Research in Computational Molecular Biology

Chapter 1 Boosting Alignment Accuracy by Adaptive Local Realignment

Chapter 2 A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes

Chapter 3 A Flow Procedure for the Linearization of Genome Sequence Graphs

Chapter 4 Dynamic Alignment-Free and Reference-Free Read Compression

Chapter 5 A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

Chapter 6 Determining the Consistency of Resolved Triplets and Fan Triplets

Chapter 7 Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?

Chapter 8 Resolving Multicopy Duplications de novo Using Polyploid Phasing

Chapter 9 A Bayesian Active Learning Experimental Design for Inferring Signaling Networks

Chapter 10 $$BBK^*$$ (Branch and Bound over $$K^*$$ ): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces

Chapter 11 Superbubbles, Ultrabubbles and Cacti

Chapter 12 EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices

Chapter 13 A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference

Chapter 14 Towards Recovering Allele-Specific Cancer Genome Graphs

Chapter 15 Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability

Chapter 16 Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

Chapter 18 Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-learning Predictive Model

Chapter 19 Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies

Chapter 20 The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data

Chapter 21 Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding

Chapter 22 aBayesQR: A Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity