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Establishing a distance between genomes is a significant problem in computational genomics, because its solution can be used to establish evolutionary relationships including phylogeny. The "double cut and join" (DCJ) model of chromosomal…
We compute the limiting distribution, as n approaches infinity, of the number of cycles of length between gamma n and delta n in a permutation of [n] chosen uniformly at random, for constants gamma, delta such that 1/(k+1) <= gamma < delta…
This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from probability theory. Crucially, this distance estimate provides a genuine metric on genome space. We develop the…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
We study the problem of partitioning a small sample of $n$ individuals from a mixture of $k$ product distributions over a Boolean cube $\{0, 1\}^K$ according to their distributions. Each distribution is described by a vector of allele…
To model the destruction of a resilient network, Cai, Holmgren, Devroye and Skerman introduced the $k$-cut model on a random tree, as an extension to the classic problem of cutting down random trees. Berzunza, Cai and Holmgren later proved…
We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
In this paper, the transfer matrix technique using the $k$-matching vector is developed to compute the number of $k$-matchings in an arbitrary graph which can be constructed by successive amalgamations over sets of cardinality two. This…
A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S|that contains a representation of each element in S exactly once as a substring. If S is the set of k-subsets of [n] = {1, 2, . . . , n}, it is…
Graphs are extremely versatile and ubiquitous mathematical structures with potential to model a wide range of domains. For this reason, graph problems have been of interest since the early days of computer science. Some of these problems…
String Kernel (SK) techniques, especially those using gapped $k$-mers as features (gk), have obtained great success in classifying sequences like DNA, protein, and text. However, the state-of-the-art gk-SK runs extremely slow when we…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
Structural properties of evolving random graphs are investigated. Treating linking as a dynamic aggregation process, rate equations for the distribution of node to node distances (paths) and of cycles are formulated and solved analytically.…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
We consider the problem of enumerating the permutations containing exactly $k$ occurrences of a pattern of length 3. This enumeration has received a lot of interest recently, and there are a lot of known results. This paper presents an…
Consider a random permutation of $kn$ objects that permutes $n$ disjoint blocks of size $k$ and then permutes elements within each block. Normalizing its cycle lengths by $kn$ gives a random partition of unity, and we derive the limit law…