Cancer genomics
.- Novel Driver Mutations in GCB Lymphoma Patients That Affect Transcription Factors Binding.
.- Inferring Phylogenetic Trees of Cancer Evolution from Longitudinal Single-Cell Copy Number Profiles.
Homology and Reconciliation
.- Tree decomposition for reconstructing ancestral RNA sequences of multiple families.
.- Whole-genome duplication detection with phylogenomics reconciliation: a scalable approach.
.- A Sankoff-Rousseau-like Algorithm for Minimizing Lateral Gene Transfers and Losses on Single Origin Characters.
.- tMHG-Finder: Tree-guided Maximal Homologous Group Finder for Bacterial Genomes.
Phylogenetics
.- Phylogenetic Network Diversity Parameterized by Reticulation Number and Beyond.
.- On the robustness to gene tree rooting (or lack thereof) of triplet-based species tree estimation methods.
.- Exact Counts of Binary Phylogenetic Networks with Two and Three Reticulation Events.
.- Ancestral pangenomes and their phylogenetic reconstruction.
.- QT-WEAVER: Correcting quartet distribution improves phylogenomic analyses despite gene tree estimation error.
.- Fast calculation of cherry distance on level-1 orchard networks: optimization, heuristic and implementation.
Sequence analysis
.- Detecting and Mapping Local Model Violations During Biomolecular Sequence Analysis: a RE sampling and Visual EvALuation Approach.
.- A simple way to find related sequences with position-specific probabilities.
.- Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks.
Epidemiology
.- Residual immunity and seasonality of an epidemic.
.- Adapting the cov2clusters tool for clustering MPOXV whole genome sequences.
Genome evolution
.- Probability-based sequence comparison finds the oldest ever nuclear mitochondrial DNA segments in mammalian genomes.
.- Unraveling Insect Immunity: A Cross-Order Comparative Genomic Analysis of Key Immune Proteins.
.- Analyzing Sequence Similarity Distributions in Salmonidae: A Branching Process Approach.
.- Evolutionary Reconstruction of Hormone-bHLH Regulatory Networks in Solanaceae: Phylogenomic Insights from PSTVd-Tomato Interactions.
