Categorizing water for LCA inventory

Purpose  

As impact assessment methods for water use in LCA evolve, so must inventory methods. Water categories that consider water quality must be defined within life cycle inventory. The method presented here aims to establish water categories by source, quality parameter and user.     

New resampling method for evaluating stability of clusters

Background  

Hierarchical clustering is a widely applied tool in the analysis of microarray gene expression data. The assessment of cluster stability is a major challenge in clustering procedures. Statistical methods are required to distinguish between real and random clusters. Several methods for assessing cluster stability have been published, including resampling methods such as the bootstrap.     

Implications for domain fusion protein-protein interactions based on structural information

Background  

Several in silico methods exist that were developed to predict protein interactions from the copious amount of genomic and proteomic data. One of these methods is Domain Fusion, which has proven to be effective in predicting functional links between proteins.     

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

Background  

As more methods are developed to analyze RNA-profiling data, assessing their performance using control datasets becomes increasingly important.     

BioInfer: a corpus for information extraction in the biomedical domain

Background  

Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora.     

An interactive tool for visualization of relationships between gene expression profiles

Background  

Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques.     

A comparison of probe-level and probeset models for small-sample gene expression data

Background  

Statistical methods to tentatively identify differentially expressed genes in microarray studies typically assume larger sample sizes than are practical or even possible in some settings.     

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.     

The Flp double cross system a simple efficient procedure for cloning DNA fragments

Background  

While conventional cloning methods using restriction enzymes and polynucleotide ligase are adequate for most DNAs, fragments made by the polymerase chain reaction are difficult to clone because the amplifying DNA polymerase tends to add untemplated nucleotides to the 3'-termini of the amplified strands. Conservative site-specific recombinases offer an efficient alternative to conventional cloning methods.     

Word correlation matrices for protein sequence analysis and remote homology detection

Background  

Classification of protein sequences is a central problem in computational biology. Currently, among computational methods discriminative kernel-based approaches provide the most accurate results. However, kernel-based methods often lack an interpretable model for analysis of discriminative sequence features, and predictions on new sequences usually are computationally expensive.     

A novel method for prokaryotic promoter prediction based on DNA stability

Background  

In the post-genomic era, correct gene prediction has become one of the biggest challenges in genome annotation. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. This work presents a novel prokaryotic promoter prediction method based on DNA stability.     

SignS: a parallelized,open-source,freely available,web-based tool for gene selection and molecular signatures for survival and censored data

Background  

Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data.     

Preferred analysis methods for Affymetrix GeneChips. II. An expanded,balanced, wholly-defined spike-in dataset

Background  

Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.     

Sample size calculation for microarray experiments with blocked one-way design

Background  

One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment effects in microarray experiments.     

A high-level 3D visualization API for Java and ImageJ

Background  

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.     

R/BHC: fast Bayesian hierarchical clustering for microarray data

Background  

Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained.     

TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis

Background  

Computational enzyme design is far from being applicable for the general case. Due to computational complexity and limited knowledge of the structure-function interplay, heuristic methods have to be used.     

GOPET: A tool for automated predictions of Gene Ontology terms

Background  

Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions.