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 adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. RESULTS:We offer BAGEL (Bayesian Analysis of Gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1015-8
更新日期:2016-04-16 00:00:00
abstract:BACKGROUND:Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the missing heritability, i.e. heritability of phenotypes so far not accounted for by single genetic vari...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1006-9
更新日期:2016-04-08 00:00:00
abstract:BACKGROUND:RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of dif...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0994-9
更新日期:2016-03-31 00:00:00
abstract:BACKGROUND:Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0991-z
更新日期:2016-03-24 00:00:00
abstract:BACKGROUND:Enhancers are stretches of DNA (100-1000 bp) that play a major role in development gene expression, evolution and disease. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (CRMs). Although the binding ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0980-2
更新日期:2016-03-18 00:00:00
abstract:BACKGROUND:Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is crucial to assess in silico the options as well as the impact of various crossing schemes and breedi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0906-z
更新日期:2016-02-06 00:00:00
abstract:BACKGROUND:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibil...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0917-9
更新日期:2016-02-06 00:00:00
abstract:BACKGROUND:The nonparametric trend test (NPT) is well suitable for identifying the genetic variants associated with quantitative traits when the trait values do not satisfy the normal distribution assumption. If the genetic model, defined according to the mode of inheritance, is known, the NPT derived under the given g...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0888-x
更新日期:2016-01-28 00:00:00
abstract:BACKGROUND:Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mouse models revealed delayed maturation of neuronal morphology and autonomous as well as non-cell auton...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0859-7
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The main network reconstruction approaches are either based on Bayesian scores, which enable the ranking...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0856-x
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0887-y
更新日期:2016-01-20 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:A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging ty...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0875-7
更新日期:2016-01-16 00:00:00
abstract:BACKGROUND:Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0847-y
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying protein folds and domains. Although some methods have been presented to the protein solvent accessibilit...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0851-2
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relations...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0866-8
更新日期:2016-01-05 00:00:00
abstract:BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0832-5
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0836-1
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the regulatory relationships, High-Order Dynamic Bayesian Network (HO-DBN) is a good model of GRN. Howeve...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0823-6
更新日期:2015-11-25 00:00:00
abstract:BACKGROUND:Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA's 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incor...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0815-6
更新日期:2015-11-18 00:00:00
abstract:BACKGROUND:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0794-7
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0807-6
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0810-y
更新日期:2015-11-04 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:Numerous tools have been developed to predict the fitness effects (i.e., neutral, deleterious, or beneficial) of genetic variants on corresponding proteins. However, prediction in terms of whether a variant causes the variant bearing protein to lose the original function or gain new function is also needed f...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0781-z
更新日期:2015-10-30 00:00:00
abstract:BACKGROUND:GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that G...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0773-z
更新日期:2015-10-23 00:00:00
abstract:BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0751-5
更新日期:2015-10-22 00:00:00
abstract:BACKGROUND:This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0689-7
更新日期:2015-09-15 00:00:00
abstract:BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0681-2
更新日期:2015-08-19 00:00:00
abstract:BACKGROUND:Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0688-8
更新日期:2015-08-14 00:00:00
abstract:BACKGROUND:The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0660-7
更新日期:2015-07-30 00:00:00
abstract:BACKGROUND:Genetic variations predispose individuals to hereditary diseases, play important role in the development of complex diseases, and impact drug metabolism. The full information about the DNA variations in the genome of an individual is given by haplotypes, the ordered lists of single nucleotide polymorphisms (...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0651-8
更新日期:2015-07-16 00:00:00
abstract:BACKGROUND:The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to se...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0630-0
更新日期:2015-06-20 00:00:00
abstract:BACKGROUND:People with an autistic spectrum disorder (ASD) display a variety of characteristic behavioral traits, including impaired social interaction, communication difficulties and repetitive behavior. This complex neurodevelopment disorder is known to be associated with a combination of genetic and environmental fa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0622-0
更新日期:2015-06-06 00:00:00
abstract:BACKGROUND:Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. RESULTS:We have found l...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0612-2
更新日期:2015-06-02 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 Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0613-1
更新日期:2015-05-28 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:Deep mutational scanning is a technique to estimate the impacts of mutations on a gene by using deep sequencing to count mutations in a library of variants before and after imposing a functional selection. The impacts of mutations must be inferred from changes in their counts after selection. RESULTS:I desc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0590-4
更新日期:2015-05-20 00:00:00
abstract:BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0592-2
更新日期:2015-05-13 00:00:00