Related papers: Haplotype Assembly: An Information Theoretic View
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…
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…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
Persistent homology provides information about the lifetime of homology classes along a filtration of cell complexes. Persistence barcode is a graphical representation of such information. A filtration might be determined by time in a set…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
Higher-dimensional rewriting systems are tools to analyse the structure of formally reducing terms to normal forms, as well as comparing the different reduction paths that lead to those normal forms. This higher structure can be captured by…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on…
A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper we take a few initial steps towards a description of this object, which may be…
The remarkable success of foundation models has sparked growing interest in their application to single-cell biology. Models like Geneformer and scGPT promise to serve as versatile tools in this specialized field. However, representing a…