BMC Bioinformatics - Volume 12, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

In Thomas' formalism for modeling gene regulatory networks (GRNs), branching time, where a state can have more than one possible future, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

In genome-wide association studies, it is widely accepted that multilocus methods are more powerful than testing single-nucleotide polymorphisms (SNPs) one at a time. Among statistical approaches considering many predictors simultaneously, scan statistics are an effective tool for detec

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

Liquid chromatography-mass spectrometry (LC-MS) utilizing the high-resolution power of an orbitrap is an important analytical technique for both metabolomics and proteomics. Most important feature of the orbitrap is excellent mass accuracy. Thus, it is necessary to convert raw data to a

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs.

Results

LAVA identifies combinations of six pr

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

Remote homology detection is a hard computational problem. Most approaches have trained computational models by using either full protein sequences or multiple sequence alignments (MSA), including all positions. However, when we deal with proteins in the "twilight zone" we can observe t

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analys

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools a

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes amon

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

When a large number of candidate variables are present, a dimension reduction procedure is usually conducted to reduce the variable space before the subsequent analysis is carried out. The goal of dimension reduction is to find a list of candidate genes with a more operable length ideal

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011

Abstract

Background

Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data so

Journal: BMC Bioinformatics, vol. 12, no. Preprint, 2011