Abstract:
BACKGROUND:Extensive studies have been carried out on Caenorhabditis elegans as a model organism to elucidate mechanisms of aging and the effects of perturbing known aging-related genes on lifespan and behavior. This research has generated large amounts of experimental data that is increasingly difficult to integrate and analyze with existing databases and domain knowledge. To address this challenge, we demonstrate a scalable and effective approach for automatic evidence gathering and evaluation that leverages existing experimental data and literature-curated facts to identify genes involved in aging and lifespan regulation in C. elegans. RESULTS:We developed a semantic knowledge base for aging by integrating data about C. elegans genes from WormBase with data about 2005 human and model organism genes from GenAge and 149 genes from GenDR, and with the Bio2RDF network of linked data for the life sciences. Using HyQue (a Semantic Web tool for hypothesis-based querying and evaluation) to interrogate this knowledge base, we examined 48,231 C. elegans genes for their role in modulating lifespan and aging. HyQue identified 24 novel but well-supported candidate aging-related genes for further experimental validation. CONCLUSIONS:We use semantic technologies to discover candidate aging genes whose effects on lifespan are not yet well understood. Our customized HyQue system, the aging research knowledge base it operates over, and HyQue evaluations of all C. elegans genes are freely available at http://hyque.semanticscience.org .
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Callahan A,Cifuentes JJ,Dumontier Mdoi
10.1186/s12859-015-0469-4subject
Has Abstractpub_date
2015-02-07 00:00:00pages
40issn
1471-2105pii
10.1186/s12859-015-0469-4journal_volume
16pub_type
杂志文章abstract:BACKGROUND:We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how thi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-430
更新日期:2010-08-18 00:00:00
abstract:BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0618-9
更新日期:2015-05-29 00:00:00
abstract:BACKGROUND:The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1608-x
更新日期:2017-03-27 00:00:00
abstract:BACKGROUND:Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1790-x
更新日期:2017-09-13 00:00:00
abstract:BACKGROUND:In omics data integration studies, it is common, for a variety of reasons, for some individuals to not be present in all data tables. Missing row values are challenging to deal with because most statistical methods cannot be directly applied to incomplete datasets. To overcome this issue, we propose a multip...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1273-5
更新日期:2016-10-03 00:00:00
abstract:BACKGROUND:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0611-3
更新日期:2015-05-22 00:00:00
abstract:BACKGROUND:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-117
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2463-0
更新日期:2018-12-28 00:00:00
abstract:BACKGROUND:Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-164
更新日期:2005-06-29 00:00:00
abstract:BACKGROUND:Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-153
更新日期:2012-06-28 00:00:00
abstract:BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...
journal_title:BMC bioinformatics
pub_type: 临床试验,杂志文章
doi:10.1186/s12859-019-2667-y
更新日期:2019-02-28 00:00:00
abstract:BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-142
更新日期:2008-03-06 00:00:00
abstract:BACKGROUND:Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-127
更新日期:2004-09-09 00:00:00
abstract:BACKGROUND:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S2-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to sc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2642-7
更新日期:2019-02-18 00:00:00
abstract:BACKGROUND:The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for model...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-436
更新日期:2008-10-16 00:00:00
abstract:BACKGROUND:Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such representations, the cell is considered as a system composed of interlocked sub...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03637-9
更新日期:2020-07-23 00:00:00
abstract:BACKGROUND:Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows conve...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0759-x
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:Mammalian germ cells undergo meiosis to produce sperm or eggs, haploid cells that are primed to meet and propagate life. Meiosis is initiated by retinoic acid and meiotic prophase is the first and most complex stage of meiosis when homologous chromosomes pair to exchange genetic information. Errors in meiosi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-72
更新日期:2013-02-27 00:00:00
abstract:BACKGROUND:Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-287
更新日期:2008-06-18 00:00:00
abstract:BACKGROUND:While biomedical text mining is emerging as an important research area, practical results have proven difficult to achieve. We believe that an important first step towards more accurate text-mining lies in the ability to identify and characterize text that satisfies various types of information needs. We rep...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-356
更新日期:2006-07-25 00:00:00
abstract:BACKGROUND:Selecting a parsimonious set of informative genes to build highly generalized performance classifier is the most important task for the analysis of tumor microarray expression data. Many existing gene pair evaluation methods cannot highlight diverse patterns of gene pairs only used one strategy of vertical c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0893-0
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-343
更新日期:2010-06-24 00:00:00
abstract:BACKGROUND:The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS) which can also be isolated and characterized. Each DIS corr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-19
更新日期:2005-01-27 00:00:00
abstract:BACKGROUND:Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstrom...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2083-8
更新日期:2018-02-23 00:00:00
abstract:BACKGROUND:The miRNAs, a class of short approximately 22-nucleotide non-coding RNAs, often act post-transcriptionally to inhibit mRNA expression. In effect, they control gene expression by targeting mRNA. They also help in carrying out normal functioning of a cell as they play an important role in various cellular proc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-266
更新日期:2013-09-04 00:00:00
abstract:BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2469-7
更新日期:2018-12-28 00:00:00
abstract:BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-264
更新日期:2008-06-05 00:00:00
abstract:BACKGROUND:Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2416-7
更新日期:2018-11-30 00:00:00
abstract:BACKGROUND:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-173
更新日期:2004-10-29 00:00:00