Research in Computational Molecular Biology

Chapter 1 An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

Chapter 2 Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning

Chapter 3 ModHMM: A Modular Supra-Bayesian Genome Segmentation Method

Chapter 4 Learning Robust Multi-label Sample Specific Distances for Identifying HIV-1 Drug Resistance

Chapter 5 MethCP : Differentially Methylated Region Detection with Change Point Models

Chapter 6 On the Complexity of Sequence to Graph Alignment

Chapter 7 Minimization-Aware Recursive $$K^{*}$$ K ∗ ( $${ MARK}^{*}$$ MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape

Chapter 8 Sparse Binary Relation Representations for Genome Graph Annotation

Chapter 9 How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories

Chapter 10 Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

Chapter 11 Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data

Chapter 12 OMGS: Optical Map-Based Genome Scaffolding

Chapter 13 Fast Approximation of Frequent k -mers and Applications to Metagenomics

Chapter 14 De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm

Chapter 15 A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer

Chapter 16 Disentangled Representations of Cellular Identity

Chapter 17 RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature