Related papers: Exploring gene content with pangene graphs
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing…
We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Gene Regulatory Networks (GRNs) are intricate biological systems that control gene expression and regulation in response to environmental and developmental cues. Advances in computational biology, coupled with high throughput sequencing…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Living cells are the product of gene expression programs that involve the regulated transcription of thousands of genes. The elucidation of transcriptional regulatory networks in thus needed to understand the cell's working mechanism, and…
Gene set collections are a common ground to study the enrichment of genes for specific phenotypic traits. Gene set enrichment analysis aims to identify genes that are over-represented in gene sets collections and might be associated with a…
The biological roles of gene sets are used to group them into collections. These collections are often characterized by being high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
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…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
Evolutionary algorithms (EAs) simulate natural selection but have two main limitations: (1) they rarely update individuals based on global correlations, limiting comprehensive learning; (2) they struggle with balancing exploration and…
The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to communicate such findings, not all of…
Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…
Histone modifications play a critical role in gene regulation. Consequently, predicting gene expression from histone modification signals is a highly motivated problem in epigenetics. We build upon the work of DeepChrome by Singh et al.…
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of disease subtypes. Analyses of these data are becoming ever more…
Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…