Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions/deletions and gene order rearrangements. Reconstruction of phylogeny based on gene order changes has been limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many Chloroplast ge...

A dynamic programming algorithm is developed for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree. To date, exhaustive algorithms that find the most likely set of ancestral states (joint reconstruction) have running times that scale exponentially with the number of sequences and are thus limited to very few taxa. The time requirement of o...

The Brassicaceae family includes important crop plants as well as the model plant Arabidopsis thaliana. The evolutionary history of this family is characterized by a number of whole genome duplications (WGDs), and the relationships within the family have been a matter of study and debate for decades. Recent multi-gene phylogenetic analyses have revealed that the Brassicaceae family can be divid...

A challenging task in computational biology is the reconstruction of genomic sequences of extinct ancestors, given the phylogenetic tree and the sequences at the leafs. This task is best solved by calculating the most likely estimate of the ancestral sequences, along with the most likely edge lengths. We deal with this problem and also the variant in which the phylogenetic tree in addition to t...

Like other RNA viruses, coxsackievirus B5 (CVB5) exists as circulating heterogeneous populations of genetic variants. In this study, we present the reconstruction and characterization of a probable ancestral virion of CVB5. Phylogenetic analyses based on capsid protein-encoding regions (the VP1 gene of 41 clinical isolates and the entire P1 region of eight clinical isolates) of CVB5 revealed tw...

Anterior cruciate ligament (ACL) reconstruction surgery has significantly evolved in recent years. This has led to development of new technologies that facilitate the diagnosis of ACL injury and the application of state of the art methods for treatment. In particular, individualized anatomical ACL reconstruction aims to restore native ACL function. Treatment is tailored to each patient based on...