Gene finding in novel genomes

Background  

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.     

Motif-guided sparse decomposition of gene expression data for regulatory module identification

Background  

Genes work coordinately as gene modules or gene networks. Various computational approaches have been proposed to find gene modules based on gene expression data; for example, gene clustering is a popular method for grouping genes with similar gene expression patterns. However, traditional gene clustering often yields unsatisfactory results for regulatory module identification because the resulting gene clusters are co-expressed but not necessarily co-regulated.     

Automatic generation of gene finders for eukaryotic species

Background  

The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically generate species-specific gene finders and to re-train them as the quantity and quality of reliable gene annotation grows.     

Multivariate analysis of microarray data: differential expression and differential connection

Background  

Typical analysis of microarray data ignores the correlation between gene expression values. In this paper we present a model for microarray data which specifically allows for correlation between genes. As a result we combine gene network ideas with linear models and differential expression.     

Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA – a Bayesian approach

Background  

Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge.     

A new measure for functional similarity of gene products based on Gene Ontology

Background  

Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role.     

An accurate and interpretable model for siRNA efficacy prediction

Background  

The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. Although considerable progress has been made recently in understanding how the RNAi pathway mediates gene silencing, the design of potent siRNAs remains challenging.     

RCAS-RNAi: A loss-of-function method for the developing chick retina

Background  

The embryonic chick provides an excellent model system for studies of development. However, it has lacked an efficient loss-of-function method for studies of gene function.     

Effects of sample size on robustness and prediction accuracy of a prognostic gene signature

Background  

Few overlap between independently developed gene signatures and poor inter-study applicability of gene signatures are two of major concerns raised in the development of microarray-based prognostic gene signatures. One recent study suggested that thousands of samples are needed to generate a robust prognostic gene signature.     

Multiconstrained gene clustering based on generalized projections

Background  

Gene clustering for annotating gene functions is one of the fundamental issues in bioinformatics. The best clustering solution is often regularized by multiple constraints such as gene expressions, Gene Ontology (GO) annotations and gene network structures. How to integrate multiple pieces of constraints for an optimal clustering solution still remains an unsolved problem.     

Comparative transcriptomics in <Emphasis Type="Italic">Yersinia pestis</Emphasis>: a global view of environmental modulation of gene expression

Background  

Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro.     

In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles

Background  

In silico candidate gene prioritisation (CGP) aids the discovery of gene functions by ranking genes according to an objective relevance score. While several CGP methods have been described for identifying human disease genes, corresponding methods for prokaryotic gene function discovery are lacking. Here we present two prokaryotic CGP methods, based on phylogenetic profiles, to assist with this task.     

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

Background  

The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies.     

Polymorphism and selection of rpoS in pathogenic Escherichia coli

Background  

Though RpoS is important for survival of pathogenic Escherichia coli in natural environments, polymorphism in the rpoS gene is common. However, the causes of this polymorphism and consequential physiological effects on gene expression in pathogenic strains are not fully understood.     

<Emphasis Type="Italic">BMP-2</Emphasis> gene-fibronectin-apatite composite layer enhances bone formation

Background  

Safe and efficient gene transfer systems are needed for tissue engineering. We have developed an apatite composite layer including the bone morphogenetic protein-2 (BMP-2) gene and fibronectin (FB), and we evaluated its ability to induce bone formation.     

A systemic gene silencing method suitable for high throughput,reverse genetic analyses of gene function in fern gametophytes

Background  

Ceratopteris richardii is a useful experimental system for studying gametophyte development and sexual reproduction in plants. However, few tools for cloning mutant genes or disrupting gene function exist for this species. The feasibility of systemic gene silencing as a reverse genetics tool was examined in this study.