D. Posada

Single-cell phylogenies reveal deviations from clock-like, neutral evolution in cancer and healthy tissues

This study uses single-cell DNA sequencing to test for neutral evolution in cancer and healthy tissues, finding deviations from a clock-like model in many datasets.

The evolution of two transmissible leukaemias colonizing the coasts of Europe

This study investigates the origin and evolution of two transmissible leukaemias in common cockles, identifying clonal origins, mutational signatures, and genomic instability.

Transcriptome landscape of kleptoplastic sea slug Elysia viridis

This study reports the transcriptome of the kleptoplastic sea slug Elysia viridis, identifying genes related to stress response and ROS quenching, and functional annotations for a large portion of its protein-coding sequences.

Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Phylovar improves scalability and accuracy of SNV detection in scDNAseq data by leveraging phylogenetic information, outperforming existing methods in speed and precision.

Interpreting dN/dS under different selective regimes in cancer evolution

This study examines how dN/dS ratios in cancer genomics differ under various selective pressures and highlights limitations in interpreting selection coefficients from these ratios.

Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

This study uses gene tree-species tree reconciliation on a large dataset to determine the root of the eukaryotic tree of life, supporting a root between Opisthokonta and all other eukaryotes.

Rapid evolution and biogeographic spread in a colorectal cancer

This study uses a model-based framework to analyze the evolutionary and biogeographic history of colorectal cancer, finding early monoclonal metastasis and rapid population expansion.

Selective pressures on human cancer genes along the evolution of mammals

The paper identifies 63 cancer genes under positive selection in mammals, enriched in DNA repair, and links germline selection to hereditary cancer risk.