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Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to ...
Gene expression microarrays are a prominent experimental tool in functional genomics which has opened the opportunity for gaining global, systems-level understanding of transcriptional networks. Experiments th...
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
This article is part of a Supplement: Volume 6 Supplement 3
Baum-Welch training is an expectation-maximisation algorithm for training the emission and transition probabilities of hidden Markov models in a fully automated way. It can be employed as long as a training se...
There has been much evidence recently for a link between transcriptional regulation and chromosomal gene order, but the relationship between genomic organization, regulation and gene function in higher eukaryo...
Procedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material. Such procedures require the design of large sets of probes ...
There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have ...
Biological processes are carried out by coordinated modules of interacting molecules. As clustering methods demonstrate that genes with similar expression display increased likelihood of being associated with ...
Protein structure research often deals with the comparison of two or more structures of the same protein, for instance when handling alternative structure models for the same protein, point mutants, molecule m...
A promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins invol...
Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming algorithm for a novel and non-trivial ...
The Erratum to this article has been published in BMC Bioinformatics 2006 7:214
The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, th...
The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to ...
We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a quantitative measure of structural similarity ...
The allele frequencies of single-nucleotide polymorphisms (SNPs) are needed to select an optimal subset of common SNPs for use in association studies. Sequence-based methods for finding SNPs with allele freque...
The currently used k th order Markov models estimate the probability of generating a single nucleotide conditional upon the immediately preceding (gap = 0) k units. However, ...
Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical sp...
Accurate assignment of genes to pathways is essential in order to understand the functional role of genes and to map the existing pathways in a given genome. Existing algorithms predict pathways by extrapolati...
Whole-genome sequencing projects are rapidly producing an enormous number of new sequences. Consequently almost every family of proteins now contains hundreds of members. It has thus become necessary to develo...
Cells react to changing intra- and extracellular signals by dynamically modulating complex biochemical networks. Cellular responses to extracellular signals lead to changes in gene and protein expression. Sinc...
A typical microarray experiment has many sources of variation which can be attributed to biological and technical causes. Identifying sources of variation and assessing their magnitude, among other factors, ar...
To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques a...
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