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Detection of adaptive amino acid changes in proteins under recent short-term selection is of great interest for researchers studying microevolutionary processes in microbial pathogens or any other biological s...
Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding s...
Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what proper...
Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make compari...
RNA interference (RNAi) is a naturally occurring phenomenon that results in the suppression of a target RNA sequence utilizing a variety of possible methods and pathways. To dissect the factors that result in ...
Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expressio...
Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describ...
Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thous...
RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we d...
G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore represent key phar...
The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations ...
The fundamental role that intrinsic stochasticity plays in cellular functions has been shown via numerous computational and experimental studies. In the face of such evidence, it is important that intracellula...
3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become incre...
High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets ...
This article is part of a Supplement: Volume 8 Supplement 5
Identification of protein interacting sites is an important task in computational molecular biology. As more and more protein sequences are deposited without available structural information, it is strongly de...
This article is part of a Supplement: Volume 8 Supplement 5
Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in order to identify genes and their alterna...
This article is part of a Supplement: Volume 8 Supplement 5
Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly an...
This article is part of a Supplement: Volume 8 Supplement 5
Recent development of mass spectrometry technology enabled the analysis of complex peptide mixtures. A lot of effort is currently devoted to the identification of biomarkers in human body fluids like serum or ...
This article is part of a Supplement: Volume 8 Supplement 5
This work explores the quantitative characteristics of the local transcriptional regulatory network based on the availability of time dependent gene expression data sets.
This article is part of a Supplement: Volume 8 Supplement 5
Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using para...
This article is part of a Supplement: Volume 8 Supplement 5
Reverse engineering cellular networks is currently one of the most challenging problems in systems biology. Dynamic Bayesian networks (DBNs) seem to be particularly suitable for inferring relationships between...
This article is part of a Supplement: Volume 8 Supplement 5
This article is part of a Supplement: Volume 8 Supplement 5
A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally...
In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called ...
There exist many segmentation techniques for genomic sequences, and the segmentations can also be based on many different biological features. We show how to evaluate and compare the quality of segmentations o...
Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigati...
One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed us...
Cellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental researc...
Relating features of protein sequences to structural hinges is important for identifying domain boundaries, understanding structure-function relationships, and designing flexibility into proteins. Efforts in t...
With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the ...
Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial ...
Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN...
Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is there...
This article is part of a Supplement: Volume 8 Supplement 4
An accurate description of protein shape derived from protein structure is necessary to establish an understanding of protein-ligand interactions, which in turn will lead to improved methods for protein-ligand...
This article is part of a Supplement: Volume 8 Supplement 4
Protein-protein interaction has been used to complement traditional sequence homology to elucidate protein function. Most existing approaches only make use of direct interactions to infer function, and some ha...
This article is part of a Supplement: Volume 8 Supplement 4
Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various ex...
This article is part of a Supplement: Volume 8 Supplement 4
Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation in the function prediction process. Bacteriophage genomes are an example that cannot be ea...
This article is part of a Supplement: Volume 8 Supplement 4
Many protein sequences are still poorly annotated. Functional characterization of a protein is often improved by the identification of its interaction partners. Here, we aim to predict protein-protein interact...
This article is part of a Supplement: Volume 8 Supplement 4
Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited b...
This article is part of a Supplement: Volume 8 Supplement 4
Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we demonstrate t...
This article is part of a Supplement: Volume 8 Supplement 4
Predicting a protein's structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing new representations for protein sequences, cal...
This article is part of a Supplement: Volume 8 Supplement 4
This article is part of a Supplement: Volume 8 Supplement 4
Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archa...
The size and magnitude of the metabolome, the ratio between individual metabolites and the response of metabolic networks is controlled by multiple cellular factors. A tight control over metabolite ratios will...
Recent analyses have suggested that many genes possess multiple transcription start sites (TSSs) that are differentially utilized in different tissues and cell lines. We have identified a huge number of TSSs m...
The nucleotide sequence flanking the translation initiation codon (start codon context) affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation ini...
Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been ...
TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organi...
When conducting multiple hypothesis tests, it is important to control the number of false positives, or the False Discovery Rate (FDR). However, there is a tradeoff between controlling FDR and maximizing power...
The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-l...
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