Related papers: Fundamental Limits of Pooled-DNA Sequencing
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
We investigate the capacity of noisy frequency-based channels, motivated by DNA data storage in the short-molecule regime, where information is encoded in the frequency of items types rather than their order. The channel output is a…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
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…
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
DNA samples are often pooled, either by experimental design, or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of…
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…