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The Ruby programming language has a lot to offer to any scientist with electronic data to process. Not only is the initial learning curve very shallow, but its reflection and meta-programming capabilities allo...
Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and err...
Transcriptional regulation is an important part of regulatory control in eukaryotes. Even if binding motifs for transcription factors are known, the task of finding binding sites by scanning sequences is plagu...
Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high qu...
With the rapid development of high-throughput genotyping technologies, efficient methods for identifying linked regions using high-density SNP genotype data have become more and more important. Recently, a det...
The p53 protein is a master regulator that controls the transcription of many genes in various pathways in response to a variety of stress signals. The extent of this regulation depends in part on the binding ...
One essential step in the massive analysis of transcriptomic profiles is the calculation of the correlation coefficient, a value used to select pairs of genes with similar or inverse transcriptional profiles a...
Regularized regression methods such as principal component or partial least squares regression perform well in learning tasks on high dimensional spectral data, but cannot explicitly eliminate irrelevant featu...
Hidden Markov models and hidden Boltzmann models are employed in computational biology and a variety of other scientific fields for a variety of analyses of sequential data. Whether the associated algorithms a...
Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By determining uncertainties from Affymetrix GeneChip data and propagating these...
Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy ...
The detection of true significant cases under multiple testing is becoming a fundamental issue when analyzing high-dimensional biological data. Unfortunately, known multitest adjustments reduce their statistic...
DNA sequence binding motifs for several important transcription factors happen to be self-overlapping. Many of the current regulatory site identification methods do not explicitly take into account the overlap...
It is extremely important and challenging to identify the sites that are responsible for functional specification or diversification in protein families. In this study, a rigorous comparative benchmarking prot...
Translational initiation site (TIS) prediction is a very important and actively studied topic in bioinformatics. In order to complete a comparative analysis, it is desirable to have several benchmark data sets...
Progress in the life sciences cannot be made without integrating biomedical knowledge on numerous genes in order to help formulate hypotheses on the genetic mechanisms behind various biological phenomena, incl...
The detection of enriched DNA or RNA fragments by tiling microarrays has become more and more popular. These microarrays contain a high number of small probes covering genomic loci. However, to achieve high co...
Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy nu...
Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that exist in yeast, the best char...
Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitat...
One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential) gene lists from multiple experiments for common or unique underlying biological themes. A ...
Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology ...
Large-scale statistical analyses have become hallmarks of post-genomic era biological research due to advances in high-throughput assays and the integration of large biological databases. One accompanying issu...
Identifying the catalytic residues in enzymes can aid in understanding the molecular basis of an enzyme's function and has significant implications for designing new drugs, identifying genetic disorders, and e...
A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produ...
Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protei...
Protein secretion is a cell translocation process of major biological and technological significance. The secretion and downstream processing of proteins by recombinant cells is of great commercial interest. T...
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
This article is part of a Supplement: Volume 10 Supplement 7
Prior to cluster analysis or genetic network analysis it is customary to filter, or remove genes considered to be irrelevant from the set of genes to be analyzed. Often genes whose variation across samples is ...
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 genom...
Quality assessment of microarray data is an important and often challenging aspect of gene expression analysis. This task frequently involves the examination of a variety of summary statistics and diagnostic p...
The tumor suppressor p53 plays pivotal roles in tumorigenesis suppression. Although oscillations of p53 have been extensively studied, the mechanism of p53 pulses and their physiological roles in DNA damage re...
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