Related papers: Just-DNA-Seq, open-source personal genomics platfo…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based…
For most diseases, building large databases of labeled genetic data is an expensive and time-demanding task. To address this, we introduce genetic Generative Adversarial Networks (gGAN), a semi-supervised approach based on an innovative GAN…
A major challenge in biomedical data science is to identify the causal genes underlying complex genetic diseases. Despite the massive influx of genome sequencing data, identifying disease-relevant genes remains difficult as individuals with…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read count variability. These estimates are…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
Sharing diverse genomic and other biomedical datasets is critical to advance scientific discoveries and their equitable translation to improve human health. However, data sharing remains challenging in the context of legacy datasets,…
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…
Introduction: Big data in healthcare must be exploited to achieve a substantial increase in efficiency and competitiveness. Especially the analysis of patient-related data possesses huge potential to improve decision-making processes.…
Human placenta is a complex and heterogeneous organ interfacing between the mother and the fetus that supports fetal development. Alterations to placental structural components are associated with various pregnancy complications. To reveal…
Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost has led to an exponential…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…