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:Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1928-x
更新日期:2017-11-28 00:00:00
abstract:BACKGROUND:In bioinformatics community, many tasks associate with matching a set of protein query sequences in large sequence datasets. To conduct multiple queries in the database, a common used method is to run BLAST on each original querey or on the concatenated queries. It is inefficient since it doesn't exploit the...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1938-8
更新日期:2017-11-21 00:00:00
abstract:BACKGROUND:The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1910-7
更新日期:2017-11-21 00:00:00
abstract:BACKGROUND:The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1870-y
更新日期:2017-11-15 00:00:00
abstract:BACKGROUND:The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced,...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1911-6
更新日期:2017-11-10 00:00:00
abstract:BACKGROUND:An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1865-8
更新日期:2017-10-23 00:00:00
abstract:BACKGROUND:Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenom...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1826-2
更新日期:2017-10-16 00:00:00
abstract:BACKGROUND:DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1860-0
更新日期:2017-10-12 00:00:00
abstract:BACKGROUND:Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical e...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1805-7
更新日期:2017-10-03 00:00:00
abstract:BACKGROUND:One approach to improving the personalized treatment of cancer is to understand the cellular signaling transduction pathways that cause cancer at the level of the individual patient. In this study, we used unsupervised deep learning to learn the hierarchical structure within cancer gene expression data. Deep...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1798-2
更新日期:2017-10-03 00:00:00
abstract:BACKGROUND:Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. R...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1841-3
更新日期:2017-09-30 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:Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little simila...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1795-5
更新日期:2017-08-25 00:00:00
abstract:BACKGROUND:Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is required to model the non-uniformity. Also, the properties of sequencing read counts can be leveraged to...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1780-z
更新日期:2017-08-09 00:00:00
abstract:BACKGROUND:Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replica...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1774-x
更新日期:2017-08-07 00:00:00
abstract:BACKGROUND:The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where seq...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1751-4
更新日期:2017-07-17 00:00:00
abstract:BACKGROUND:Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often repre...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1740-7
更新日期:2017-07-11 00:00:00
abstract:BACKGROUND:Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1742-5
更新日期:2017-07-11 00:00:00
abstract:BACKGROUND:In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front informatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1733-6
更新日期:2017-07-10 00:00:00
abstract:BACKGROUND:Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream analysis will be. During the last few years, major efforts have been made towards improving the qua...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1735-4
更新日期:2017-06-30 00:00:00
abstract:BACKGROUND:Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional g...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1662-4
更新日期:2017-06-07 00:00:00
abstract:BACKGROUND:The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Health Organization (WHO) proposed classification that assigns multi-level codes to compounds based on th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1660-6
更新日期:2017-06-07 00:00:00
abstract:BACKGROUND:Bioluminescent proteins (BLPs) widely exist in many living organisms. As BLPs are featured by the capability of emitting lights, they can be served as biomarkers and easily detected in biomedical research, such as gene expression analysis and signal transduction pathways. Therefore, accurate identification o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1709-6
更新日期:2017-06-05 00:00:00
abstract:BACKGROUND:PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate est...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1686-9
更新日期:2017-06-02 00:00:00
abstract:BACKGROUND:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has beco...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1705-x
更新日期:2017-05-31 00:00:00
abstract:BACKGROUND:Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1685-x
更新日期:2017-05-26 00:00:00
abstract:BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1691-z
更新日期:2017-05-25 00:00:00
abstract:BACKGROUND:It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1678-9
更新日期:2017-05-18 00:00:00
abstract:BACKGROUND:Analyses of molecular high-throughput data often lack in robustness, i.e. results are very sensitive to the addition or removal of a single observation. Therefore, the identification of extreme observations is an important step of quality control before doing further data analysis. Standard outlier detection...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1645-5
更新日期:2017-05-02 00:00:00
abstract:BACKGROUND:Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1616-x
更新日期:2017-04-11 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:Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipeli...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1592-1
更新日期:2017-03-20 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactom...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1585-0
更新日期:2017-03-16 00:00:00
abstract:BACKGROUND:The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the simila...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1473-7
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1466-6
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing. RESULTS:We propose s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1539-6
更新日期:2017-03-02 00:00:00
abstract:BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1518-y
更新日期:2017-02-23 00:00:00
abstract:BACKGROUND:Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the assoc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1499-x
更新日期:2017-02-02 00:00:00
abstract:BACKGROUND:Dystrophinopathy is one of the most common human monogenic diseases which results in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Mutations in the dystrophin gene are responsible for both DMD and BMD. However, the clinical phenotypes and treatments are quite different in these two m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1504-4
更新日期:2017-02-02 00:00:00
abstract:BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1493-3
更新日期:2017-02-02 00:00:00