Abstract:
:High-throughput next-generation sequencing (NGS) technologies have rapidly generated a large volume of genomic data. To aid the development and evaluation of new statistical models and computational methods, NGS-based simulators have been proposed to construct better experimental workflows. However, the comparative performance of these NGS simulators remains unclear. In this review, we conducted a comprehensive investigation of NGS simulators for various sequencing techniques, including DNA sequencing, metagenomic sequencing, RNA-seq, ChIP-seq and bisulfite sequencing for methylation.
journal_name
Brief Funct Genomicsjournal_title
Briefings in functional genomicsauthors
Zhao M,Liu D,Qu Hdoi
10.1093/bfgp/elw012subject
Has Abstractpub_date
2017-05-01 00:00:00pages
121-128issue
3eissn
2041-2649issn
2041-2657pii
elw012journal_volume
16pub_type
杂志文章,评审abstract::Recent data have revealed that the paradigmatic tumour suppressor gene RB1 on chromosome 13 is preferentially expressed from the maternal allele. Imprinted expression of RB1 is linked to a differentially methylated CpG island in intron 2 of this gene (CpG 85). On the paternal chromosome, CpG 85 is unmethylated and act...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elq014
更新日期:2010-07-01 00:00:00
abstract::In the current era of epigenetics research, we have observed many examples of epigenetic modifications, like histone modification and DNA methylation, in various fatal diseases. These include solid tumors, hematological malignancies and viral infections with DNA or RNA viruses. The purpose of this review is to summari...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/ely021
更新日期:2018-11-26 00:00:00
abstract::The Notch signalling pathway plays crucial roles in cardiac development and postnatal cardiac homoeostasis. Gain- and loss-of-function approaches indicate that Notch promotes or inhibits cardiogenesis in a stage-dependent manner. However, the molecular mechanisms are poorly defined because many downstream effectors re...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt036
更新日期:2014-01-01 00:00:00
abstract::The presence of microchimeric cells is known for >100 years and well documented since decades. Earlier, microchimeric cells were mainly used for cell-based non-invasive prenatal diagnostics during early pregnancy. Microchimeric cells are also present beyond delivery and are associated to various autoimmune diseases, t...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elx027
更新日期:2018-07-01 00:00:00
abstract::Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding R...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elx018
更新日期:2018-01-01 00:00:00
abstract::Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions betwee...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elp049
更新日期:2010-01-01 00:00:00
abstract::The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particula...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv040
更新日期:2016-03-01 00:00:00
abstract::Research on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes report...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elz024
更新日期:2020-03-23 00:00:00
abstract::The Human Cell Atlas is a large, international consortium that aims to identify and describe every cell type in the human body. The comprehensive cellular maps that arise from this ambitious effort have the potential to transform many aspects of fundamental biology and clinical practice. Here, we discuss the technical...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elx029
更新日期:2018-07-01 00:00:00
abstract::The epitome of any genome research is to identify all the existing genes in a genome and investigate their roles. Various techniques have been applied to unveil the functions either by silencing or over-expressing the genes by targeted expression or random mutagenesis. Rice is the most appropriate model crop for gener...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elw041
更新日期:2017-07-01 00:00:00
abstract::In order to better understand several cellular processes, it is helpful to study how various components make up the system. This systems perspective is supported by several modelling tools including network analysis. Networks of protein-protein interactions (PPI networks) offer a way to depict, visualize and quantify ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els035
更新日期:2012-11-01 00:00:00
abstract::A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of 'carotenoids and apocarotenoids' is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide repr...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elz037
更新日期:2020-01-22 00:00:00
abstract::Defects in the initial establishment of cardiogenic cell fate are likely to contribute to pervasive human congenital cardiac abnormalities. However, the molecular underpinnings of nascent cardiac fate induction have proven difficult to decipher. In this review we explore the participation of extracellular, cellular an...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt034
更新日期:2014-01-01 00:00:00
abstract::Piwi-interacting RNAs (piRNAs) and CRISPR RNAs (crRNAs) are two recently discovered classes of small noncoding RNA that are found in animals and prokaryotes, respectively. Both of these novel RNA species function as components of adaptive immune systems that protect their hosts from foreign nucleic acids-piRNAs repres...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els016
更新日期:2012-07-01 00:00:00
abstract::Genome editing allows for the versatile genetic modification of somatic cells, germ cells and embryos. In particular, CRISPR/Cas9 is worldwide used in biomedical research. Although the first report on Cas9-mediated gene modification in human embryos focused on the prevention of a genetic disease in offspring, it raise...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv053
更新日期:2017-01-01 00:00:00
abstract::DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been develope...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw029
更新日期:2016-11-01 00:00:00
abstract::Molecular network data are increasingly becoming available, necessitating the development of well performing computational tools for their analyses. Such tools enabled conceptually different approaches for exploring human diseases to be undertaken, in particular, those that study the relationship between a multitude o...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/els037
更新日期:2012-11-01 00:00:00
abstract::The specificity of protein-DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, s...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elu043
更新日期:2015-01-01 00:00:00
abstract::Gene Set Enrichment (GSE) is a computational technique which determines whether a priori defined set of genes show statistically significant differential expression between two phenotypes. Currently, the gene sets used for GSE are derived from annotation or pathway databases, which often contain computationally based ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elq021
更新日期:2010-12-01 00:00:00
abstract::The use of genetically isolated populations can empower next-generation association studies. In this review, we discuss the advantages of this approach and review study design and analytical considerations of genetic association studies focusing on isolates. We cite successful examples of using population isolates in ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elu022
更新日期:2014-09-01 00:00:00
abstract::Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw010
更新日期:2016-11-01 00:00:00
abstract::Coronary artery disease (CAD) and ischemic stroke are the two most predominant forms of cardiovascular diseases (CVDs) caused by genetic, epigenetic and environmental risk factors. Although studies on the impact of 'epigenetics' in CVDs is not new, its effects are increasingly being realized as a key regulatory determ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elz043
更新日期:2020-07-29 00:00:00
abstract::The evolution of next-generation sequencing technologies has facilitated the detection of causal genetic variants in diseases previously undiagnosed at a molecular level. However, in genome sequencing studies, the identification of disease genes among a candidate gene list is often difficult because of the large numbe...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/ely033
更新日期:2019-02-14 00:00:00
abstract::The involvement of epigenetic processes in the origin and progression of cancer is now widely appreciated. Consequently, targeting the enzymatic machinery that controls the epigenetic regulation of the genome has emerged as an attractive new strategy for therapeutic intervention. The development of epigenetic drugs re...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt002
更新日期:2013-05-01 00:00:00
abstract::Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big data. A huge amount of high dimensional and complex structured data has made it no longer applicable for conventional machine learning algorithms. Fortunately, deep learning technology can contribute toward resolving these chall...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/ely030
更新日期:2019-02-14 00:00:00
abstract::Less than 2% of the human genome DNA is composed of protein-coding genes, although the majority of the human genome is transcribed, indicating the transcripts mostly are noncoding RNAs. Those noncoding RNAs with length between 200 nt and 200 kb are categorized as long noncoding RNA (lncRNA). Around 30 000 lncRNAs have...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv049
更新日期:2016-05-01 00:00:00
abstract::The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. In Ar...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elw007
更新日期:2017-03-01 00:00:00
abstract::Lysine N-ε-acetylation is a post-translational modification that regulates the function of histone and non-histone proteins. In several malignancies, histone acetyltransferase (HAT) activities are disturbed as a consequence of various genetic or epigenetic alterations. In particular, HATs can function as tumor suppres...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els065
更新日期:2013-05-01 00:00:00
abstract::Epigenetic memory represents a natural mechanism whereby the identity of a cell is maintained through successive cell cycles, allowing the specification and maintenance of differentiation during development and in adult cells. Cancer is a loss or reversal of the stable differentiated state of adult cells and may be me...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt011
更新日期:2013-05-01 00:00:00
abstract::Prostate cancer (PCa) is the second most commonly diagnosed malignancy in men in the Western world and the second leading cause of cancer-related deaths among men worldwide. Although most cancers have the potential to metastasize under appropriate conditions, PCa favors the skeleton as a primary site of metastasis, su...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt021
更新日期:2013-09-01 00:00:00