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Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at a...
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...
We generalized penalized canonical correlation analysis for analyzing microarray gene-expression measurements for checking completeness of known metabolic pathways and identifying candidate genes for incorpora...
Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of ...
Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with ...
Many integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function. Computational methods that pr...
The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR) and Extraction...
The Audic-Claverie method [1] has been and still continues to be a popular approach for detection of differentially expressed genes in the SAGE framework. The method is based on the assumption that under the null...
SSWAP (S imple S emantic W eb A rchitecture and P rotocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on ...
Alterations in the number of copies of genomic DNA that are common or recurrent among diseased individuals are likely to contain disease-critical genes. Unfortunately, defining common or recurrent copy number ...
A central task in contemporary biosciences is the identification of biological processes showing response in genome-wide differential gene expression experiments. Two types of analysis are common. Either, one ...
Differential coexpression is a change in coexpression between genes that may reflect 'rewiring' of transcriptional networks. It has previously been hypothesized that such changes might be occurring over time i...
Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been employed to examine features such as protein binding and histone modifications on a genome-wide scale in a variety of cell types. Array data ...
Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments ...
One of the most neglected areas of biomedical Text Mining (TM) is the development of systems based on carefully assessed user needs. We have recently investigated the user needs of an important task yet to be ...
Prediction of antigenic epitopes on protein surfaces is important for vaccine design. Most existing epitope prediction methods focus on protein sequences to predict continuous epitopes linear in sequence. Only...
Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector ...
Gene sets are widely used to interpret genome-scale data. Analysis techniques that make better use of the correlation structure of microarray data while addressing practical "n<p" concerns could provide a real...
High-throughput sequencing technology has become popular and widely used to study protein and DNA interactions. Chromatin immunoprecipitation, followed by sequencing of the resulting samples, produces large am...
To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be ...
Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is av...
The major histocompatibility complex (MHC) molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to...
MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pa...
Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have b...
The ability to predict drug sensitivity in cancer is one of the exciting promises of pharmacogenomic research. Several groups have demonstrated the ability to predict drug sensitivity by integrating chemo-sens...
The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in ...
Functional magnetic resonance imaging (fMRI) is a technology used to detect brain activity. Patterns of brain activation have been utilized as biomarkers for various neuropsychiatric applications. Detecting de...
The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of dive...
The availability of up-to-date, executable, evidence-based medical knowledge is essential for many clinical applications, such as pharmacovigilance, but executable knowledge is costly to obtain and update. Aut...
Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for trans...
Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to under...
This study describes a large-scale manual re-annotation of data samples in the Gene Expression Omnibus (GEO), using variables and values derived from the National Cancer Institute thesaurus. A framework is des...
Large repositories of biomedical research data are most useful to translational researchers if their data can be aggregated for efficient queries and analyses. However, inconsistent or non-existent annotations...
Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to ...
The decision environment for cancer care is becoming increasingly complex due to the discovery and development of novel genomic tests that offer information regarding therapy response, prognosis and monitoring...
Current outcome predictors based on "molecular profiling" rely on gene lists selected without consideration for their molecular mechanisms. This study was designed to demonstrate that we could learn about gene...
The osteocyte is a type of cell that appears to be one of the key endocrine regulators of bone metabolism and a key responder to initiate bone formation and remodeling. Identifying the regulatory networks in o...
Physicians use clinical and physiological data to treat patients every day, and it is essential for treating a patient appropriately. However, medical sources of clinical physiological data are only now starti...
Chronic renal diseases are currently classified based on morphological similarities such as whether they produce predominantly inflammatory or non-inflammatory responses. However, such classifications do not r...
Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate...
Gene interactions play a central role in transcriptional networks. Many studies have performed genome-wide expression analysis to reconstruct regulatory networks to investigate disease processes. Since biologi...
Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray appl...
The disparate results from the methods commonly used to determine differential expression in Affymetrix microarray experiments may well result from the wide variety of probe set and probe level models employed...
Wiki technology has become a ubiquitous mechanism for dissemination of information, and places strong emphasis on collaboration. We aimed to leverage wiki technology to allow small groups of researchers to col...
The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for ...
The definition of a hypothetical protein is a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. Hypothetical proteins constit...
Many different cluster methods are frequently used in gene expression data analysis to find groups of co-expressed genes. However, cluster algorithms with the ability to visualize the resulting clusters are us...
Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire prote...
Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-t...
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Citation Impact 2023
Journal Impact Factor: 2.9
5-year Journal Impact Factor: 3.6
Source Normalized Impact per Paper (SNIP): 0.821
SCImago Journal Rank (SJR): 1.005
Speed 2023
Submission to first editorial decision (median days): 12
Submission to acceptance (median days): 146
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