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Cellular phone is one of the most developing technological artifacts today. The evolution occurs through random innovation. Our effort is trying to view the evolution of this artifact from memetics. By constructing a phylomemetic tree based…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
Boissonnat and Pritam introduced an algorithm to reduce a filtration of flag (or clique) complexes, which can in particular speed up the computation of its persistent homology. They used so-called edge collapse to reduce the input flag…
In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…
In this paper we introduce the phylogenetic scan test (PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial (DTM) model. DTM models the microbiome data through a cascade of…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Selecting the most relevant or informative features is a key issue in actual machine learning problems. Since an exhaustive search is not feasible even for a moderate number of features, an intelligent search strategy must be employed for…
In this paper, we present an algorithm that enumerates a certain class of signed permutations, referred to as grid signed permutation classes. In the case of permutations, the corresponding grid classes are of interest because they are…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Principal components (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples sampled from a given environment. However, a classical application of…
In recent years the importance of finding a meaningful pattern from huge datasets has become more challenging. Data miners try to adopt innovative methods to face this problem by applying feature selection methods. In this paper we propose…
Evolutionary algorithms solve problems by simulating the evolution of a population of candidate solutions. We focus on evolving permutations for ordering problems like the traveling salesperson problem (TSP), as well as assignment problems…
A first step in exploring population structure in crop plants and other organisms is to define the number of subpopulations that exist for a given data set. The genetic marker data sets being generated have become increasingly large over…
Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…
The design and the implementation of a genetic algorithm are described. The applicability domain is on structure-activity relationships expressed as multiple linear regressions and predictor variables are from families of structure-based…