Related papers: Intra-Chromosomal Potentials from Nucleosomal Posi…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
Many measurement modalities which perform imaging by probing an object pixel-by-pixel, such as via Photoacoustic Microscopy, produce a multi-dimensional feature (typically a time-domain signal) at each pixel. In principle, the many degrees…
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
We develop a Genetic Programming-based methodology that enables discovery of novel functional forms for classical inter-atomic force-fields, used in molecular dynamics simulations. Unlike previous efforts in the field, that fit only the…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…
Chromatin is a complex of DNA, RNA and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
Genetic algorithms are a well-known method for tackling the problem of variable selection. As they are non-parametric and can use a large variety of fitness functions, they are well-suited as a variable selection wrapper that can be applied…
In this contribution, the clustering procedure based on K-Means algorithm is studied as an inverse problem, which is a special case of the illposed problems. The attempts to improve the quality of the clustering inverse problem drive to…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
Based on an analysis of the short range chemical environment of each atom in a system, standard machine learning based approaches to the construction of interatomic potentials aim at determining directly the central quantity which is the…
Deep Learning models have transformed various domains, including the healthcare sector, particularly biomedical image classification by learning intricate features and enabling accurate diagnostics pertaining to complex diseases. Recent…
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…
Genetic algorithms are a powerful tool in optimization for single and multi-modal functions. This paper provides an overview of their fundamentals with some analytical examples. In addition, we explore how they can be used as a parameter…