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In genetical genomics studies, it is important to jointly analyze gene expression data and genetic variants in exploring their associations with complex traits, where the dimensionality of gene expressions and genetic variants can both be…
Let $G$ and $G_1, G_2, \ldots , G_t$ be given graphs. By $G\rightarrow (G_1, G_2, \ldots , G_t)$ we mean if the edges of $G$ are arbitrarily colored by $t$ colors, then for some $i$, $1\leq i\leq t$, the spanning subgraph of $G$ whose edges…
The linear spline growth model (LSGM), which approximates complex patterns using at least two linear segments, is a popular tool for examining nonlinear change patterns. Among such models, the linear-linear piecewise change pattern is the…
Many types of tumors exhibit chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletionsare also observed. Typically, a region that is aberrant in…
We have analyzed the relations between the mutational pressure, recombination and selection pressure in the bit-string model with sexual reproduction. For specific sets of these parameters we have found three phase transitions with one…
This paper provides a framework in order to statistically model sequences from human genome, which is allowing a formulation to synthesize gene sequences. We start by converting the alphabetic sequence of genome to decimal sequence by…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in…
This paper develops a simplified model for sexual replication within the quasispecies formalism. We assume that the genomes of the replicating organisms are two-chromosomed and diploid, and that the fitness is determined by the number of…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
Gene expression prediction plays a vital role in transcriptome-wide association studies (TWAS), which seek to establish associations between tissue gene expression and complex traits. Traditional models rely on genetic variants in close…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
The relationship between the size of the whole and the size of the parts in language and music is known to follow Menzerath-Altmann law at many levels of description (morphemes, words, sentences...). Qualitatively, the law states that…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
Researchers in genetics and other life sciences commonly use permutation tests to evaluate differences between groups. Permutation tests have desirable properties, including exactness if data are exchangeable, and are applicable even when…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…