Algorithms for Computational Biology

Genomics.- Parallel Generalized Su x Tree Construction for Genomic Data.- A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions.- Heuristics for Reversal Distance between Genomes with Duplicated Genes.- Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics.- Gaps and Runs in Syntenic Alignments.- Phylogenetics.- Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology.- Combining Networks Using Cherry Picking Sequences.- Linear Time Algorithm for Tree-Child Network Containment.- PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals.- TreeSolve: Rapid Error-Correction of Microbial Gene Trees.- RNA-Seq and Other Biological Processes.- Time Series Adjustment Enhancement of Hierarchical Modeling of Arabidopsis Thaliana Gene Interactions.- BESTox: A Convolutional Neural Network Regression Model Based on Binary-Encoded SMILES for Acute Oral Toxicity Predictionof Chemical Compounds.- Stratified Test Alleviates Batch Effects in Single-Cell Data.- A Topological Data Analysis Approach on Predicting Phenotypes from Gene Expression Data.- BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance.