Related papers: Seven clusters in genomic triplet distributions

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…

Cluster analysis has proved to be an invaluable tool for the exploratory and unsupervised analysis of high dimensional datasets. Among methods for clustering, hierarchical approaches have enjoyed substantial popularity in genomics and other…

Extracting an understanding of the underlying system from high dimensional data is a growing problem in science. Discovering informative and meaningful features is crucial for clustering, classification, and low dimensional data embedding.…

In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…

Graph clustering is a fundamental problem in unsupervised learning, with numerous applications in computer science and in analysing real-world data. In many real-world applications, we find that the clusters have a significant high-level…

Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…

Clustering algorithms are one of the main analytical methods to detect patterns in unlabeled data. Existing clustering methods typically treat samples in a dataset as points in a metric space and compute distances to group together similar…

Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic…

We present a detailed study of the morphological features of 22 rich galaxy clusters. Our sample is constructed from a cross-correlation of optical (Abell+APM) data with X-ray (0.1 - 2.4) keV ROSAT pointed observations. We systematically…

Nowadays, data are generated massively and rapidly from scientific fields as bioinformatics, neuroscience and astronomy to business and engineering fields. Cluster analysis, as one of the major data analysis tools, is therefore more…

Segmentation of a colour image composed of different kinds of texture regions can be a hard problem, namely to compute for an exact texture fields and a decision of the optimum number of segmentation areas in an image when it contains…

The correct identification of clusters is crucial for an accurate monitoring of the spread of a disease and also in many other natural, social and physical phenomena which exhibit an epidemic structure. Nevertheless, even when an accurate…

A fundamental property of complex networks is the tendency for edges to cluster. The extent of the clustering is typically quantified by the clustering coefficient, which is the probability that a length-2 path is closed, i.e., induces a…

In this paper, we address the problem of identifying protein functionality using the information contained in its aminoacid sequence. We propose a method to define sequence similarity relationships that can be used as input for…

Predictive clustering trees (PCTs) are a well established generalization of standard decision trees, which can be used to solve a variety of predictive modeling tasks, including structured output prediction. Combining them into ensembles…

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of…

Spectral clustering is a powerful technique for clustering high-dimensional data, utilizing graph-based representations to detect complex, non-linear structures and non-convex clusters. The construction of a similarity graph is essential…

Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…

Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…

We propose a change-point detection method for large scale multiple testing problems with data having clustered signals. Unlike the classic change-point setup, the signals can vary in size within a cluster. The clustering structure on the…