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The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
In the past decade, transcriptome data have become an important component of many phylogenetic studies. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and…
Medical image classification has developed rapidly under the impetus of the convolutional neural network (CNN). Due to the fixed size of the receptive field of the convolution kernel, it is difficult to capture the global features of…
Microarray technology is known as one of the most important tools for collecting DNA expression data. This technology allows researchers to investigate and examine types of diseases and their origins. However, microarray data are often…
Understanding the global organization of complicated and high dimensional data is of primary interest for many branches of applied sciences. It is typically achieved by applying dimensionality reduction techniques mapping the considered…
Along with the flourish of the information age, massive amounts of data are generated day by day. Due to the large-scale and high-dimensional characteristics of these data, it is often difficult to achieve better decision-making in…
Causal effects are often characterized with population summaries. These might provide an incomplete picture when there are heterogeneous treatment effects across subgroups. Since the subgroup structure is typically unknown, it is more…
Disruptive technologies provides unparalleled opportunities to contribute to the identifications of many aspects in pervasive healthcare, from the adoption of the Internet of Things through to Machine Learning (ML) techniques. As a powerful…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
Usage data of a group of users distributed across a number of categories, such as songs, movies, webpages, links, regular household products, mobile apps, games, etc. can be ultra-high dimensional and massive in size. More often this kind…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Systematic reviews and mapping studies are critical to synthesize research, identify gaps, and guide future work, but are often labor-intensive and time-consuming. Existing tools provide partial support for specific steps, leaving much of…
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for experiments to enhance understanding of biological mechanisms…
Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
We discuss two new approaches to extract relevant biological information on the Transcription Factors (and in particular to identify their binding sequences) from the statistical distribution of oligonucleotides in the upstream region of…