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:Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. RESULTS:We introduce Accucopy, a method t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03924-5
更新日期:2021-01-15 00:00:00
abstract:BACKGROUND:Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03939-y
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene express...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03810-0
更新日期:2020-12-30 00:00:00
abstract:BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03928-1
更新日期:2020-12-17 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03896-6
更新日期:2020-12-16 00:00:00
abstract:BACKGROUND:We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model to discriminate CD8+ T cell epitopes. RESULTS:We first assembled an epitope dataset consisting of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03782-1
更新日期:2020-12-14 00:00:00
abstract:BACKGROUND:The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3184-8
更新日期:2020-12-09 00:00:00
abstract:BACKGROUND:Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, e...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03824-8
更新日期:2020-12-03 00:00:00
abstract:BACKGROUND:Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03906-7
更新日期:2020-12-02 00:00:00
abstract:BACKGROUND:DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03865-z
更新日期:2020-12-01 00:00:00
abstract:BACKGROUND:Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a connected subnetwork of a global interaction network that best encompasses significant individual c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03572-9
更新日期:2020-11-18 00:00:00
abstract:BACKGROUND:Antibodies revolutionized cancer treatment over the past decades. Despite their successfully application, there are still challenges to overcome to improve efficacy, such as the heterogeneous distribution of antibodies within tumors. Tumor microenvironment features, such as the distribution of tumor and othe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03854-2
更新日期:2020-11-17 00:00:00
abstract:BACKGROUND:Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03668-2
更新日期:2020-11-11 00:00:00
abstract:BACKGROUND:Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03809-7
更新日期:2020-11-09 00:00:00
abstract:BACKGROUND:High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of pr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03827-5
更新日期:2020-11-04 00:00:00
abstract:BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03777-y
更新日期:2020-10-20 00:00:00
abstract:BACKGROUND:Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain uncharted. Thus, in-depth study of the epi-transcriptomic patterns of m6A may provide insights into ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03787-w
更新日期:2020-10-09 00:00:00
abstract:BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03691-3
更新日期:2020-09-30 00:00:00
abstract:BACKGROUND:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03690-4
更新日期:2020-09-30 00:00:00
abstract:BACKGROUND:Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to improve. RESULTS:Here we expand on the common base method to develop procedures for testing linear re...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03696-y
更新日期:2020-09-29 00:00:00
abstract:BACKGROUND:Positron Emission Tomography (PET) is increasingly utilized in radiomics studies for treatment evaluation purposes. Nevertheless, lesion volume identification in PET images is a critical and still challenging step in the process of radiomics, due to the low spatial resolution and high noise level of PET imag...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03647-7
更新日期:2020-09-16 00:00:00
abstract:BACKGROUND:Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context, computational models and computer simulations are one of the available research tools that epidemi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03648-6
更新日期:2020-09-16 00:00:00
abstract:BACKGROUND:De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence dif...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03740-x
更新日期:2020-09-14 00:00:00
abstract:BACKGROUND:S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in their functions. Regulatory glutathionylation of proteins is a controllable and reversible process a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03571-w
更新日期:2020-09-14 00:00:00
abstract:BACKGROUND:A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can provide a new perspective for the diagnosis and treatment of diseases. The main function of many ln...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03721-0
更新日期:2020-09-03 00:00:00
abstract:BACKGROUND:The improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximize the impact of these genomics studies, it is important that data from biological samples will becom...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03694-0
更新日期:2020-09-03 00:00:00
abstract:BACKGROUND:Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experimen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03561-y
更新日期:2020-08-21 00:00:00
abstract:BACKGROUND:Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03564-9
更新日期:2020-08-21 00:00:00
abstract:BACKGROUND:While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03702-3
更新日期:2020-08-10 00:00:00
abstract:BACKGROUND:The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D sh...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03654-8
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03667-3
更新日期:2020-07-28 00:00:00
abstract:BACKGROUND:Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although vi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03599-y
更新日期:2020-07-24 00:00:00
abstract:BACKGROUND:The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares control the error of output, e.g., the last release of fastPHASE program (1.4.8) lacks such an option. In ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03589-0
更新日期:2020-07-24 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:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03646-8
更新日期:2020-07-21 00:00:00
abstract:BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03639-7
更新日期:2020-07-14 00:00:00
abstract:BACKGROUND:A recently proposed method for estimating qPCR amplification efficiency E analyzes fluorescence intensity ratios from pairs of points deemed to lie in the exponential growth region on the amplification curves for all reactions in a dilution series. This method suffers from a serious problem: The resulting ra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03604-4
更新日期:2020-07-08 00:00:00
abstract:BACKGROUND:Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target proteins. In recent studies, handcrafted features, similarity metrics and machine learning methods have...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3518-6
更新日期:2020-07-06 00:00:00
abstract:BACKGROUND:Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to save lives. In this paper, a comparative analysis of different classifiers was performed for the classi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03626-y
更新日期:2020-07-02 00:00:00
abstract:BACKGROUND:As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03577-4
更新日期:2020-06-29 00:00:00