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Phonon localization is a phenomenon that influences numerous material properties in condensed matter physics. Anderson localization brings rise to localized atomic-scale phonon interferences in disordered lattices with an influence limited…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…
The length and time scales of atomistic simulations are limited by the computational cost of the methods used to predict material properties. In recent years there has been great progress in the use of machine learning algorithms to develop…
We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster,…
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…
Structural defects are ubiquitous in condensed matter, and not always a nuisance. For example, they underlie phenomena such as Anderson localization and hyperuniformity, and they are now being exploited to engineer novel materials. Here, we…
All genes on the human Y-chromosome were studied using fractal dimension and Shannon entropy. Clear outlier clusters were identified. Among these were 6 sequences that have since been withdrawn as CDSs and 1 additional sequence that is not…
With a view toward addressing the explosive growth in the computational demands of nuclear structure and reactions modeling, we develop a novel quantum algorithm for neutron-nucleus simulations with general potentials, which provides…
Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic…
In order to efficiently explore the chemical space of all possible small molecules, a common approach is to compress the dimension of the system to facilitate downstream machine learning tasks. Towards this end, we present a data driven…
The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated…
The opportunistic fungal pathogen Candida albicans causes serious hematogenic hospital acquired candidiasis with worldwide impact on public health. Because of its importance as a nosocomial etiologic agent, C. albicans genome has been…
Machine Learning methods have of late made significant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in…
Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…
Fast and high quality document clustering is an important task in organizing information, search engine results obtaining from user query, enhancing web crawling and information retrieval. With the large amount of data available and with a…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
The detection of genomic regions unusually rich in a given pattern is an important undertaking in the analysis of next generation sequencing data. Recent studies of chromosomal translocations in activated B lymphocytes have identified…
Among the genetic algorithms generally used for optimization problems in the recent decades, quantum-inspired variants are known for fast and high-fitness convergence and small resource requirement. Here the application to the patient…