Abstract:
BACKGROUND:Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. RESULTS:The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. CONCLUSIONS:ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section) and at: http://www.alice-dsl.net/evgeniy.vainshtein/ICEP/
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Vainshtein Y,Sanchez M,Brazma A,Hentze MW,Dandekar T,Muckenthaler MUdoi
10.1186/1471-2105-11-112subject
Has Abstractpub_date
2010-03-01 00:00:00pages
112issn
1471-2105pii
1471-2105-11-112journal_volume
11pub_type
杂志文章abstract:BACKGROUND:Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similar...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-379
更新日期:2007-10-10 00:00:00
abstract:BACKGROUND:Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, fo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-257
更新日期:2006-05-18 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:Innovations in biological and biomedical imaging produce complex high-content and multivariate image data. For decision-making and generation of hypotheses, scientists need novel information technology tools that enable them to visually explore and analyze the data and to discuss and communicate results or f...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-297
更新日期:2011-07-21 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:Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure eleme...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-510
更新日期:2006-11-21 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:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S11-S16
更新日期:2014-01-01 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:Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative interactions cannot be readily obtained from interaction data, so these must be generated. In protein-pr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S1-S57
更新日期:2009-01-30 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:The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise and contaminant peaks. It is widely accepted that a valid primary peak tends to have high intensity an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-346
更新日期:2011-08-17 00:00:00
abstract:BACKGROUND:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S10-S6
更新日期:2012-06-25 00:00:00
abstract:BACKGROUND:Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed based on amino acid compositions or on the N-terminal characteristics (signal peptides) of proteins. Ho...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-152
更新日期:2005-06-17 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:Frequent pattern mining analysis applied on microarray dataset appears to be a promising strategy for identifying relationships between gene expression levels. Unfortunately, too many itemsets (co-expressed genes) are identified by this analysis method since it does not consider the importance of each gene w...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-230
更新日期:2013-07-21 00:00:00
abstract:BACKGROUND:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0466-7
更新日期:2015-02-12 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: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: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:Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-220
更新日期:2010-04-29 00:00:00
abstract:BACKGROUND:Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the databas...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S18-S6
更新日期:2015-01-01 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:Amplified fragment length polymorphism (AFLP) is a PCR-based technique that involves restriction of genomic DNA followed by ligation of adaptors to the fragments generated and selective PCR amplification of a subset of these fragments. The amplified fragments are separated on a sequencing gel and visualized ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-4-7
更新日期:2003-02-25 00:00:00
abstract:BACKGROUND:De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis work...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2174-6
更新日期:2018-07-09 00:00:00
abstract:BACKGROUND:Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., conti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-275
更新日期:2010-05-21 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:The rapid growth of protein-protein interaction (PPI) data has led to the emergence of PPI network analysis. Despite advances in high-throughput techniques, the interactomes of several model organisms are still far from complete. Therefore, it is desirable to expand these interactomes with ortholog-based and...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S12-S11
更新日期:2008-12-12 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:Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-41
更新日期:2008-01-24 00:00:00