相关论文: Barnacle: An Assembly Algorithm for Clone-based Se…

Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…

We consider the problem of sequencing a set of positive numbers. We try to find the optimal sequence to maximize the variance of its partial sums. The optimal sequence is shown to have a beautiful structure. It is interesting to note that…

In this paper we present an efficient algorithm to produce a provably dense sample of a smooth compact variety. The procedure is partly based on computing $\textit{bottlenecks}$ of the variety. Using geometric information such as the…

A key problem in constrained random verification (CRV) concerns generation of input stimuli that result in good coverage of the system's runs in targeted corners of its behavior space. Existing CRV solutions however provide no formal…

The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…

Generating logical form equivalents of human language is a fresh way to employ neural architectures where long short-term memory effectively captures dependencies in both encoder and decoder units. The logical form of the sequence usually…

Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…

Sequence to Sequence models struggle at compositionality and systematic generalisation even while they excel at many other tasks. We attribute this limitation to their failure to internalise constructions conventionalised form meaning…

In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…

To cluster sequences given only their read-set representations, one may try to reconstruct each one from the corresponding read set, and then employ conventional (dis)similarity measures such as the edit distance on the assembled sequences.…

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…

DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…

Community detection in complex networks is a topic of considerable recent interest within the scientific community. For dealing with the problem that genetic algorithm are hardly applied to community detection, we propose a genetic…

The dominant approach to sequence generation is to produce a sequence in some predefined order, e.g. left to right. In contrast, we propose a more general model that can generate the output sequence by inserting tokens in any arbitrary…

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…

Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…

With distributed computing and mobile applications, synchronizing diverging replicas of data structures is a more and more common problem. We use algebraic methods to reason about filesystem operations, and introduce a simplified definition…

This paper provides a framework in order to statistically model sequences from human genome, which is allowing a formulation to synthesize gene sequences. We start by converting the alphabetic sequence of genome to decimal sequence by…