Related papers: Physics-based signal analysis of genome sequences:…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
In this paper, we present two variations of an algorithm for signal reconstruction from one-bit or two-bit noisy observations of the discrete Fourier transform (DFT). The one-bit observations of the DFT correspond to the sign of its real…
Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…
The importance of the working document is that it allows the analysis of information and cases associated with (SARS-CoV-2) COVID-19, based on the daily information generated by the Government of Mexico through the Secretariat of Health,…
Future SARS-CoV-2 virus outbreak COVID-XX might possibly occur during the next years. However the pathology in humans is so recent that many clinical aspects, like early detection of complications, side effects after recovery or early…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
Identifying mutations of SARS-CoV-2 strains associated with their phenotypic changes is critical for pandemic prediction and prevention. We compared an explainable convolutional neural network (CNN) approach and the traditional genome-wide…
Gene-gene interactions are often regarded as playing significant roles in influencing variabilities of complex traits. Although much research has been devoted to this area, to date a comprehensive statistical model that addresses the…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Since the coronavirus disease (COVID-19) outbreak in December 2019, studies have been addressing diverse aspects in relation to COVID-19 and Variant of Concern 202012/01 (VOC 202012/01) such as potential symptoms and predictive tools.…
Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built…
Many control and detection applications require real-time analysis of signals from sensors, in order to quickly and accurately act upon events revealed by the sensors. Such signal analysis benefits from statistical models of signal and…
With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new…
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…
While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain…
Cancers are mainly caused by somatic genomic alterations (SGAs) that perturb cellular signaling systems and eventually activate oncogenic processes. Therefore, understanding the functional impact of SGAs is a fundamental task in cancer…
Considering vast amounts of genomic sequences of mostly unknown functionality, in-silico prediction of functional regions is an important enterprise. Many genomic browsers employ GC content, which was observed to be elevated in gene-rich…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the sharp differences in virus distributions across…
Compartmental models provide simple and efficient tools to analyze the relevant transmission processes during an outbreak, to produce short-term forecasts or transmission scenarios, and to assess the impact of vaccination campaigns.…