相关论文: Identifying DNA motifs based on match and mismatch…

Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…

In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…

Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…

Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…

Protein complexes involved in DNA mismatch repair appear to diffuse along dsDNA in order to locate a hemimethylated incision site via a dissociative mechanism. Here, we study the probability that these complexes locate a given target site…

Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the…

Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…

In most computer vision and image analysis problems, it is necessary to define a similarity measure between two or more different objects or images. Template matching is a classic and fundamental method used to score similarities between…

Kinship verification aims to find out whether there is a kin relation for a given pair of facial images. Kinship verification databases are born with unbalanced data. For a database with N positive kinship pairs, we naturally obtain N(N-1)…

Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…

Gene expression datasets are usually of high dimensionality and therefore require efficient and effective methods for identifying the relative importance of their attributes. Due to the huge size of the search space of the possible…

While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated…

In many classification problems, we want a classifier that is robust to a range of non-semantic transformations. For example, a human can identify a dog in a picture regardless of the orientation and pose in which it appears. There is…

Discriminative patterns are association patterns that occur with disproportionate frequency in some classes versus others, and have been studied under names such as emerging patterns and contrast sets. Such patterns have demonstrated…

DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…

Aptamers, short synthetic RNA/DNA molecules binding specific targets with high affinity and specificity, are utilized in an increasing spectrum of bio-medical applications. Aptamers are identified in vitro via the Systematic Evolution of…

Discriminative pattern mining is an essential task of data mining. This task aims to discover patterns which occur more frequently in a class than other classes in a class-labeled dataset. This type of patterns is valuable in various…

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…