A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods

Background  

The Golden Spike data set has been used to validate a number of methods for summarizing Affymetrix data sets, sometimes with seemingly contradictory results. Much less use has been made of this data set to evaluate differential expression methods. It has been suggested that this data set should not be used for method comparison due to a number of inherent flaws.     

In search of functional association from time-series microarray data based on the change trend and level of gene expression

Background  

The increasing availability of time-series expression data opens up new possibilities to study functional linkages of genes. Present methods used to infer functional linkages between genes from expression data are mainly based on a point-to-point comparison. Change trends between consecutive time points in time-series data have been so far not well explored.     

Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks

Background  

Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data.     

Revealing biases inherent in recombination protocols

Background  

The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing.     

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background  

The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.     

FRASS: the web-server for RNA structural comparison

Background  

The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.     

Using diffusion distances for flexible molecular shape comparison

Background  

Many molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition.     

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis

Background  

In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods.     

A tool for comparing different statistical methods on identifying differentially expressed genes

Background  

Many different statistical methods have been developed to deal with two group comparison microarray experiments. Most often, a substantial number of genes may be selected or not, depending on which method was actually used. Practical guidance on the application of these methods is therefore required. We developed a procedure based on bootstrap and a criterion to allow viewing and quantifying differences between method-dependent selections. We applied this procedure on three datasets that cover a range of possible sample sizes to compare three well known methods, namely: t-test, LPE and SAM.     

A comparison of parametric models for the investigation of the shape of cognitive change in the older population

Background  

Cognitive decline is a major threat to well being in later life. Change scores and regression based models have often been used for its investigation. Most methods used to describe cognitive decline assume individuals lose their cognitive abilities at a constant rate with time. The investigation of the parametric curve that best describes the process has been prevented by restrictions imposed by study design limitations and methodological considerations. We propose a comparison of parametric shapes that could be considered to describe the process of cognitive decline in late life.     

PALSSE: A program to delineate linear secondary structural elements from protein structures

Background  

The majority of residues in protein structures are involved in the formation of α-helices and β-strands. These distinctive secondary structure patterns can be used to represent a protein for visual inspection and in vector-based protein structure comparison. Success of such structural comparison methods depends crucially on the accurate identification and delineation of secondary structure elements.     

Which is the best method of sterilization of tumour bone for reimplantation? a biomechanical and histopathological study

Introduction  

Sterilization and re-usage of tumour bone for reconstruction after tumour resection is now gaining popularity in the East. This recycle tumour bone needs to be sterilized in order to eradicate the tumour cells before re-implantation for limb salvage procedures. The effect of some of these treatments on the integrity and sterility of the bone after treatment has been published but there has yet been a direct comparison between the various methods of sterilization to determine the one method that gives the best tumour kill without compromising the bone's structural integrity.     

Alignment of protein structures in the presence of domain motions

Background  

Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used.     

IDSS: deformation invariant signatures for molecular shape comparison

Background  

The conventional superposition methods use an ordinary least squares (LS) fit for structural comparison of two different conformations of the same protein. The main problem of the LS fit that it is sensitive to outliers, i.e. large displacements of the original structures superimposed.     

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

Background  

Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.     

ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification

Background  

Current classification of protein folds are based, ultimately, on visual inspection of similarities. Previous attempts to use computerized structure comparison methods show only partial agreement with curated databases, but have failed to provide detailed statistical and structural analysis of the causes of these divergences.     

Precise detection of rearrangement breakpoints in mammalian chromosomes

Background  

Genomes undergo large structural changes that alter their organisation. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. We developed a method to precisely delimit rearrangement breakpoints on a genome by comparison with the genome of a related species. Contrary to current methods which search for synteny blocks and simply return what remains in the genome as breakpoints, we propose to go further and to investigate the breakpoints themselves in order to refine them.     

Microarray analysis of relative gene expression stability for selection of internal reference genes in the rhesus macaque brain

Background  

Normalization of gene expression data refers to the comparison of expression values using reference standards that are consistent across all conditions of an experiment. In PCR studies, genes designated as "housekeeping genes" have been used as internal reference genes under the assumption that their expression is stable and independent of experimental conditions. However, verification of this assumption is rarely performed. Here we assess the use of gene microarray analysis to facilitate selection of internal reference sequences with higher expression stability across experimental conditions than can be expected using traditional selection methods.     

Effects of scanning sensitivity and multiple scan algorithms on microarray data quality

Background  

Maximizing the utility of DNA microarray data requires optimization of data acquisition through selection of an appropriate scanner setting. To increase the amount of useable data, several approaches have been proposed that incorporate multiple scans at different sensitivities to reduce the quantification error and to minimize effects of saturation. However, no direct comparison of their efficacy has been made. In the present study we compared individual scans at low, medium and high sensitivity with three methods for combining data from multiple scans (either 2-scan or 3-scan cases) using an actual dataset comprising 40 technical replicates of a reference RNA standard.