Deep learning in omics: a survey and guideline.

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：: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：:A central environment and interface for microRNA (miRNA) registry and repository and a general standardized framework for their systematic annotation was established over a decade ago. However, the numbers of experimentally and computationally identified miRNAs are swiftly accumulating, and new aspects of miRNA-mediat...

journal_title：Briefings in functional genomics

authors： Budak H,Bulut R,Kantar M,Alptekin B

更新日期：2016-01-01 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

authors： Cota CD,Segade F,Davidson B

更新日期：2014-01-01 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：: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：: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：: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：: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：: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：: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：: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：: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：: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：: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 growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine a...

journal_title：Briefings in functional genomics

authors： Machyna M,Simon MD

更新日期：2018-03-01 00:00:00

abstract：:Premature termination of transcription, or attenuation, is an efficient RNA-based regulatory strategy that is commonly used in bacterial organisms. Attenuators are generally located in the 50 untranslated regions of genes or operons and combine a Rho-independent terminator, controlling transcription, with an RNA eleme...

journal_title：Briefings in functional genomics

authors： Naville M,Gautheret D

更新日期：2010-03-01 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：: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：: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

authors： Liu H,Li S,Wang X,Zhu J,Wei Y,Wang Y,Wen Y,Wang L,Huang Y,Zhang B,Shang S,Zhang Y

更新日期：2016-11-01 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：: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

authors： Sharma AR,Shashikiran U,Uk AR,Shetty R,Satyamoorthy K,Rai PS

更新日期：2020-07-29 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

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

authors： Alyousfi D,Baralle D,Collins A

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

authors： Bartke T,Borgel J,DiMaggio PA

更新日期：2013-05-01 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：: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

authors： Di Cerbo V,Schneider R

更新日期：2013-05-01 00:00:00

abstract：:Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize th...

journal_title：Briefings in functional genomics

authors： Viljakainen L

更新日期：2015-11-01 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

authors： Stormo GD,Zuo Z,Chang YK

更新日期：2015-01-01 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

authors： Grob S

更新日期：2020-03-23 00:00:00