相关论文: TwoPaCo: An efficient algorithm to build the compa…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
The format of graphing algorithms for genomic data has been a debate in recent biotechnology. In this paper, we discuss the construction of population graphs using said genomic data. We first examine the GENPOFAD distance measurement,…
A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine…
Bipartite graphs are a prevalent modeling tool for real-world networks, capturing interactions between vertices of two different types. Within this framework, bicliques emerge as crucial structures when studying dense subgraphs: they are…
Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture…
The compact genetic algorithm is an Estimation of Distribution Algorithm for binary optimisation problems. Unlike the standard Genetic Algorithm, no cross-over or mutation is involved. Instead, the compact Genetic Algorithm uses a virtual…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
The merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
High dimensional correlated binary data arise in many areas, such as observed genetic variations in biomedical research. Data simulation can help researchers evaluate efficiency and explore properties of different computational and…
Analyzing interconnection structures among underlying entities or objects in a dataset through the use of graph analytics has been shown to provide tremendous value in many application domains. However, graphs are not the primary…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…
In many scientific and engineering applications, one has to solve not one but a sequence of instances of the same problem. Often times, the problems in the sequence are linked in a way that allows intermediate results to be reused. A…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
We introduce a decomposition method for the distributed calculation of exact Euclidean Minimum Spanning Trees in high dimensions (where sub-quadratic algorithms are not effective), or more generalized geometric-minimum spanning trees of…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…