Abstract:
:Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Quintales L,Vázquez E,Antequera Fdoi
10.1093/bib/bbu037subject
Has Abstractpub_date
2015-07-01 00:00:00pages
576-87issue
4eissn
1467-5463issn
1477-4054pii
bbu037journal_volume
16pub_type
杂志文章abstract:BACKGROUND:Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. METHODS:We assessed the global status of Mtb WGS and developed a 3-week training co...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa246
更新日期:2020-10-03 00:00:00
abstract::Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become incre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw072
更新日期:2017-11-01 00:00:00
abstract::The number of bioinformatics tools and resources that support molecular and cell biology approaches is continuously expanding. Moreover, systems and network biology analyses are accompanied more and more by integrated bioinformatics methods. Traditional information-centered university teaching methods often fail, as (...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt024
更新日期:2013-09-01 00:00:00
abstract::A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially b...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz065
更新日期:2020-07-15 00:00:00
abstract::Despite The Central Dogma states the destiny of gene as 'DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic information but also, surprisingly, join in intracellular vital movement as a regulator of gene expression. Bioinformatics has contributed to knowledge for a series of em...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa023
更新日期:2020-04-06 00:00:00
abstract::The outbreak caused by the novel coronavirus SARS-CoV-2 has been declared a global health emergency. G-quadruplex structures in genomes have long been considered essential for regulating a number of biological processes in a plethora of organisms. We have analyzed and identified 25 four contiguous GG runs (G2NxG2NyG2N...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa114
更新日期:2020-06-01 00:00:00
abstract:BACKGROUND:The most frequently mutated gene pairs in pancreatic adenocarcinoma (PAAD) are KRAS and TP53, and our goal is to illustrate the multiomics and molecular dynamics landscapes of KRAS/TP53 mutation and also to obtain prospective novel drugs for KRAS- and TP53-mutated PAAD patients. Moreover, we also made an att...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa149
更新日期:2020-07-31 00:00:00
abstract::Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of cis-regulatory elements such as microRNA (miRNA) target sites in the 3'-untranslated region (3'-UTRs) of genes. Although previous computational APA studies focused on a subset of genes strongly affected by APA (APA genes), we ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa191
更新日期:2020-08-26 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::We discuss and review different ways to map cellular components and their temporal interaction with other such components to different non-spatially explicit mathematical models. The essential choices made in the literature are between discrete and continuous state spaces, between rule and event-based state updates an...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbp062
更新日期:2010-01-01 00:00:00
abstract::Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studi...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa113
更新日期:2020-07-01 00:00:00
abstract::Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systemat...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbr076
更新日期:2012-09-01 00:00:00
abstract::Deoxyribonucleic acid replication is one of the most crucial tasks taking place in the cell, and it has to be precisely regulated. This process is initiated in the replication origins (ORIs), and thus it is essential to identify such sites for a deeper understanding of the cellular processes and functions related to t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa304
更新日期:2020-11-25 00:00:00
abstract::Posttranscriptional crosstalk and communication between RNAs yield large regulatory competing endogenous RNA (ceRNA) networks via shared microRNAs (miRNAs), as well as miRNA synergistic networks. The ceRNA crosstalk represents a novel layer of gene regulation that controls both physiological and pathological processes...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx137
更新日期:2019-07-19 00:00:00
abstract::The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of ...
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::Effectively representing Medical Subject Headings (MeSH) headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. In this paper, we converted the MeSH tree ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa037
更新日期:2020-03-31 00:00:00
abstract::Despite gene expression programs being notoriously complex, RNA abundance is usually assumed as a proxy for transcriptional activity. Recently developed approaches, able to disentangle transcriptional and post-transcriptional regulatory processes, have revealed a more complex scenario. It is now possible to work out h...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa389
更新日期:2020-12-22 00:00:00
abstract::Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of qua...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbp056
更新日期:2010-05-01 00:00:00
abstract::Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. T...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs074
更新日期:2014-07-01 00:00:00
abstract::Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa162
更新日期:2020-08-11 00:00:00
abstract::Protein remote homology detection is one of the most fundamental and central problems for the studies of protein structures and functions, aiming to detect the distantly evolutionary relationships among proteins via computational methods. During the past decades, many computational approaches have been proposed to sol...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbw108
更新日期:2018-03-01 00:00:00
abstract::Information Integrator is an extension to IBM's relational database DB2, which uses data federation to provide benefits to molecular biology researchers through two unique capabilities: increased flexibility in combining data from disparate sources, and SQL access to non-SQL data, easing the task of automating data an...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/4.4.375
更新日期:2003-12-01 00:00:00
abstract::Cell lines are widely used as in vitro models of tumorigenesis. However, an increasing number of researchers have found that cell lines differ from their sourced tumour samples after long-term cell culture. The application of unsuitable cell lines in experiments will affect the experimental accuracy and the treatment ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbw082
更新日期:2017-05-01 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:MOTIVATION:Computational methods accelerate drug discovery and play an important role in biomedicine, such as molecular property prediction and compound-protein interaction (CPI) identification. A key challenge is to learn useful molecular representation. In the early years, molecular properties are mainly calculated b...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa266
更新日期:2020-11-04 00:00:00
abstract::Despite its central role in the adaptation and microevolution of traits, the genetic architecture of phenotypic plasticity, i.e. multiple phenotypes produced by a single genotype in changing environments, remains elusive. We know little about the genes that underlie the plastic response of traits to the environment, t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbs009
更新日期:2013-01-01 00:00:00
abstract::Cell-penetrating peptides (CPPs) facilitate the delivery of therapeutically relevant molecules, including DNA, proteins and oligonucleotides, into cells both in vitro and in vivo. This unique ability explores the possibility of CPPs as therapeutic delivery and its potential applications in clinical therapy. Over the l...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bby124
更新日期:2020-03-23 00:00:00
abstract::Heterophylly, i.e. morphological changes in leaves along the axis of an individual plant, is regarded as a strategy used by plants to cope with environmental change. However, little is known of the extent to which heterophylly is controlled by genes and how each underlying gene exerts its effect on heterophyllous vari...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx011
更新日期:2018-07-20 00:00:00
abstract::Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa031
更新日期:2020-04-08 00:00:00
abstract::Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and m...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw081
更新日期:2017-11-01 00:00:00