Related papers: Do Read Errors Matter for Genome Assembly?
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
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 this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been…
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…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…
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…
In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs…
Generative adversarial networks (GANs) generate data based on minimizing a divergence between two distributions. The choice of that divergence is therefore critical. We argue that the divergence must take into account the hypothesis set and…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
The Generative Adversarial Network (GAN) has achieved great success in generating realistic (real-valued) synthetic data. However, convergence issues and difficulties dealing with discrete data hinder the applicability of GAN to text. We…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…