A Two-Stage Poisson Model for Testing RNA-Seq Data

Articles in the same Issue

1. Invited Editorial
2. Measurement of Evidence and Evidence of Measurement
3. Article
4. Fully Moderated T-statistic for Small Sample Size Gene Expression Arrays
5. Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains
6. Assessing Modularity Using a Random Matrix Theory Approach
7. Choice of Summary Statistic Weights in Approximate Bayesian Computation
8. Genetic Linkage Analysis in the Presence of Germline Mosaicism
9. Fitting Boolean Networks from Steady State Perturbation Data
10. Adaptive Elastic-Net Sparse Principal Component Analysis for Pathway Association Testing
11. Bayesian Learning from Marginal Data in Bionetwork Models
12. Unsupervised Classification for Tiling Arrays: ChIP-chip and Transcriptome
13. Multiple Testing in Candidate Gene Situations: A Comparison of Classical, Discrete, and Resampling-Based Procedures
14. Modeling Read Counts for CNV Detection in Exome Sequencing Data
15. Multiscale Characterization of Signaling Network Dynamics through Features
16. A Calibrated Multiclass Extension of AdaBoost
17. False Discovery Rate Estimation for Stability Selection: Application to Genome-Wide Association Studies
18. A Markov-Chain Model for the Analysis of High-Resolution Enzymatically ¹⁸O-Labeled Mass Spectra
19. Repeated Measures Semiparametric Regression Using Targeted Maximum Likelihood Methodology with Application to Transcription Factor Activity Discovery
20. Learning Monotonic Genotype-Phenotype Maps
21. A Comparison of Multifactor Dimensionality Reduction and L₁-Penalized Regression to Identify Gene-Gene Interactions in Genetic Association Studies
22. Accuracy and Computational Efficiency of a Graphical Modeling Approach to Linkage Disequilibrium Estimation
23. Learning from Past Treatments and Their Outcome Improves Prediction of In Vivo Response to Anti-HIV Therapy
24. A Three Component Latent Class Model for Robust Semiparametric Gene Discovery
25. Log-Linear Modelling of Protein Dipeptide Structure Reveals Interesting Patterns of Side-Chain-Backbone Interactions
26. A Robust Statistical Method to Detect Null Alleles in Microsatellite and SNP Datasets in Both Panmictic and Inbred Populations
27. Large Sample Approximations of Probabilities of Correct Evolutionary Tree Estimation and Biases of Maximum Likelihood Estimation
28. Interval Estimation of Familial Correlations from Pedigrees
29. Information Metrics in Genetic Epidemiology
30. Linear Combination Test for Hierarchical Gene Set Analysis
31. Exploratory Analysis of Multiple Omics Datasets Using the Adjusted RV Coefficient
32. Application of the Lasso to Expression Quantitative Trait Loci Mapping
33. A Variance-Components Model for Distance-Matrix Phylogenetic Reconstruction
34. Imputation Estimators Partially Correct for Model Misspecification
35. On the Statistical Properties of SGoF Multitesting Method
36. Meta-Analysis of Family-Based and Case-Control Genetic Association Studies that Use the Same Cases
37. A Non-Parametric Method for Detecting Specificity Determining Sites in Protein Sequence Alignments
38. Performance of Matrix Representation with Parsimony for Inferring Species from Gene Trees
39. Disequilibrium Coefficient: A Bayesian Perspective
40. Analyzing Time-Course Microarray Data Using Functional Data Analysis - A Review
41. The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq
42. Inferring Gene Networks using Robust Statistical Techniques
43. A Two-Stage Poisson Model for Testing RNA-Seq Data
44. Quantifying the Relative Contribution of the Heterozygous Class to QTL Detection Power
45. The Joint Null Criterion for Multiple Hypothesis Tests
46. Multiple Imputation of Missing Phenotype Data for QTL Mapping
47. Sparse Canonical Covariance Analysis for High-throughput Data
48. Comparison of Clinical Subgroup aCGH Profiles through Pseudolikelihood Ratio Tests
49. Random Forests for Genetic Association Studies
50. Deviance Information Criteria for Model Selection in Approximate Bayesian Computation
51. High-Dimensional Regression and Variable Selection Using CAR Scores
52. Surveying the Manifold Divergence of an Entire Protein Class for Statistical Clues to Underlying Biochemical Mechanisms
53. Smoothing Gene Expression Data with Network Information Improves Consistency of Regulated Genes
54. Entropy Based Genetic Association Tests and Gene-Gene Interaction Tests
55. Weighted Lasso with Data Integration
56. MA-SNP -- A New Genotype Calling Method for Oligonucleotide SNP Arrays Modeling the Batch Effect with a Normal Mixture Model
57. A Modified Maximum Contrast Method for Unequal Sample Sizes in Pharmacogenomic Studies