相关论文: Finding Sequence Features in Tissue-specific Seque…

This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen…

Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…

Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…

The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a…

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…

Motifs are the most repetitive/frequent patterns of a time-series. The discovery of motifs is crucial for practitioners in order to understand and interpret the phenomena occurring in sequential data. Currently, motifs are searched among…

Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…

This article introduces idMotif, a visual analytics framework designed to aid domain experts in the identification of motifs within protein sequences. Motifs, short sequences of amino acids, are critical for understanding the distinct…

Time series prediction is of great significance in many applications and has attracted extensive attention from the data mining community. Existing work suggests that for many problems, the shape in the current time series may correlate an…

Discovery of transcription factor binding sites is a much explored and still exploring area of research in functional genomics. Many computational tools have been developed for finding motifs and each of them has their own advantages as…

Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network…

Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network…

The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown…

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets…

Many time series, particularly health data streams, can be best understood as a sequence of phenomenon or events, which we call \textit{motifs}. A time series motif is a short trace segment which may implicitly capture an underlying…

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…

In the age of social computing, finding interesting network patterns or motifs is significant and critical for various areas such as decision intelligence, intrusion detection, medical diagnosis, social network analysis, fake news…

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…