Bioinformatics

The largest family of transcription factors in mammals is of Cys ₂ His ₂ zinc finger-proteins, each with an NH ₂ -terminal KRAB motif. Extensive expansions of this family have occurred in separate mammalian lineages, with ~400 such genes known in ...

Motivation: Of the ~200 proteins that have been identified for the vaccinia virus (VACV) genome, many are currently listed as having an unknown function, and seven of these are also found in all other poxvirus genomes that have been sequenced. The ...

Motivation: Due to the growing number of completely sequenced genomes, functional annotation of proteins becomes a more and more important issue. Here, we describe a method for the prediction of sites within protein domains, which are part of protein-...

Motivation: Predicting cis -regulatory modules (CRMs) in higher eukaryotes is a challenging computational task. Commonly used methods to predict CRMs based on the signal of transcription factor binding sites (TFBS) are limited by prior information ...

Motivation: Likelihood ratio approximants (LRA) have been widely used for model comparison in statistics. The present study was undertaken in order to explore their utility as a scoring (ranking) function in the classification of protein sequences.

...

Motivation: Many computational methods for identifying regulatory elements use a likelihood ratio between motif and background models. Often, the methods use a background model of independent bases. At least two different Markov background models ...

Motivation: Modeling of protein interactions is often possible from known structures of related complexes. It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units ...

Motivation: Microarrays datasets frequently contain a large number of missing values (MVs), which need to be estimated and replaced for subsequent data mining. The focus of the paper is to study the effects of different MV treatments for cDNA ...

Motivation: The diverse microarray datasets that have become available over the past several years represent a rich opportunity and challenge for biological data mining. Many supervised and unsupervised methods have been developed for the analysis of ...

Motivation: The identification of the change of gene expression in multifactorial diseases, such as breast cancer is a major goal of DNA microarray experiments. Here we present a new data mining strategy to better analyze the marginal difference in ...

Motivation: A steadily increasing number of experiments with microarrays stimulate the further development of the statistical methods of the analysis of gene expression data. One of the central problems in this area is detecting differential gene ...

Motivation: Although numerous algorithms have been developed for microarray segmentation, extensive comparisons between the algorithms have acquired far less attention. In this study, we evaluate the performance of nine microarray segmentation ...

Motivation: With the generation of a wealth of information, detailing cellular components, their functions and interactions, there is a growing need for the development of new computational tools capable of interpreting these data within spatial and ...

Motivation: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an ...

Motivation: Annotation databases are widely used as public repositories of biological knowledge. However, most of these resources have been developed by independent groups which used different designs and different identifiers for the same biological ...

Motivation: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the ...

Summary: ChromoScan is an implementation of a genome-based scan statistic that detects genomic regions, which are statistically significant for targeted measurements, such as genetic associations with disease, gene expression profiles, DNA copy ...

Summary: Identification of disordered regions in polypeptide chains is very important because such regions are essential for protein function. A new parameter, namely mean packing density of residues has been introduced to detect disordered regions ...

Summary: Chromosomal translocations are common in cancer, and in some cases may be causal in the progression of the disease. Using microarrays, in which the expression of thousands of genes are simultaneously measured, could potentially allow one to ...

Summary: BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are ...

Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative processing procedure that comprises five major ...

Motivation: Based on a gene classification into hierarchical categories ('BINs'), MapMan was originally developed to display Arabidopsis thaliana gene expression in a functional context. We have created a bioinformatics system to extend MapMan to ...

Summary: ssSNPer is a novel user-friendly web interface that provides easy determination of the number and location of untested HapMap SNPs, in the region surrounding a tested HapMap SNP, which are statistically similar and would thus produce ...

Summary: MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual ...

Motivation: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted format.

Summary: Two modules, SBMLSupportLayout and ...

Summary: Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks for a number of organisms. To grapple with ...

Summary: Biologists and other scientists routinely need to know times of divergence between species and to construct phylogenies calibrated to time (timetrees). Published studies reporting time estimates from molecular data have been increasing ...