Related papers: Locating recombination hot spots in genomic sequen…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Recent developments in integrated photonics technology are opening the way to the fabrication of complex linear optical interferometers. The application of this platform is ubiquitous in quantum information science, from quantum simulation…
Medical data classification is typically a challenging task due to imbalance between classes. In this paper, we propose an approach to classify dermatoscopic images from HAM10000 (Human Against Machine with 10000 training images) dataset,…
We analyze 14,651 HIV1 reverse transcriptase (HIV RT) sequences from the Stanford HIV Drug Resistance Database labeled with treatment regimen in order to study the evolution this enzyme under drug selection in the clinic. Our goal is to…
Detecting communities in complex networks can shed light on the essential characteristics and functions of the modeled phenomena. This topic has attracted researchers of various fields from both academia and industry. Among the different…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. The past decade has observed a massive growth in…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Cytotoxic T-lymphocytes (CTLs) recognize viral protein fragments displayed by major histocompatibility complex (MHC) molecules on the surface of virally infected cells and generate an anti-viral response that can kill the infected cells.…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
We propose a new, more actionable view of neural network interpretability and data analysis by leveraging the remarkable matching effectiveness of representations derived from deep networks, guided by an approach for class-conditional…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effect on gene expression: expression quantitative trait locus (eQTL) hotspots. We describe a set of exploratory graphical…
In segmentation problems, inference on change-point position and model selection are two difficult issues due to the discrete nature of change-points. In a Bayesian context, we derive exact, non-asymptotic, explicit and tractable formulae…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…