Related papers: Constrained Consensus Sequence Algorithm for DNA A…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
Algorithms for community detection are usually stochastic, leading to different partitions for different choices of random seeds. Consensus clustering has proven to be an effective technique to derive more stable and accurate partitions…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
The goal of constraint-based sequence mining is to find sequences of symbols that are included in a large number of input sequences and that satisfy some constraints specified by the user. Many constraints have been proposed in the…
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…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
Preference orderings are orderings of a set of items according to the preferences (of judges). Such orderings arise in a variety of domains, including group decision making, consumer marketing, voting and machine learning. Measuring the…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
We propose a novel convolutional architecture, named $gen$CNN, for word sequence prediction. Different from previous work on neural network-based language modeling and generation (e.g., RNN or LSTM), we choose not to greedily summarize the…
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 present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…