Related papers: Seven clusters in genomic triplet distributions
A general method is described for detecting and analysing galaxy systems. The multivariate geometrical structure of the sample is studied by using an extension of the method which we introduced in a previous paper. The method is based on an…
We herein introduce a new method of interpretable clustering that uses unsupervised binary trees. It is a three-stage procedure, the first stage of which entails a series of recursive binary splits to reduce the heterogeneity of the data…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
We propose a multi-phase approach to explore network structures. In this method, structure analysis is not carried out on the observed network directly. Instead, certain similarity measures of the nodes are derived from the network firstly,…
Cluster analysis is an unsupervised learning strategy that can be employed to identify subgroups of observations in data sets of unknown structure. This strategy is particularly useful for analyzing high-dimensional data such as microarray…
Inference in clustering is paramount to uncovering inherent group structure in data. Clustering methods which assess statistical significance have recently drawn attention owing to their importance for the identification of patterns in high…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
A first step in exploring population structure in crop plants and other organisms is to define the number of subpopulations that exist for a given data set. The genetic marker data sets being generated have become increasingly large over…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Distributions of triplets in some genetic sequences are examined and found to be well described by a 2-parameter Markov process with a sparse transition matrix. The variances of all the relevant parameters are not large, indicating that…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome…
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
Globular Clusters (GCs) have historically been subdivided in either two (disk/halo) or three (disk/inner-halo/outer-halo) groups based on their orbital, chemical and internal physical properties. The qualitative nature of this subdivision…
A hierarchical scheme for clustering data is presented which applies to spaces with a high number of dimension ($N_{_{D}}>3$). The data set is first reduced to a smaller set of partitions (multi-dimensional bins). Multiple clustering…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…
In this short paper, it is shown that the multiplet structure of the standard genetic code is derivable from the total number of nucleotides contained in 64 codons, 192, a small number. The degeneracy class-number is derived as the number…
Phase-change materials (PCMs) such as Ge-Sb-Te alloys are widely used in non-volatile memory applications due to their rapid and reversible switching between amorphous and crystalline states. However, their functional properties are…