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Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological o...
Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine. Recently, some neural networks-based methods have been proposed to classify biomedic...
This article is part of a Supplement: Volume 21 Supplement 13
Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledg...
A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure suc...
This article is part of a Supplement: Volume 14 Supplement 11
Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more gener...
This article is part of a Supplement: Volume 21 Supplement 23
Extraction of adverse drug events from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Existing...
This article is part of a Supplement: Volume 22 Supplement 11
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...
The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortu...
Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are intero...
Time delays are important factors that are often neglected in gene regulatory network (GRN) inference models. Validating time delays from knowledge bases is a challenge since the vast majority of biological da...
This article is part of a Supplement: Volume 15 Supplement 2
The analysis of gene expression from time series underpins many biological studies. Two basic forms of analysis recur for data of this type: removing inactive (quiet) genes from the study and determining which...
In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structu...
Machine learning approaches have been applied in the procedures of RNA sequence features extraction and classification in a computational way, which may supplement experimental approaches more efficiently. Recent...
The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers u...
Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with ...
Adverse drug events (ADEs) constitute one of the leading causes of post-therapeutic death and their identification constitutes an important challenge of modern precision medicine. Unfortunately, the onset and ...
This article is part of a Supplement: Volume 17 Supplement 13
Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generat...
Automated text classification has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often difficult and expensive. ...
Numerous publicly available biomedical databases derive data by curating from literatures. The curated data can be useful as training examples for information extraction, but curated data usually lack the exac...
This article is part of a Supplement: Volume 17 Supplement 1
The Erratum to this article has been published in BMC Bioinformatics 2016 17:84
The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles ar...
Due to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function inference remains a fundamental challenge in computational biology. Currently,...
The number of corpora, collections of structured texts, has been increasing, as a result of the growing interest in the application of natural language processing methods to biological texts. Many named entity...
Genotype–phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the associatio...
The Correction to this article has been published in BMC Bioinformatics 2021 22:319
When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient sto...
Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious d...
This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear corresp...
This article is part of a Supplement: Volume 10 Supplement 10
The adverse reactions that are caused by drugs are potentially life-threatening problems. Comprehensive knowledge of adverse drug reactions (ADRs) can reduce their detrimental impacts on patients. Detecting AD...
Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene cat...
Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the comple...
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...
As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far...
This article is part of a Supplement: Volume 8 Supplement 9
The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such stud...
This article is part of a Supplement: Volume 9 Supplement 1
Event extraction from the biomedical literature is one of the most actively researched areas in biomedical text mining and natural language processing. However, most approaches have focused on ... sufficiently la...
In this work we present a novel method to extract and combine relationships between HIV drugs and mutations in viral genomes. Our extraction method is based on natural language processing (NLP) which produces gra...
Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reas...
Deep learning has become a prevalent method in identifying genomic regulatory sequences such as promoters. In a number of recent papers, the performance of deep learning models has continually been reported as...
The effectiveness of knowledge-based word sense disambiguation (WSD) approaches depends in part on the information available in the reference knowledge resource. Off the shelf, these resources are not optimize...
This article is part of a Supplement: Volume 12 Supplement 3
Metabolomics data analyses rely on the use of bioinformatics tools. Many integrated multi-functional tools have been developed for untargeted metabolomics data processing and have been widely used. More altern...
Non-biological factors give rise to unwanted variations in cDNA microarray data. There are many normalization methods designed to remove such variations. However, to date there have been few published systemat...
Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more organisms. Studies indicate that these conse...
We perform an empirical study comparing state-of-the-art traditional feature-based and neural network-based models for two core natural language processing tasks of part-of-speech (POS)...
Current proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also...
Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensio...
Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes. The field is rapidly gaining importance: it promises drugs targeted to particular subpopulatio...
This article is part of a Supplement: Volume 10 Supplement 2
Precision medicine for cancer treatment relies on an accurate pathological diagnosis. The number of known tumor classes has increased rapidly, and reliance on traditional methods of histopathologic classificat...
Nowadays, the increasing availability of omics data, due to both the advancements in the acquisition of molecular biology results and in systems biology simulation technologies, provides the bases for precisio...
This article is part of a Supplement: Volume 19 Supplement 10
Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to an...
Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integ...
This article is part of a Supplement: Volume 12 Supplement 10
N4-methylcytosine (4mC) is an important epigenetic mechanism, which regulates many cellular processes such as cell differentiation and gene expression. The knowledge about the 4mC sites is a key foundation to ...
Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We conside...
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