Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models

Articles in the same Issue

1. Article
2. Estimating Motifs Under Order Restrictions
3. Reproducible Research: A Bioinformatics Case Study
4. Generalized Rank Tests for Replicated Microarray Data
5. Stepwise Normalization of Two-Channel Spotted Microarrays
6. Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis
7. Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays
8. Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
9. Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data.
10. Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
11. Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors
12. Combined Association and Linkage Analysis for General Pedigrees and Genetic Models
13. Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data
14. The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
15. A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes
16. Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction
17. Error Distribution for Gene Expression Data
18. A General Framework for Weighted Gene Co-Expression Network Analysis
19. Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
20. Comparing Bacterial DNA Microarray Fingerprints
21. Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis
22. Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models
23. Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
24. Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data
25. FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model
26. Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation
27. Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model
28. Test on the Structure of Biological Sequences via Chaos Game Representation
29. Reverse Engineering Galactose Regulation in Yeast through Model Selection
30. Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives.
31. Weighted Analysis of Paired Microarray Experiments
32. A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles
33. A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
34. Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
35. Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes
36. Bayesian Statistical Studies of the Ramachandran Distribution
37. On Reference Designs For Microarray Experiments
38. Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors