Related papers: Haplotype Assembly: An Information Theoretic View

Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…

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…

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…

Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are two kinds of commonly used markers in Y chromosome studies of forensic and population genetics. There has been increasing interest in the cost saving strategy by…

A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…

High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…

We study the relation between the persistent homology and the spectral sequence of a filtered chain complex over a field. Our method is based on a decomposition of the persistent homology. We demonstrate that, under fairly general…

We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…

The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…

While many short read assemblers attempt to simplify the de Brujin graph by identifying and resolving variant-induced bubbles to produce a haploid mosaic result, this approach is only viable when variants are relatively rare and the bubbles…

Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…

DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

We formulate genome assembly problem as an optimization problem in which the objective function is the likelihood of the assembly given the reads.

The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…

In this paper, we solve the sample shortage problem in the human parsing task. We begin with the self-learning strategy, which generates pseudo-labels for unlabeled data to retrain the model. However, directly using noisy pseudo-labels will…

Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…