解剖学和形态学
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听力与言语-语言病理学
行为科学
心脏和心血管系统
细胞和组织工程学
临床神经病学
危重症监护医学
牙科,口腔外科和医学
皮肤病学
急诊医学
内分泌学和新陈代谢
肠胃学和肝脏学
老人病学和老年医学
卫生保健科学和服务
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免疫学
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医学,全科和内科
医学,法律
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神经系统科学
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耳鼻喉科学
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生理学
基本医疗保健
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泌尿学和肾脏学
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健康政策和服务
心理学,临床
abstract:BACKGROUND:Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0552-x
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaus...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0526-z
更新日期:2015-03-21 00:00:00
abstract:BACKGROUND:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0519-y
更新日期:2015-03-18 00:00:00
abstract:BACKGROUND:The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test stati...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0496-1
更新日期:2015-02-20 00:00:00
abstract:BACKGROUND:The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0480-9
更新日期:2015-02-19 00:00:00
abstract:BACKGROUND:Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequenc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0482-7
更新日期:2015-02-18 00:00:00
abstract:BACKGROUND:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0466-7
更新日期:2015-02-12 00:00:00
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 a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0469-4
更新日期:2015-02-07 00:00:00
abstract:BACKGROUND:N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0468-5
更新日期:2015-01-28 00:00:00
abstract:BACKGROUND:Estimation of individual ancestry from genetic data is useful for the analysis of disease association studies, understanding human population history and interpreting personal genomic variation. New, computationally efficient methods are needed for ancestry inference that can effectively utilize existing inf...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0418-7
更新日期:2015-01-16 00:00:00
abstract:BACKGROUND:Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression tra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0421-z
更新日期:2015-01-16 00:00:00
abstract::Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference, heritability estimation, and mapping disease loci. Simultaneous detection of IBD over multiple haplotypes has...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S5-S9
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S11-S4
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Dynamic programming algorithms provide exact solutions to many problems in computational biology, such as sequence alignment, RNA folding, hidden Markov models (HMMs), and scoring of phylogenetic trees. Structurally analogous algorithms compute optimal solutions, evaluate score distributions, and perform sto...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S19-S2
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the databas...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S18-S6
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Des...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S6-S3
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biologi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S6-S4
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two even...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S10-S2
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S10-S3
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0410-2
更新日期:2014-12-30 00:00:00
abstract:BACKGROUND:With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0369-z
更新日期:2014-12-14 00:00:00
abstract:BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0394-y
更新日期:2014-12-14 00:00:00
abstract:BACKGROUND:Metabolomics is one of most recent omics technologies. It has been applied on fields such as food science, nutrition, drug discovery and systems biology. For this, gas chromatography-mass spectrometry (GC-MS) has been largely applied and many computational tools have been developed to support the analysis of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0374-2
更新日期:2014-12-10 00:00:00
abstract:BACKGROUND:Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS:On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0383-1
更新日期:2014-12-10 00:00:00
abstract:BACKGROUND:Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0397-8
更新日期:2014-12-05 00:00:00
abstract:BACKGROUND:Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also n...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0392-0
更新日期:2014-11-28 00:00:00
abstract:BACKGROUND:Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS:A non-parametric Bayesian ap...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0368-0
更新日期:2014-11-21 00:00:00
abstract:BACKGROUND:Identification of the recombination hot/cold spots is critical for understanding the mechanism of recombination as well as the genome evolution process. However, experimental identification of recombination spots is both time-consuming and costly. Developing an accurate and automated method for reliably and ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-340
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0357-3
更新日期:2014-11-19 00:00:00
abstract:BACKGROUND:Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now poss...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0377-z
更新日期:2014-11-19 00:00:00
abstract:BACKGROUND:Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in co...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0379-x
更新日期:2014-11-18 00:00:00
abstract:BACKGROUND:Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0358-2
更新日期:2014-11-04 00:00:00
abstract:BACKGROUND:Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I'd rather have HIV ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-333
更新日期:2014-10-24 00:00:00
abstract:BACKGROUND:DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-337
更新日期:2014-10-18 00:00:00
abstract:BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-338
更新日期:2014-10-04 00:00:00
abstract:BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-316
更新日期:2014-09-25 00:00:00
abstract:BACKGROUND:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-268
更新日期:2014-08-08 00:00:00
abstract:BACKGROUND:Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. RESULTS:In thi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-252
更新日期:2014-07-25 00:00:00
abstract:BACKGROUND:Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging vari...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-248
更新日期:2014-07-21 00:00:00
abstract:BACKGROUND:Biological data often originate from samples containing mixtures of subpopulations, corresponding e.g. to distinct cellular phenotypes. However, identification of distinct subpopulations may be difficult if biological measurements yield distributions that are not easily separable. RESULTS:We present Multire...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-240
更新日期:2014-07-11 00:00:00