Related papers: Fundamental Limits of Pooled-DNA Sequencing
Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Training deep neural network (DNN) with noisy labels is practically challenging since inaccurate labels severely degrade the generalization ability of DNN. Previous efforts tend to handle part or full data in a unified denoising flow via…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
Counterfeiting poses a significant challenge across multiple industries, leading to financial losses and health risks. While DNA-based molecular tagging has emerged as a promising anti-counterfeiting strategy, existing methods rely on…
DNA storage has emerged as a promising solution for large-scale and long-term data preservation. Among various error types, insertions are the most frequent errors occurring in DNA sequences, where the inserted symbol is often identical or…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
Purpose Nanopore-based molecular sensing and measurement, specifically Deoxyribonucleic acid (DNA) sequencing, is advancing at a fast pace. Some embodiments have matured from coarse particle counters to enabling full human genome assembly.…
Discovering fine-grained categories from coarsely labeled data is a practical and challenging task, which can bridge the gap between the demand for fine-grained analysis and the high annotation cost. Previous works mainly focus on…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…