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The regulation of many cell functions is inherently linked to cell-cell contact interactions. However, effects of contact interactions among adherent cells can be difficult to detect with global summary statis...
Information Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are...
Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape ...
Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologica...
Biological networks characterize the interactions of biomolecules at a systems-level. One important property of biological networks is the modular structure, in which nodes are densely connected with each othe...
We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput da...
During the stages of the development of a potent drug candidate compounds can fail for several reasons. One of them, the efficacy of a candidate, can be estimated in silico if an appropriate ordinary differential...
Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through...
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
This article is part of a Supplement: Volume 10 Supplement 13
Isobaric Tags for Relative and Absolute Quantitation (iTRAQ™) [Applied Biosystems] have seen increased application in differential protein expression analysis. To facilitate the growing need to analyze iTRAQ d...
RNA-protein interactions are important for a wide range of biological processes. Current computational methods to predict interacting residues in RNA-protein interfaces predominately rely on sequence data. It ...
In contemporary biology, complex biological processes are increasingly studied by collecting and analyzing measurements of the same entities that are collected with different analytical platforms. Such data co...
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, ...
Predicting the three-dimensional structure of a protein from its amino acid sequence is currently one of the most challenging problems in bioinformatics. The internal structure of helices and sheets is highly ...
Classification using microarray datasets is usually based on a small number of samples for which tens of thousands of gene expression measurements have been obtained. The selection of the genes most significan...
Time-course microarray experiments are widely used to study the temporal profiles of gene expression. Storey et al. (2005) developed a method for analyzing time-course microarray studies that can be applied to di...
The number of protein family members defined by DNA sequencing is usually much larger than those characterised experimentally. This paper describes a method to divide protein families into subtypes purely on s...
To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes i...
Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools ar...
This article is part of a Supplement: Volume 10 Supplement 12
The cell cycle is a complex process that allows eukaryotic cells to replicate chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the G0/G1 phase, a point called the restric...
This article is part of a Supplement: Volume 10 Supplement 12
Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structur...
This article is part of a Supplement: Volume 10 Supplement 12
Due to the huge amount of information at genomic level made recently available by high-throughput experimental technologies, networks of regulatory interactions between genes and gene products, the so-called gene...
This article is part of a Supplement: Volume 10 Supplement 12
The associations existing among different biomarkers are important in clinical settings because they contribute to the characterisation of specific pathways related to the natural history of the disease, genet...
This article is part of a Supplement: Volume 10 Supplement 12
Cell motility plays a central role in development, wound-healing and tumour invasion. Cultures of eucariotic cells are a complex system where most cells move according to 'random' patterns, but may also be ind...
This article is part of a Supplement: Volume 10 Supplement 12
One of the topics of major interest in proteomics is protein identification. Protein identification can be achieved by analyzing the mass spectrum of a protein sample through different approaches. One of them,...
This article is part of a Supplement: Volume 10 Supplement 12
Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presen...
This article is part of a Supplement: Volume 10 Supplement 12
Mass spectrometry spectra, widely used in proteomics studies as a screening tool for protein profiling and to detect discriminatory signals, are high dimensional data. A large number of local maxima (a.k.a. peaks
This article is part of a Supplement: Volume 10 Supplement 12
The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in which a gene of interest is involv...
This article is part of a Supplement: Volume 10 Supplement 12
The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising ...
This article is part of a Supplement: Volume 10 Supplement 12
In the diagnosis of complex diseases such as neurological pathologies, a wealth of clinical and molecular information is often available to help the interpretation. Yet, the pieces of information are usually c...
This article is part of a Supplement: Volume 10 Supplement 12
Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in p...
This article is part of a Supplement: Volume 10 Supplement 12
Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortuna...
This article is part of a Supplement: Volume 10 Supplement 12
The design of mutants in protein functional regions, such as the ligand binding sites, is a powerful approach to recognize the determinants of specific protein activities in cellular pathways. For an exhaustiv...
This article is part of a Supplement: Volume 10 Supplement 12
The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can ...
This article is part of a Supplement: Volume 10 Supplement 12
The integration of data from multiple genome-wide assays is essential for understanding dynamic spatio-temporal interactions within cells. Such integration, which leads to a more complete view of cellular proc...
This article is part of a Supplement: Volume 10 Supplement 12
In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools a...
This article is part of a Supplement: Volume 10 Supplement 12
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