DNA methylation dynamics: identification and functional annotation.

abstract：:Since the discovery of RNA splicing in 1977 the knowledge of this important biological process has increased steadily following the identification of many of the mechanistic features of splicing: from the basic cis-acting splicing signals, through the detail composition and dynamics of the spliceosome, to the role pla...

journal_title：Briefings in functional genomics

authors： Buratti E,Baralle M,Baralle FE

更新日期：2013-01-01 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

authors： Davies MN,Meaburn EL,Schalkwyk LC

更新日期：2010-12-01 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

authors： Wang G,Liu C,Deng S,Zhao Q,Li T,Qiao S,Shen L,Zhang Y,Lü J,Meng L,Liang C,Yu Z

更新日期：2016-05-01 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

authors： Fan S,Chi W

更新日期：2016-11-01 00:00:00

abstract：:A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. We review prog...

journal_title：Briefings in functional genomics

authors： Bai Y,Dai X,Harrison AP,Chen M

更新日期：2015-03-01 00:00:00

abstract：:Hemagglutinin (HA) is a transmembrane protein of the influenza A virus and a key component in its life cycle. The protein allows the virus to enter a host cell by recognizing specific glycans attached to transmembrane proteins of the host, which leads to viral endocytosis. In recent years, significant progress has bee...

journal_title：Briefings in functional genomics

authors： Lazniewski M,Dawson WK,Szczepinska T,Plewczynski D

更新日期：2018-11-26 00:00:00

abstract：:Submitting sequences to the National Center for Biotechnology Information (NCBI) is an integral part of research and the publication process for many disciplines within the life sciences, and it will only become more important as sequencing technologies continue to improve. Here, I argue that the available infrastruct...

journal_title：Briefings in functional genomics

authors： Smith DR

更新日期：2020-12-04 00:00:00

abstract：:Chronic infection of hepatitis C virus (HCV) leads to severe life-threatening liver diseases such as cirrhosis of liver, fibrosis and hepatocellular carcinoma (HCC). Severity of the disease infects >180 million people worldwide. In recent years, many computational approaches have been proposed to study and analyze the...

journal_title：Briefings in functional genomics

authors： Ray S,Maulik U,Mukhopadhyay A

更新日期：2018-11-26 00:00:00

abstract：:Neisseria meningitidis is a strictly human pathogen and is one of the major causes of septicemia and meningitis worldwide. Functional genomics approaches have been extensively applied to study how N. meningitidis adapts to grow and survive in different human niches encountered during the infection. DNA microarrays per...

journal_title：Briefings in functional genomics

authors： Del Tordello E,Serruto D

更新日期：2013-07-01 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

authors： Huang Y,Chen DH,Liu BY,Shen WH,Ruan Y

更新日期：2017-03-01 00:00:00

abstract：:Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryo...

journal_title：Briefings in functional genomics

authors： Moriyama Y,Koshiba-Takeuchi K

更新日期：2018-09-27 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

authors： Kumar MS,Chen KC

更新日期：2012-07-01 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

authors： MacGrogan D,Luxán G,de la Pompa JL

更新日期：2014-01-01 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

authors： Hudson BD,Kulp KS,Loots GG

更新日期：2013-09-01 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

authors： Moin M,Bakshi A,Saha A,Dutta M,Kirti PB

更新日期：2017-07-01 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

authors： Zhang Z,Zhao Y,Liao X,Shi W,Li K,Zou Q,Peng S

更新日期：2019-02-14 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

authors： Ishii T

更新日期：2017-01-01 00:00:00

abstract：:RNA-seq is a methodology for RNA profiling based on next-generation sequencing that enables to measure and compare gene expression patterns at unprecedented resolution. Although the appealing features of this technique have promoted its application to a wide panel of transcriptomics studies, the fast-evolving nature o...

journal_title：Briefings in functional genomics

authors： Finotello F,Di Camillo B

更新日期：2015-03-01 00:00:00

abstract：:Gastric cancer remains the second most common cause of cancer-related death worldwide. Because of the poor prognosis of late-stage gastric cancer patients, it is imperative to develop new strategies to improve the survival rate of this disease. Currently, immunotherapy is considered as an innovative approach for cance...

journal_title：Briefings in functional genomics

authors： Zhao Q,Cao L,Guan L,Bie L,Wang S,Xie B,Chen X,Shen X,Cao F

更新日期：2019-03-22 00:00:00

abstract：:Genetic variation is crucial for successful barley improvement. Genomic technologies are improving dramatically and are providing access to the genetic diversity within this important crop species. Diverse collections of barley germplasm are being assembled and mined via genome-wide association studies and the identif...

journal_title：Briefings in functional genomics

authors： Muñoz-Amatriaín M,Cuesta-Marcos A,Hayes PM,Muehlbauer GJ

更新日期：2014-07-01 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

authors： Hou J,Acharya L,Zhu D,Cheng J

更新日期：2016-03-01 00:00:00

abstract：:Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associa...

journal_title：Briefings in functional genomics

authors： Henry RJ

更新日期：2012-01-01 00:00:00

abstract：:The human genome has an almost equal distribution of unique and transposable genetic elements. Although at the transcriptome level, a relatively higher contribution from transposable elements derived RNA has been reported. This is further highlighted with evidence from pervasive transcription. Of the total RNA, noncod...

journal_title：Briefings in functional genomics

authors： Chattopadhyay P,Srinivasa Vasudevan J,Pandey R

更新日期：2021-01-25 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

authors： Arda HE,Walhout AJ

更新日期：2010-01-01 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

authors： Kagohara LT,Stein-O'Brien GL,Kelley D,Flam E,Wick HC,Danilova LV,Easwaran H,Favorov AV,Qian J,Gaykalova DA,Fertig EJ

更新日期：2018-01-01 00:00:00

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

authors： Buiting K,Kanber D,Horsthemke B,Lohmann D

更新日期：2010-07-01 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

authors： Janjić V,Pržulj N

更新日期：2012-11-01 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

authors： Hatzikotoulas K,Gilly A,Zeggini E

更新日期：2014-09-01 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

authors： Halley-Stott RP,Gurdon JB

更新日期：2013-05-01 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

authors： Sen S,Maulik U

更新日期：2018-11-26 00:00:00