解剖学和形态学
麻醉学
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
血液学
免疫学
传染病
综合和补充性医学
医学伦理学
医学信息学
医学实验室技术
医学,全科和内科
医学,法律
医学,研究和试验
神经系统科学
护理
营养学和饮食学
产科医学和妇科医学
肿瘤学
眼科学
整形外科学
耳鼻喉科学
病理学
儿科学
周围血管疾病
药理学和药剂学
生理学
基本医疗保健
精神病学
公共、环境和职业卫生
放射学,核医学和医学成像
康复学
生殖生物学
呼吸系统
风湿病学
运动科学
外科学
毒理学
热带医学
泌尿学和肾脏学
病毒学
老年医学
健康政策和服务
心理学,临床
abstract:BACKGROUND:The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advance...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2239-6
更新日期:2018-06-25 00:00:00
abstract:BACKGROUND:A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequencing methods now becoming accessible, general network inference algorithms that were initially dev...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2217-z
更新日期:2018-06-19 00:00:00
abstract:BACKGROUND:Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with up to d mismatches and is mainly used to locate transcription factor binding sites in DNA sequenc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2242-y
更新日期:2018-06-18 00:00:00
abstract:BACKGROUND:Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2193-3
更新日期:2018-06-13 00:00:00
abstract:BACKGROUND:Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2210-6
更新日期:2018-06-11 00:00:00
abstract:BACKGROUND:Prioritizing genes according to their associations with a cancer allows researchers to explore genes in more informed ways. By far, Gene-centric or network-centric gene prioritization methods are predominated. Genes and their protein products carry out cellular processes in the context of functional modules....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2216-0
更新日期:2018-06-05 00:00:00
abstract:BACKGROUND:Drug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2167-5
更新日期:2018-05-30 00:00:00
abstract:BACKGROUND:Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is ne...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2207-1
更新日期:2018-05-23 00:00:00
abstract:BACKGROUND:PacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Due to its extremely wide range of application areas, fast sequencing simulation syste...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2208-0
更新日期:2018-05-22 00:00:00
abstract:BACKGROUND:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2185-3
更新日期:2018-05-18 00:00:00
abstract:BACKGROUND:Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2166-6
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations fo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2073-x
更新日期:2018-05-08 00:00:00
abstract:BACKGROUND:In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2171-9
更新日期:2018-05-04 00:00:00
abstract:BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2160-z
更新日期:2018-04-25 00:00:00
abstract:BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2111-8
更新日期:2018-04-19 00:00:00
abstract:BACKGROUND:Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2140-3
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:The classification of cancer subtypes is of great importance to cancer disease diagnosis and therapy. Many supervised learning approaches have been applied to cancer subtype classification in the past few years, especially of deep learning based approaches. Recently, the deep forest model has been proposed a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2095-4
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2102-9
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it rema...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2115-4
更新日期:2018-03-27 00:00:00
abstract:BACKGROUND:Analyzing Variance heterogeneity in genome wide association studies (vGWAS) is an emerging approach for detecting genetic loci involved in gene-gene and gene-environment interactions. vGWAS analysis detects variability in phenotype values across genotypes, as opposed to typical GWAS analysis, which detects v...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2061-1
更新日期:2018-03-21 00:00:00
abstract:BACKGROUND:The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS:...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2103-8
更新日期:2018-03-09 00:00:00
abstract:BACKGROUND:Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies, new protein sequences are becoming available at an extraordinary rate. The ra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2080-y
更新日期:2018-03-05 00:00:00
abstract:BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2077-6
更新日期:2018-03-01 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:Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become hu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2016-6
更新日期:2018-02-19 00:00:00
abstract:BACKGROUND:Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our motivation is inspired by label propagation algorithm and the false positive protein-protein intera...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2040-6
更新日期:2018-02-08 00:00:00
abstract:BACKGROUND:Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. RESULTS:We developed a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2037-1
更新日期:2018-02-05 00:00:00
abstract:BACKGROUND:Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. Howeve...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2044-2
更新日期:2018-01-30 00:00:00
abstract:BACKGROUND:Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted cont...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2032-6
更新日期:2018-01-25 00:00:00
abstract:BACKGROUND:The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can h...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2025-5
更新日期:2018-01-25 00:00:00
abstract:BACKGROUND:Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier pro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1998-9
更新日期:2018-01-08 00:00:00
abstract:BACKGROUND:To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibriu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-2004-2
更新日期:2018-01-02 00:00:00
abstract:BACKGROUND:Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the im...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1891-6
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:Abruptness of pigment patterns at the periphery of a skin lesion is one of the most important dermoscopic features for detection of malignancy. In current clinical setting, abrupt cutoff of a skin lesion determined by an examination of a dermatologist. This process is subjective, nonquantitative, and error-p...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1892-5
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1963-7
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the defa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1981-5
更新日期:2017-12-21 00:00:00
abstract:BACKGROUND:In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the problem of predicting protein complexes from a PPI network. This problem has two difficulties. One is r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1920-5
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1952-x
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1875-6
更新日期:2017-12-01 00:00:00
abstract:BACKGROUND:Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1943-y
更新日期:2017-11-28 00:00:00