Related papers: Anchor points for genome alignment based on Filter…

Computational approaches in historical linguistics have been increasingly applied during the past decade and many new methods that implement parts of the traditional comparative method have been proposed. Despite these increased efforts,…

In recent years the importance of finding a meaningful pattern from huge datasets has become more challenging. Data miners try to adopt innovative methods to face this problem by applying feature selection methods. In this paper we propose…

In this paper, we present a novel approach to accelerate the Bayesian inference process, focusing specifically on the nested sampling algorithms. Bayesian inference plays a crucial role in cosmological parameter estimation, providing a…

In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite…

This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…

Internet links enable users to deepen their understanding of a topic by providing convenient access to related information. However, the majority of links are unanchored -- they link to a target webpage as a whole, and readers may expend…

Estimating neuron location from extracellular recordings is essential for developing advanced brain-machine interfaces. Accurate neuron localization improves spike sorting, which involves detecting action potentials and assigning them to…

In many high-impact applications, it is important to ensure the quality of output of a machine learning algorithm as well as its reliability in comparison with the complexity of the algorithm used. In this paper, we have initiated a…

Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…

Matching and retrieving previously translated segments from a Translation Memory is the key functionality in Translation Memories systems. However this matching and retrieving process is still limited to algorithms based on edit distance…

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…

For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…

Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…

Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…

Despite evidence for the existence of engrams as memory support structures in our brains, there is no consensus framework in neuroscience as to what their physical implementation might be. Here we propose how we might design a computer…

Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…

Molecular geometry prediction of flexible molecules, or conformer search, is a long-standing challenge in computational chemistry. This task is of great importance for predicting structure-activity relationships for a wide variety of…

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are…

Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…