Abstract:
:Next generation sequencers have greatly improved our ability to mine polymorphisms and mutations out of entire (or portions of) genomes. The reliability of their outputs, though, showed to be very related to the sequencing chemistry and to deeply affect the quality of the downstream analyses. We focus here on the two-base color code chemistry of AB SOLiD sequencers and propose a comprehensive quality control methodological and software pipeline. We used existing and custom tools to detect and purge short-reads of some common flaws due to sequencing errors and chemical hitches. We apply them to a cohort of SOLiD 4 runs and measure their joint efficacy in terms of the resulting ability to detect the greatest possible number of true variants.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Castellana S,Romani M,Valente EM,Mazza Tdoi
10.1093/bib/bbs048subject
Has Abstractpub_date
2013-11-01 00:00:00pages
684-95issue
6eissn
1467-5463issn
1477-4054pii
bbs048journal_volume
14pub_type
杂志文章abstract::Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently oc...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs030
更新日期:2013-05-01 00:00:00
abstract::In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data r...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/1.2.190
更新日期:2000-05-01 00:00:00
abstract::The so-called 'omics' approaches used in modern biology aim at massively characterizing the molecular repertories of living systems at different levels. Metabolomics is one of the last additions to the 'omics' family and it deals with the characterization of the set of metabolites in a given biological system. As meta...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs055
更新日期:2013-11-01 00:00:00
abstract::Fibrosis is a key component in the pathogenic mechanism of a variety of diseases. These diseases involving fibrosis may share common mechanisms and therapeutic targets, and therefore common intervention strategies and medicines may be applicable for these diseases. For this reason, deliberately introducing anti-fibros...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa115
更新日期:2020-06-22 00:00:00
abstract::RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
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更新日期:2019-03-22 00:00:00
abstract::In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these pre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa160
更新日期:2020-08-07 00:00:00
abstract::The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by d...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2014-01-01 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2019-01-18 00:00:00
abstract::Effective drug discovery contributes to the treatment of numerous diseases but is limited by high costs and long cycles. The Quantitative Structure-Activity Relationship (QSAR) method was introduced to evaluate the activity of a large number of compounds virtually, reducing the time and labor costs required for chemic...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa276
更新日期:2020-11-03 00:00:00
abstract::Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains mass...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw088
更新日期:2017-11-01 00:00:00
abstract:MOTIVATION:Long noncoding RNAs (lncRNAs) correspond to a eukaryotic noncoding RNA class that gained great attention in the past years as a higher layer of regulation for gene expression in cells. There is, however, a lack of specific computational approaches to reliably predict lncRNA in plants, which contrast the vari...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bby034
更新日期:2019-03-25 00:00:00
abstract::The modelling of biological systems is accompanied with epistemic uncertainties that range from structural uncertainty to parametric uncertainty due to such limitations as insufficient understanding of the underlying mechanism and incomplete measurement data of a system. Fuzzy logic approaches such as fuzzy Petri nets...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bby118
更新日期:2018-12-27 00:00:00
abstract::Computational biology is essential in the process of translating biological knowledge into clinical practice, as well as in the understanding of biological phenomena based on the resources and technologies originating from the clinical environment. One such key contribution of computational biology is the discovery of...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbp008
更新日期:2009-07-01 00:00:00
abstract::Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial can...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx109
更新日期:2019-01-18 00:00:00
abstract::Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the 'uncertainty' of a solution, that is, the probability of the solution is extremely small. This situation arises for estimation problems on high-dimen...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt038
更新日期:2014-09-01 00:00:00
abstract::Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA-Seq) data. The following review includes an update regarding general methods and resources for GSA and then emphasizes GSA methods and tools...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz090
更新日期:2020-09-25 00:00:00
abstract::The Gulbenkian Training Programme in Bioinformatics has been offering hands-on training courses in Oeiras, PT for more than a decade. This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbq063
更新日期:2010-11-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 历史文章,杂志文章
doi:10.1093/bib/bbu022
更新日期:2015-03-01 00:00:00
abstract::Precision and personalized medicine will be increasingly based on the integration of various type of information, particularly electronic health records and genome sequences. The availability of cheap genome sequencing services and the information interoperability will increase the role of online bioinformatics analys...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw078
更新日期:2017-11-01 00:00:00
abstract::Since the completion of the Human Genome Project, it has been widely established that most DNA is not transcribed into proteins. These non-protein-coding regions are believed to be moderators within transcriptional and post-transcriptional processes, which play key roles in the onset of diseases. Long non-coding RNAs ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbv114
更新日期:2017-01-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2015-07-01 00:00:00
abstract::Precision medicine has changed thinking in cancer therapy, highlighting a better understanding of the individual clinical interventions. But what role do the drivers and pathways identified from pan-cancer genome analysis play in the tumor? In this letter, we will highlight the importance of in silico modeling in prec...
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pub_type: 杂志文章
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更新日期:2020-05-21 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2020-08-14 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2020-12-15 00:00:00
abstract::Correlated reaction sets (Co-Sets) are mathematically defined modules in biochemical reaction networks which facilitate the study of biological processes by decomposing complex reaction networks into conceptually simple units. According to the degree of association, Co-Sets can be classified into three types: perfect,...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2011-03-01 00:00:00
abstract::Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a number of technical and statistical problems. Possible remedies on the level of computational analysis lie in appropriate pr...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
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更新日期:2006-06-01 00:00:00
abstract::Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological lands...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2009-07-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2015-01-01 00:00:00
abstract::DNA-binding hot spot residues of proteins are dominant and fundamental interface residues that contribute most of the binding free energy of protein-DNA interfaces. As experimental methods for identifying hot spots are expensive and time consuming, computational approaches are urgently required in predicting hot spots...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz037
更新日期:2020-05-21 00:00:00
abstract::One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With...
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