Related papers: Fast ordered sampling of DNA sequence variants
Genome wide association studies directly assay 10^6 single nucleotide polymorphisms (SNPs) across a study cohort. Probabilistic estimation of additional sites by genotype imputation can increase this set of variants by 10- to 40-fold. Even…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
Deep convolutional neural networks (CNNs) have shown excellent performance in object recognition tasks and dense classification problems such as semantic segmentation. However, training deep neural networks on large and sparse datasets is…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Graph Convolutional Networks (GCNs) have become a crucial tool on learning representations of graph vertices. The main challenge of adapting GCNs on large-scale graphs is the scalability issue that it incurs heavy cost both in computation…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
The Third-Generation in DNA sequencing has emerged in the last few years using new technologies that allow the production of long-read sequences. Applications of the Third-Generation sequencing enable real-time and on-site data production,…
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…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on…
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…
Genome-wide association studies generate very large datasets that require scalable analysis algorithms. In this report we describe the GEDI software package, which implements efficient algorithms for performing several common tasks in the…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…