A protein-protein interaction network aligner study in the multi-objective domain.

Background And Objective: The protein-protein interaction (PPI) network alignment has proven to be an efficient technique in the diagnosis and prevention of certain diseases. However, the difficulty in maximizing, at the same time, the two qualities that measure the goodness of alignments (topological and biological quality) has led aligners to produce very different alignments. Thus making a comparative study among alignments of such different qualities a big challenge.

Iterative Level-0: A new and fast algorithm to traverse mating networks calculating the inbreeding and relationship coefficients.

In population medical genetics, the study of autosomal recessive disorders in highly endogamous populations is a major topic where calculating the inbreeding and relationship coefficients on mating networks is crucial. However, a challenge arises when dealing with large and complex mating networks, making their traversal difficult during the calculation process. For this calculation, we propose using Iterative Level-0 (IL0) as a new and faster algorithm that traverses mating networks more efficiently.

Automatic Update Summarization by a Multiobjective Number-One-Selection Genetic Approach.

Currently, the explosive growth of the information available on the Internet makes automatic text summarization systems increasingly important. A particularly relevant challenge is the update summarization task. Update summarization differs from traditional summarization in its dynamic nature.

PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks.

Background And Objective: Phage therapy is a resurgent strategy used in medicine and the food industry to lyse bacteria that cause damage to health or spoil a food product. Frequently, phage-bacteria infection networks have a large size, making it impossible to manually study all possible phage cocktails. Thus, this article presents an R package called PhageCocktail to automatically design efficient phage cocktails from phage-bacteria infection networks.

Systematic analysis of putative phage-phage interactions on minimum-sized phage cocktails.

The application of bacteriophages as antibacterial agents has many benefits in the "post-antibiotic age". To increase the number of successfully targeted bacterial strains, phage cocktails, instead of a single phage, are commonly formulated. Nevertheless, there is currently no consensus pipeline for phage cocktail development.

Computational design of phage cocktails based on phage-bacteria infection networks.

The misuse and overuse of antibiotics have boosted the proliferation of multidrug-resistant (MDR) bacteria, which are considered a major public health issue in the twenty-first century. Phage therapy may be a promising way in the treatment of infections caused by MDR pathogens, without the side effects of the current available antimicrobials. Phage therapy is based on phage cocktails, that is, combinations of phages able to lyse the target bacteria.

A stage-based approach to allocating water quality monitoring stations based on the WorldQual model: The Jubba River as a case study.

Ensuring adequate freshwater quality is an important aspect of integrated environmental management and sustainable development. One contribution towards this end is to monitor the water quality of river basins. An important issue in constructing a water quality monitoring network is how to allocate the stations.

Inter-Algorithm Multiobjective Cooperation for Phylogenetic Reconstruction on Amino Acid Data.

Inter-algorithm cooperative approaches are increasingly gaining interest as a way to boost the search capabilities of evolutionary algorithms (EAs). However, the growing complexity of real-world optimization problems demands new cooperative designs that implement performance-driven strategies to improve the solution quality. This article explores multiobjective cooperation to address an important problem in bioinformatics: the reconstruction of phylogenetic histories from amino acid data.

A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment.

The alignment among three or more nucleotides/amino acids sequences at the same time is known as multiple sequence alignment (MSA), a nondeterministic polynomial time (NP)-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a multiobjective version of the MSA problem wherein the goal is to simultaneously optimize the accuracy and conservation of the alignment.

Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences.

The alignment of three or more protein or nucleotide sequences is known as Multiple Sequence Alignment problem. The complexity of this problem increases exponentially with the number of sequences; therefore, many of the current approaches published in the literature suffer a computational overhead when thousands of sequences are required to be aligned. We introduce a new approach for dealing with ultra-large sets of sequences.

A Characteristic-Based Framework for Multiple Sequence Aligners.

The multiple sequence alignment is a well-known bioinformatics problem that consists in the alignment of three or more biological sequences (protein or nucleic acid). In the literature, a number of tools have been proposed for dealing with this biological sequence alignment problem, such as progressive methods, consistency-based methods, or iterative methods; among others. These aligners often use a default parameter configuration for all the input sequences to align.

Finding Patterns in Protein Sequences by Using a Hybrid Multiobjective Teaching Learning Based Optimization Algorithm.

Proteins are molecules that form the mass of living beings. These proteins exist in dissociated forms like amino-acids and carry out various biological functions, in fact, almost all body reactions occur with the participation of proteins. This is one of the reasons why the analysis of proteins has become a major issue in biology.

Gene variants and haplotypes modifying transcription factor binding sites in the human cyclooxygenase 1 and 2 (PTGS1 and PTGS2) genes.

Cyclooxygenases (prostaglandin-endoperoxide synthases, (EC 1.14.99.

DNA strand generation for DNA computing by using a multi-objective differential evolution algorithm.

In this paper, we use an adapted multi-objective version of the differential evolution (DE) metaheuristics for the design and generation of reliable DNA libraries that can be used for computation. DNA sequence design is a very relevant task in many recent research fields, e.g.

Applying a multiobjective metaheuristic inspired by honey bees to phylogenetic inference.

The development of increasingly popular multiobjective metaheuristics has allowed bioinformaticians to deal with optimization problems in computational biology where multiple objective functions must be taken into account. One of the most relevant research topics that can benefit from these techniques is phylogenetic inference. Throughout the years, different researchers have proposed their own view about the reconstruction of ancestral evolutionary relationships among species.

Fast decision algorithms in low-power embedded processors for quality-of-service based connectivity of mobile sensors in heterogeneous wireless sensor networks.

When a mobile wireless sensor is moving along heterogeneous wireless sensor networks, it can be under the coverage of more than one network many times. In these situations, the Vertical Handoff process can happen, where the mobile sensor decides to change its connection from a network to the best network among the available ones according to their quality of service characteristics. A fitness function is used for the handoff decision, being desirable to minimize it.

Parallel Niche Pareto AlineaGA--an evolutionary multiobjective approach on multiple sequence alignment.

Multiple sequence alignment is one of the most recurrent assignments in Bioinformatics. This method allows organizing a set of molecular sequences in order to expose their similarities and their differences. Although exact methods exist for solving this problem, their use is limited by the computing demands which are necessary for exploring such a large and complex search space.