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This article addresses the problem of interoperation of heterogeneous bioinformatics databases.
Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual...
Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. ...
The relationship between disease susceptibility and genetic variation is complex, and many different types of data are relevant. We describe a web resource and database that provides and integrates as much inf...
Gene expression and transcription factor (TF) binding data have been used to reveal gene transcriptional regulatory networks. Existing knowledge of gene regulation can be presented using gene connectivity netw...
Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to ...
As a reversible and dynamic post-translational modification (PTM) of proteins, phosphorylation plays essential regulatory roles in a broad spectrum of the biological processes. Although many studies have been ...
Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the poten...
Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subse...
Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number...
The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations which is not always desirable f...
We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field...
Serial Analysis of Gene Expressions (SAGE) produces gene expression measurements on a discrete scale, due to the finite number of molecules in the sample. This means that part of the variance in SAGE data shou...
Genetic markers hold great promise for refining our ability to establish precise prognostic prediction for diseases. The development of comprehensive gene expression microarray technology has allowed the selec...
Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the ...
As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources.
This article is part of a Supplement: Volume 7 Supplement 1
Biologists regularly search DNA or protein databases for sequences that share an evolutionary or functional relationship with a given query sequence. Traditional search methods, such as BLAST and PSI-BLAST, fo...
This article is part of a Supplement: Volume 7 Supplement 1
Support Vector Machines (SVMs) – using a variety of string kernels – have been successfully applied to biological sequence classification problems. While SVMs achieve high classification accuracy they lack int...
This article is part of a Supplement: Volume 7 Supplement 1
Sequence homologs are an important source of information about proteins. Amino acid profiles, representing the position-specific mutation probabilities found in profiles, are a richer encoding of biological se...
This article is part of a Supplement: Volume 7 Supplement 1
Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such netw...
This article is part of a Supplement: Volume 7 Supplement 1
Neuronal communication is tightly regulated in time and in space. The neuronal transmission takes place in the nerve terminal, at a specialized structure called the synapse. Following neuronal activation, an e...
This article is part of a Supplement: Volume 7 Supplement 1
We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the ...
This article is part of a Supplement: Volume 7 Supplement 1
Prediction of human cell response to anti-cancer drugs (compounds) from microarray data is a challenging problem, due to the noise properties of microarrays as well as the high variance of living cell response...
This article is part of a Supplement: Volume 7 Supplement 1
Many different aspects of cellular signalling, trafficking and targeting mechanisms are mediated by interactions between proteins and peptides. Representative examples are MHC-peptide complexes in the immune s...
This article is part of a Supplement: Volume 7 Supplement 1
The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experimentalists in the search for no...
This article is part of a Supplement: Volume 7 Supplement 1
Computing exact multipoint LOD scores for extended pedigrees rapidly becomes infeasible as the number of markers and untyped individuals increase. When markers are excluded from the computation, significant po...
This article is part of a Supplement: Volume 7 Supplement 1
Current methods of analyzing Affymetrix GeneChip® microarray data require the estimation of probe set expression summaries, followed by application of statistical tests to determine which genes are differentially...
T cells recognize a complex between a specific major histocompatibility complex (MHC) molecule and a particular pathogen-derived epitope. A given epitope will elicit a response only in individuals that express...
Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is spa...
The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize e...
Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of t...
The incorporation of statistical models that account for experimental variability provides a necessary framework for the interpretation of microarray data. A robust experimental design coupled with an analysis...
Statistical methods for identifying positively selected sites in protein coding regions are one of the most commonly used tools in evolutionary bioinformatics. However, they have been limited by not taking the...
Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and util...
The rapid growth of protein interactome data has elevated the necessity and importance of network analysis tools. However, unlike pure text data, network search spaces are of exponential complexity. This poses...
RNA editing is one of several post-transcriptional modifications that may contribute to organismal complexity in the face of limited gene complement in a genome. One form, known as C → U editing, appears to exist...
The Erratum to this article has been published in BMC Bioinformatics 2006 7:406
The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They a...
Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch-like pairwise alignment methods. We intro...
Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changin...
Phytochromes are photoreceptors, discovered in plants, that control a wide variety of developmental processes. They have also been found in bacteria and fungi, but for many species their biological role remain...
Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natura...
Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require...
The characterization of the relationship between a longitudinal response process and a time-to-event has been a pressing challenge in biostatistical research. This has emerged as an important issue in genetic ...
Short oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operati...
Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult...
With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and th...
Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is...
In bio-systems, genes, proteins and compounds are related to each other, thus forming complex networks. Although each organism has its individual network, some organisms contain common sub-networks based on fu...
Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem.
Does a relationship exist between a protein's evolutionary rate and its number of interactions? This relationship has been put forward many times, based on a biological premise that a highly interacting protei...
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