Related papers: The combinatorics of overlapping genes
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Neural codes allow the brain to represent, process, and store information about the world. Combinatorial codes, comprised of binary patterns of neural activity, encode information via the collective behavior of populations of neurons. A…
Proving capacity for networks without feedback or cooperation usually involves two fundamental random coding techniques: superposition coding and binning. Although conceptually very different, these two techniques often achieve the same…
Hypergraphs tackle the limitations of traditional graphs by introducing {\em hyperedges}. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges. Also, the underlying message-passing…
2-level polytopes naturally appear in several areas of pure and applied mathematics, including combinatorial optimization, polyhedral combinatorics, communication complexity, and statistics. In this paper, we present a study of some 2-level…
Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show some notable general features including essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly…
This article proposes a cognitive mechanism of humour of general applicability, not restricted to verbal communication. It is indebted to Raskin's concept of script overlap, and conforms to the incongruity-resolution theoretical framework,…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
We study the problem of learning a Bayesian network (BN) of a set of variables when structural side information about the system is available. It is well known that learning the structure of a general BN is both computationally and…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Hypergraphs are structures that can be decomposed or described; in other words they are recursively countable. Here, we get exact and asymptotic enumeration results on hypergraphs by means of exponential generating functions. The number of…