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Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented ...
Serial Analysis of Gene Expression (SAGE) is a high-throughput method for inferring mRNA expression levels from the experimentally generated sequence based tags. Standard analyses of SAGE data, however, ignore...
Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence dat...
Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is ...
The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research co...
The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher t...
Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation...
Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent tech...
Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different st...
The original article was published in BMC Bioinformatics 2006 7:S10
Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nuc...
In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Rényi ent...
The majority of common diseases are multi-factorial and modified by genetically and mechanistically complex polygenic interactions and environmental factors. High-throughput genome-wide studies like linkage an...
Domains are the basic functional units of proteins. It is believed that protein-protein interactions are realized through domain interactions. Revealing multi-domain cooperation can provide deep insights into ...
Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinati...
Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that i...
Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein s...
In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be inval...
The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain i...
Motif discovery aims to detect short, highly conserved patterns in a collection of unaligned DNA or protein sequences. Discriminative motif finding algorithms aim to increase the sensitivity and selectivity of...
A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes. For instance, connectivity, clustering c...
As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as en...
Biological sequence repeats arranged in tandem patterns are widespread in DNA and proteins. While many software tools have been designed to detect DNA tandem repeats (TRs), useful algorithms for identifying pr...
By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. T...
An important and yet rather neglected question related to bioinformatics predictions is the estimation of the amount of data that is needed to allow reliable predictions. Bioinformatics predictions are usually...
Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is e...
Deficiencies in microarray technology cause unwanted variation in the hybridization signal, obscuring the true measurements of intracellular transcript levels. Here we describe a general method that can improv...
Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will co...
The NF-κ B regulatory network controls innate immune response by transducing variety of pathogen-derived and cytokine stimuli into well defined single-cell gene regulatory events.
Safety assessment of genetically modified (GM) food, with regard to allergenic potential of transgene-encoded xenoproteins, typically involves several different methods, evaluation by digestibility being one t...
An important goal of comparative genomics is the identification of functional elements through conservation analysis. Phylo-HMM was recently introduced to detect conserved elements based on multiple genome ali...
The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computationa...
In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical resea...
As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms...
With DNA microarray data, selecting a compact subset of discriminative genes from thousands of genes is a critical step for accurate classification of phenotypes for, e.g., disease diagnosis. Several widely us...
In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor ...
Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in unaffected individuals as polymorphi...
Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been estab...
In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important compu...
A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level.
With the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across multiple studies.
The set of extreme pathways (ExPa), {p i }, defines the convex basis vectors used for the mathematical characterization of the null space of the stoichiometric matrix for bio...
Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology mode...
This article is part of a Supplement: Volume 8 Supplement 6
Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of applica...
This article is part of a Supplement: Volume 8 Supplement 6
This is an introductory review on how genes interact to produce biological functions. Transcriptional interactions involve the binding of proteins to regulatory DNA. Specific binding sites can be identified by...
This article is part of a Supplement: Volume 8 Supplement 6
The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cel...
This article is part of a Supplement: Volume 8 Supplement 6
In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used method...
This article is part of a Supplement: Volume 8 Supplement 6
Computational analysis of eukaryotic promoters is one of the most difficult problems in computational genomics and is essential for understanding gene expression profiles and reverse-engineering gene regulatio...
This article is part of a Supplement: Volume 8 Supplement 6
Considering that 80 genomes have been sequenced, providing us with the static information of the genome, it is still a long way to reveal the relationship between complex genotypes and phenotypes. The transcri...
This article is part of a Supplement: Volume 8 Supplement 6
This article is part of a Supplement: Volume 8 Supplement 6
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