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Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach…
Neurons have a polarized structure, including dendrites and axons, and compartment-specific functions can be affected by dwelling mitochondria. It is known that the morphology of mitochondria is closely related to the functions of neurons…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
Cell-free DNA (cfDNA) analysis is a powerful, minimally invasive tool for monitoring disease progression, treatment response, and early detection. A major challenge, however, is accurately determining the tissue of origin, especially in…
Recently, scientists from The Craig J. Venter Institute reported construction of very long DNA molecules using a variety of experimental procedures adopting a number of working hypotheses. Finding a mathematical rule for generation of such…
Mitochondria are complex organelles, and their proteomics analysis requires a combination of techniques. The emphasis in this chapter is made first on mitochondria preparation from cultured mammalian cells, then on the separation of the…
Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of…
The proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the…
Vertebrae localization, segmentation and identification in CT images is key to numerous clinical applications. While deep learning strategies have brought to this field significant improvements over recent years, transitional and…
High-resolution connectomics data allows for the identification of dysfunctional mitochondria which are linked to a variety of diseases such as autism or bipolar. However, manual analysis is not feasible since datasets can be petabytes in…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
Vertebral detection and segmentation are critical steps for treatment planning in spine surgery and radiation therapy. Accurate identification and segmentation are complicated in imaging that does not include the full spine, in cases with…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
The complementary DNA (cDNA) sequence is considered to be the magic biometric technique for personal identification. In this paper, we present a new method for cDNA recognition based on the artificial neural network (ANN). Microarray…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…