski , M. S. , Liu , J. S. , Neuwald , A. F. and Wootton , J. C. 1994 . “A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences,” . Proceedings of the 27th Annual Hawaii International Conference on Systems Science , 5 : 245 – 254 .
   Google Scholar
• Lawrence , C. E. and Reilly , A. A. 1990a . “An Expectation Maximization (EM) Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymer Sequences,” . Proteins: Structure, Function, and Genetics , 7 : 41 – 51 .
   PubMed Web of Science ®Google Scholar
• Lawrence , C. E. and Reilly , A. A. 1990b . “Misaligned (Shuffled) Data Analysis With Application to Gene Regulation,” , State University of New York at Albany, School of Public Health, Dept. of Biometry and Statistics . Technical Report No. 3
   Google Scholar
• Lawrence , C. E. and Reilly , A. A. 1993 . “Likelihood Inferences With Uncertain Indices,” , State University of New York at Albany, School of Public Health, Dept. of Biometry and Statistics . Technical Report No. 121
   Google Scholar
• Lewin , B. 1990 . Genes IV , Oxford , , UK : Oxford University Press .
   Google Scholar
• Little , R. J. A. and Rubin , D. B. 1987 . Statistical Analysis with Missing Data , New York : John Wiley .
   Google Scholar
• Liu , J. 1994 . “The Collapsed Gibbs Sampler in Bayesian Computations With Applications to Gene Regulation,” . Journal of the American Statistical Association , 89 : 958 – 966 .
   Web of Science ®Google Scholar
• McGillem , C. D. and Aumon , J. I. 1987 . “Analysis of Event Related Potentials,” . In Methods of Analysis of Brain Electrical and Magnetic Signals , Edited by: Givins , A. S. and Remond , A. New York : Elsevier .
   Google Scholar
• Queen , C. M. , Wegman , N. and Korn , L. J. 1982 . “Improvements to a Program for DNA Analysis: A Procedure to Find Homologies Among Many Sequences,” . Nucleic Acids Research , 10 : 449 – 456 .
   Google Scholar
• Redner , R. A. and Walker , H. F. 1984 . “Mixture Densities, Maximum Likelihood, and the EM Algorithm,” . Society for Industrial and Applied Mathematics , 26 : 195 – 239 .
   Google Scholar
• Schuler , G. D. , Altschul , S. F. and Lipman , D. J. 1991 . “A Workbench for Multiple Alignment Construction and Analysis,” . Proteins: Structure, Function, and Genetics , 9 : 180 – 190 .
   PubMed Web of Science ®Google Scholar
• Self , S. G. and Liang , K. Y. 1987 . “Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests Under Nonstandard Conditions,” . Journal of the American Statistical Association , 82 : 605 – 610 .
   Web of Science ®Google Scholar
• Smith , H. O. , Annau , T. M. and Chandrasegaran , S. 1990 . “Finding Sequence Motifs in Groups of Functionally Related Proteins,” . Proceedings of the National Academy of Science , 87 : 826 – 830 .
   Google Scholar
• Staden , R. 1989 . “Methods for Discovering Novel Motifs in Nucleic Acid Sequences,” . Computer Applications in the Biosciences , 5 : 293 – 298 .
   Google Scholar
• Stormo , G. D. and Hartzell , G. W. 1989 . “Identifying Protein Binding Sites From Unaligned DNA Fragments,” . Proceedings of the National Academy of Sciences , 86 : 1183 – 1187 .
   PubMed Web of Science ®Google Scholar
• Vingron , M. and Argos , P. 1991 . “Motif Recognition and Alignment for Many Sequences by Comparison of Dot Matrices,” . Journal of Molecular Biology , 218 : 33 – 43 .
   PubMedGoogle Scholar
• Waterman , M. S. 1989 . “Consensus Patterns in Sequences,” . In Mathematical Methods for DNA Sequences , Edited by: Waterman , M. S. 94 – 115 . Boca Raton , FL : CRC Press .
   Google Scholar
• Wüthrick , K. 1986 . NMR of Proteins and Nucleic Acids , New York : John Wiley .
   Google Scholar