BMC Bioinformatics - Volume 10, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms is still incomplete and currently a topic of intense research.

Results

I

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

It is known that transcription factors frequently act together to regulate gene expression in eukaryotes. In this paper we describe a computational analysis of transcription factor site dependencies in human, mouse and rat genomes.

Results

Our approach for quantifying tendencies of

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

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.

Results

We have developed TransCent, a computational enzyme design method sup

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analys

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of e

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

The majority of ovarian cancer biomarker discovery efforts focus on the identification of proteins that can improve the predictive power of presently available diagnostic tests. We here show that metabolomics, the study of metabolic changes in biological systems, can also provide charac

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

Molecular genotyping of bacteria has revolutionized the study of tuberculosis epidemiology, yet these established laboratory techniques typically require subjective and laborious interpretation by trained professionals. In the context of a Tuberculosis Case Contact study in The Gambia w

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

We propose an efficient and biologically sensitive algorithm based on repeated random walks (RRW) for discovering functional modules, e.g., complexes and pathways, within large-scale protein networks. Compared to existing cluster identification techniques, RRW implicitly makes use of ne

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identify

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009

Abstract

Background

A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb). We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium

Journal: BMC Bioinformatics, vol. 10, no. Preprint, 2009