Related papers: Reducibility of Gene Patterns in Ciliates using th…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating…
The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Golden Gate cloning has become a powerful and widely used DNA assembly method. Its modular nature and the reusability of standardized parts allow rapid construction of transcription units and multi-gene constructs. Importantly, its modular…
We build networks of genetic similarity in which the nodes are organisms sampled from biological populations. The procedure is illustrated by constructing networks from genetic data of a marine clonal plant. An important feature in the…
Cellular automata are discrete and computational models thatcan be shown as general models of complexity. They are used in varied applications to derive the generalized behavior of the presented model. In this paper we have took one such…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique,…
Discovering genes with similar functions across diverse biomedical contexts poses a significant challenge in gene representation learning due to data heterogeneity. In this study, we resolve this problem by introducing a novel model called…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic…
Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of…
Bioinformatics encompass storing, analyzing and interpreting the biological data. Most of the challenges for Machine Learning methods like Cellular Automata is to furnish the functional information with the corresponding biological…
The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Graphlet analysis is an approach to network analysis that is particularly popular in bioinformatics. We show how to set up a system of linear equations that relate the orbit counts and can be used in an algorithm that is significantly…
Motivation: The consistent amount of different types of omics data requires novel methods of analysis and data integration. In this work we describe Regression2Net, a computational approach to analyse gene expression and methylation…