Abstract:
BACKGROUND:Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2DE images. To reduce the errors of spot quantification in 2DE images, a novel brightness correction method based on gradient interval histogram (GIH) is proposed in this paper. RESULTS:First, GIH equalization is proposed to enhance the protein spot edges, especially the weak protein spots in the 2DE image. Second, to eliminate the overall brightness shift, GIH matching is applied to the 2DE images that need to be compared. Finally, the proposed method is verified by subjective quality evaluation and quantitative analysis of protein spots in real 2DE images. CONCLUSIONS:The experimental results show that the average error of the quantification of corresponding protein spots in the resulting image pairs is less than 3%, which is significantly superior to that of the existing methods.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Ou Q,Xiao J,Yu L,Wu K,Xiong Bdoi
10.1186/s12859-020-3432-ysubject
Has Abstractpub_date
2020-03-19 00:00:00pages
117issue
1issn
1471-2105pii
10.1186/s12859-020-3432-yjournal_volume
21pub_type
杂志文章abstract:BACKGROUND:Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understanding the structure and function of these fundamental cellular networks and essential for the emerging ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-199
更新日期:2004-12-16 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:Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites. RESULTS:We propose to identify and group similar profiles using tw...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-237
更新日期:2005-09-28 00:00:00
abstract:BACKGROUND:Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3510-1
更新日期:2020-05-29 00:00:00
abstract:BACKGROUND:Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology all...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-241
更新日期:2006-05-04 00:00:00
abstract:BACKGROUND:It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool wh...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-218
更新日期:2008-04-28 00:00:00
abstract:BACKGROUND:The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appea...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-4-41
更新日期:2003-09-11 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:Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), expe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-224
更新日期:2011-06-02 00:00:00
abstract:BACKGROUND:The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challeng...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-186
更新日期:2009-06-18 00:00:00
abstract:BACKGROUND:The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-76
更新日期:2004-06-09 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: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:Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms. RESULTS:In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architectur...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2276-1
更新日期:2018-08-13 00:00:00
abstract:BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-55
更新日期:2004-05-07 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: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:Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-153
更新日期:2012-06-28 00:00:00
abstract:BACKGROUND:Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-63
更新日期:2006-02-09 00:00:00
abstract:BACKGROUND:Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profil...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-184
更新日期:2006-04-03 00:00:00
abstract:BACKGROUND:Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distribution of biological resources and related data collected by 28 European culture collections. Linki...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-S4-S23
更新日期:2005-12-01 00:00:00
abstract:BACKGROUND:An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. RESULTS:The bioinformatics library libcov is a collection of C++ classe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-138
更新日期:2005-06-06 00:00:00
abstract:BACKGROUND:Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained. RESULTS:We present an R/Bioconductor port of a fast novel algorithm for...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-242
更新日期:2009-08-06 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:Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-38
更新日期:2009-01-29 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:Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-237
更新日期:2006-05-02 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: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:SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations foun...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-309
更新日期:2009-09-23 00:00:00