Related papers: Upper Bounds to Genome Rearrangement Problem using…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
Sequence representations supporting queries $access$, $select$ and $rank$ are at the core of many data structures. There is a considerable gap between the various upper bounds and the few lower bounds known for such representations, and how…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
In this paper we address two optimization problems arising in the design of genomic assays based on universal tag arrays. First, we address the universal array tag set design problem. For this problem, we extend previous formulations to…
An important problem when modeling gene networks lies in the identification of parameters, even if we consider a purely discrete framework as the one of Ren\'e Thomas. Here we are interested in the exhaustive search of all parameter values…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
A key property underlying the success of evolutionary algorithms (EAs) is their global search behavior, which allows the algorithms to `jump' from a current state to other parts of the search space, thereby avoiding to get stuck in local…
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…
Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
This paper proposes an algorithmic framework for various reconfiguration problems using zero-suppressed binary decision diagrams (ZDDs), a data structure for families of sets. In general, a reconfiguration problem checks if there is a…
In prefix coding over an infinite alphabet, methods that consider specific distributions generally consider those that decline more quickly than a power law (e.g., Golomb coding). Particular power-law distributions, however, model many…
While the theoretical analysis of evolutionary algorithms (EAs) has made significant progress for pseudo-Boolean optimization problems in the last 25 years, only sporadic theoretical results exist on how EAs solve permutation-based…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
While neuroevolution (evolving neural networks) has a successful track record across a variety of domains from reinforcement learning to artificial life, it is rarely applied to large, deep neural networks. A central reason is that while…
Previous compact representations of permutations have focused on adding a small index on top of the plain data $<\pi(1), \pi(2),...\pi(n)>$, in order to efficiently support the application of the inverse or the iterated permutation. In this…
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. The past decade has observed a massive growth in…