Comparative Genomics

.- Combinatorics of Genome Rearrangements.

.- Time Complexity and Relaxation Gap for the Rank Median of Three Genomes.
.- Quantifying the Rearrangement Complexity of Pangenomes.
.- Breakpoint Medians and Antimedians for Signed Genomes.

.- Genome Evolution and Reconstruction.

.- Reconstructing the Constituent Genomes of the Ancestral Angiosperm Pangenome.
.- A Multi-flow Approach for Binning Circular Plasmids from Short-reads Assembly Graphs.
.- Modeling the Mutational Dynamics of Very Short Tandem Repeats.

.- Phylogenetics I: Inferring Gene and Species Histories.

.- Theoretical and Empirical Performance of Pseudo-likelihood-based Bayesian Inference of Species Trees under the Multispecies Coalescent.
.- wQFM-GDL Enables Accurate Quartet-based Genome-scale Species Tree Inference Under Gene Duplication and Loss.
.- On the Consistency of Duplication, Loss, and Deep Coalescence Gene Tree Parsimony Costs under the Multispecies Coalescent.
.- Gene Repertoire Evolution Minimizing Episodes of Gains and Losses.

.- Phylogenetics II: Comparing and Evaluating Phylogenies.

.- Similarities, Differences and Biases in Cophylogenetic Models for Host-Symbiont Coevolution.
.- Gabriele Di Palma, Catherine Matias and Blerina Sinaimeri On the Comparison of LGT Networks and Tree-based Networks.
.- k-Nearest Common Leaves Algorithm for Phylogenetic Tree Completion.
.- Cherry Picking Distance Between Binary Orchards Parameterized by Level.

.- Machine Learning in Genomics.

.- DipGNNome: Diploid de novo Genome Assembly with Geometric Deep Learning and Beam-search.
.- GNNome-Decision: Enhancing GNN Training for de novo Genome Assembly by Targeting Decision Nodes.
.- FIREFLY: PHYlogeny-informed REpresentation Learning to Estimate PHyLogenetic dIstances.
.- Detecting Outlier Subtrees of Gene Trees Using SPR Moves and Machine Learning.
.- "Frustratingly Easy" Domain Adaptation for Cross-species Transcription Factor Binding Prediction.