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Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments,...
It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an i...
Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is...
The accurate detection of differentially expressed (DE) genes has become a central task in microarray analysis. Unfortunately, the noise level and experimental variability of microarrays can be limiting. While...
Linear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, ...
Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in...
PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a se...
This article is part of a Supplement: Volume 9 Supplement 4
With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms...
This article is part of a Supplement: Volume 9 Supplement 4
Protein identification is one of the most challenging problems in proteomics. Tandem mass spectrometry provides an important tool to handle the protein identification problem.
This article is part of a Supplement: Volume 9 Supplement 4
Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, a key role is played by ...
This article is part of a Supplement: Volume 9 Supplement 4
Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically appro...
This article is part of a Supplement: Volume 9 Supplement 4
Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks....
This article is part of a Supplement: Volume 9 Supplement 4
Research in life sciences is benefiting from a large availability of formal description techniques and analysis methodologies. These allow both the phenomena investigated to be precisely modeled and virtual ex...
This article is part of a Supplement: Volume 9 Supplement 4
The recent availability of high-throughput data in molecular biology has increased the need for a formal representation of this knowledge domain. New ontologies are being developed to formalize knowledge, e.g....
This article is part of a Supplement: Volume 9 Supplement 4
Amines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accu...
This article is part of a Supplement: Volume 9 Supplement 4
Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly ma...
This article is part of a Supplement: Volume 9 Supplement 4
Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles i...
This article is part of a Supplement: Volume 9 Supplement 4
The engineering of ontologies, especially with a view to a text-mining use, is still a new research field. There does not yet exist a well-defined theory and technology for ontology construction. Many of the o...
This article is part of a Supplement: Volume 9 Supplement 4
This article is part of a Supplement: Volume 9 Supplement 4
The original article was published in BMC Bioinformatics 2007 8:S6
The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens/hundreds of different conditions. In microarray data, genes with similar functions usually co-express ...
In DNA microarray experiments, discovering groups of genes that share similar transcriptional characteristics is instrumental in functional annotation, tissue classification and motif identification. However, ...
Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The evolutionary conservation of co-ex...
The increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Nam...
With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in o...
Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a...
Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput geno...
Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths a...
Missing values frequently pose problems in gene expression microarray experiments as they can hinder downstream analysis of the datasets. While several missing value imputation approaches are available to the ...
Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing mo...
During the last decade, the use of microarrays to assess the transcriptome of many biological systems has generated an enormous amount of data. A common technique used to organize and analyze microarray data i...
Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not onl...
Determining the function of uncharacterized proteins is a major challenge in the post-genomic era due to the problem's complexity and scale. Identifying a protein's function contributes to an understanding of ...
This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The process of matching peptide sequenc...
Microarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology. This new technique uses pooled DNA, thereby reducing costs...
With the advent of high throughput biotechnology data acquisition platforms such as micro arrays, SNP chips and mass spectrometers, data sets with many more variables than observations are now routinely being ...
Microarray pre-processing usually consists of normalization and summarization. Normalization aims to remove non-biological variations across different arrays. The normalization algorithms generally require the...
Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.
Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-...
Comparative genomics aims to detect signals of evolutionary conservation as an indicator of functional constraint. Surprisingly, results of the ENCODE project revealed that about half of the experimentally ver...
Haplotype reconstruction is important in linkage mapping and association mapping of quantitative trait loci (QTL). One widely used statistical approach for haplotype reconstruction is simulated annealing (SA),...
In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical...
This article is part of a Supplement: Volume 9 Supplement 3
This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a g...
This article is part of a Supplement: Volume 9 Supplement 3
This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is ...
This article is part of a Supplement: Volume 9 Supplement 3
Much effort is currently made to develop the Gene Ontology (GO). Due to the dynamic nature of information it addresses, GO undergoes constant updates whose results are released at regular intervals as separate...
This article is part of a Supplement: Volume 9 Supplement 3
Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. Howe...
This article is part of a Supplement: Volume 9 Supplement 3
Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or...
This article is part of a Supplement: Volume 9 Supplement 3
Efficient features play an important role in automated text classification, which definitely facilitates the access of large-scale data. In the bioscience field, biological structures and terminologies are des...
This article is part of a Supplement: Volume 9 Supplement 3
In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other sema...
This article is part of a Supplement: Volume 9 Supplement 3
This article is part of a Supplement: Volume 9 Supplement 3
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