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The analysis of gene sets has become a popular topic in recent times, with researchers attempting to improve the interpretability and reproducibility of their microarray analyses through the inclusion of suppl...
There is accumulating evidence that the milieu of repeat elements and other non-genic sequence features at a given chromosomal locus, here defined as the genome environment, can play an important role in regul...
Post translational modifications (PTMs) occur in the vast majority of proteins and are essential for function. Prediction of the sequence location of PTMs enhances the functional characterisation of proteins. ...
One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metab...
The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advant...
Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing su...
The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current app...
Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regu...
Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the prolifer...
The Structural Descriptor Database (SDDB) is a web-based tool that predicts the function of proteins and functional site positions based on the structural properties of related protein families. Structural ali...
Designing small-molecule kinase inhibitors with desirable selectivity profiles is a major challenge in drug discovery. A high-throughput screen for inhibitors of a given kinase will typically yield many compou...
DNA microarrays, which determine the expression levels of tens of thousands of genes from a sample, are an important research tool. However, the volume of data they produce can be an obstacle to interpretation...
In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of mi...
Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to...
This article is part of a Supplement: Volume 9 Supplement 11
Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizi...
This article is part of a Supplement: Volume 9 Supplement 11
Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annot...
This article is part of a Supplement: Volume 9 Supplement 11
Previous studies of named entity recognition have shown that a reasonable level of recognition accuracy can be achieved by using machine learning models such as conditional random fields or support vector mach...
This article is part of a Supplement: Volume 9 Supplement 11
Like text in other domains, biomedical documents contain a range of terms with more than one possible meaning. These ambiguities form a significant obstacle to the automatic processing of biomedical texts. Pre...
This article is part of a Supplement: Volume 9 Supplement 11
Term identification is the task of grounding ambiguous mentions of biomedical named entities in text to unique database identifiers. Previous work on term identification has focused on studying species-specifi...
This article is part of a Supplement: Volume 9 Supplement 11
When term ambiguity and variability are very high, dictionary-based Named Entity Recognition (NER) is not an ideal solution even though large-scale terminological resources are available. Many researches on stati...
This article is part of a Supplement: Volume 9 Supplement 11
Chemical named entities represent an important facet of biomedical text.
This article is part of a Supplement: Volume 9 Supplement 11
The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-ba...
This article is part of a Supplement: Volume 9 Supplement 11
Automated extraction of protein-protein interactions (PPI) is an important and widely studied task in biomedical text mining. We propose a graph kernel based approach for this task. In contrast to earlier appr...
This article is part of a Supplement: Volume 9 Supplement 11
This article is part of a Supplement: Volume 9 Supplement 11
An important emerging trend in the analysis of microarray data is to incorporate known pathway information a priori. Expression level "summaries" for pathways, obtained from the expression data for the genes c...
By using a standard Support Vector Machine (SVM) with a Sequential Minimal Optimization (SMO) method of training, Naïve Bayes and other machine learning algorithms we are able to distinguish between two classe...
Large-scale compilation of gene expression microarray datasets across diverse biological phenotypes provided a means of gathering a priori knowledge in the form of identification and annotation of bimodal gene...
DNA microarrays contain thousands of different probe sequences represented on their surface. These are designed in such a way that potential cross-hybridization reactions with non-target sequences are minimize...
The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence o...
For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny...
Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment.
Recently, microarray data analyses using functional pathway information, e.g., gene set enrichment analysis (GSEA) and significance analysis of function and expression (SAFE), have gained recognition as a way ...
Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientif...
The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or prot...
Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and...
Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microar...
Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and so...
High-throughput screening of pharmaceutical compound activity in tissue culture experiments requires time-consuming repeated analysis of the large amounts of data generated. Automation of the evaluation proced...
The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a ...
The epidermal physiology results from a complex regulated homeostasis of keratinocyte proliferation, differentiation and death and is tightly regulated by a specific protein expression during cellular maturati...
Researchers interested in analysing the expression patterns of functionally related genes usually hope to improve the accuracy of their results beyond the boundaries of currently available experimental data. G...
Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to...
Metabolomics, or metabonomics, refers to the quantitative analysis of all metabolites present within a biological sample and is generally carried out using NMR spectroscopy or Mass Spectrometry. Such analysis ...
Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use...
Various measures of semantic similarity of terms in bio-ontologies such as the Gene Ontology (GO) have been used to compare gene products. Such measures of similarity have been used to annotate uncharacterized...
Probability based statistical learning methods such as mutual information and Bayesian networks have emerged as a major category of tools for reverse engineering mechanistic relationships from quantitative bio...
Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity ...
Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is ...
This article is part of a Supplement: Volume 9 Supplement 10
This article is part of a Supplement: Volume 9 Supplement 10
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