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In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…

Mutation is one of the most important stages of the genetic algorithm because of its impact on the exploration of global optima, and to overcome premature convergence. There are many types of mutation, and the problem lies in selection of…

In order to identify clusters of objects with features transformed by unknown affine transformations, we develop a Bayesian cluster process which is invariant with respect to certain linear transformations of the feature space and able to…

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

We present TripNet, a method for constructing phylogenetic networks from triplets. We will present the motivations behind our approach and its theoretical and empirical justification. To demonstrate the accuracy and efficiency of TripNet,…

Cancer genomes exhibit a large number of different alterations that affect many genes in a diverse manner. It is widely believed that these alterations follow combinatorial patterns that have a strong connection with the underlying…

This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…

A Genetic Algorithm (GA) is proposed in which each member of the population can change schemata only with its neighbors according to a rule. The rule methodology and the neighborhood structure employ elements from the Cellular Automata (CA)…

The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…

Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…

In many optical metrology techniques, fringe pattern analysis is the central algorithm for recovering the underlying phase distribution from the recorded fringe patterns. Despite extensive research efforts for decades, how to extract the…

We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. We compare the number of operations along the evolutionary trajectory to the DCJ distance of the genome from its ancestor…

Cluster analysis which focuses on the grouping and categorization of similar elements is widely used in various fields of research. Inspired by the phenomenon of atomic fission, a novel density-based clustering algorithm is proposed in this…

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…

Time course microarray data provide insight about dynamic biological processes. While several clustering methods have been proposed for the analysis of these data structures, comparison and selection of appropriate clustering methods are…

In scientific visualization, scalar fields are often compared through edit distances between their merge trees. Typical tasks include ensemble analysis, feature tracking and symmetry or periodicity detection. Tree edit distances represent…

Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way…

In an exploration paper, {\it L. Chen, Algorithms for Deforming and Contracting Simply Connected Discrete Closed Manifolds (I)}, we designed algorithms for deforming and contracting a simply connected discrete closed manifold to a discrete…

The classification of different patterns of network evolution, for example in brain connectomes or social networks, is a key problem in network inference and modern data science. Building on the notion of a network's Euclidean mirror, which…