Abstract:
:Extracting inherent valuable knowledge from omics big data remains as a daunting problem in bioinformatics and computational biology. Deep learning, as an emerging branch from machine learning, has exhibited unprecedented performance in quite a few applications from academia and industry. We highlight the difference and similarity in widely utilized models in deep learning studies, through discussing their basic structures, and reviewing diverse applications and disadvantages. We anticipate the work can serve as a meaningful perspective for further development of its theory, algorithm and application in bioinformatic and computational biology.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Tang B,Pan Z,Yin K,Khateeb Adoi
10.3389/fgene.2019.00214subject
Has Abstractpub_date
2019-03-26 00:00:00pages
214issn
1664-8021journal_volume
10pub_type
杂志文章,评审abstract::Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2011.00054
更新日期:2011-08-31 00:00:00
abstract::Hematopoiesis results in the correct formation of all the different blood cell types. In mammals, it starts from specific hematopoietic stem and precursor cells residing in the bone marrow. Mature blood cells are responsible for supplying oxygen to every cell of the organism and for the protection against pathogens. T...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00348
更新日期:2018-08-31 00:00:00
abstract::Known as the "fifth RNA nucleotide", pseudouridine (Ψ or psi) is the first-discovered and most abundant RNA modification occurring at the Uridine site, and it plays a prominent role in a number of biological processes. Thousands of Ψ sites have been identified within different biological contexts thanks to the advance...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00088
更新日期:2020-03-12 00:00:00
abstract::During plant-pathogen interactions, pathogens secrete many rapidly evolving, small secreted proteins (SSPs) that can modify plant defense and permit pathogens to colonize plant tissue. The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), one of the most important foliar diseas...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00469
更新日期:2020-05-12 00:00:00
abstract::The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptiv...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00140
更新日期:2014-05-20 00:00:00
abstract::I present here an in-depth, although non-exhaustive, review of two topics in molecular dating. Clock models, which describe the evolution of the rate of evolution, are considered first. Some of the shortcomings of popular approaches-uncorrelated clock models in particular-are presented and discussed. Autocorrelated mo...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00526
更新日期:2020-05-27 00:00:00
abstract::The southern muriqui (Brachyteles arachnoides) is the largest neotropical primate. This species is endemic to Brazil and is currently critically endangered due to its habitat destruction. The genetic basis underlying adaptive traits of New World monkeys has been a subject of interest to several investigators, with sig...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00831
更新日期:2020-07-31 00:00:00
abstract::Obesity has become a major public health issue which is caused by a combination of genetic and environmental factors. Genome-wide DNA methylation studies have identified that DNA methylation at Cytosine-phosphate-Guanine (CpG) sites are associated with obesity. However, subsequent functional validation of the results ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00663
更新日期:2018-12-19 00:00:00
abstract::Challenges in diagnosing primary immunodeficiency are numerous and diverse, with current whole-exome and whole-genome sequencing approaches only able to reach a molecular diagnosis in 25-60% of cases. We assess these problems and discuss how RNA-focused analysis has expanded and improved in recent years and may now be...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.01204
更新日期:2019-12-11 00:00:00
abstract::Undergraduate students in the biomedical sciences are often interested in future health-focused careers. This presents opportunities for instructors in genetics, molecular biology, and cancer biology to capture their attention using lab experiences built around clinically relevant data. As biomedical science in genera...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.573992
更新日期:2020-12-16 00:00:00
abstract::Long non-coding RNAs (lncRNAs) are transcripts which are usually more than 200 nt in length, and which do not have the protein-coding capacity. LncRNAs can be categorized based on their generation from distinct DNA elements, or derived from specific RNA processing pathways. During the past several decades, dramatic pr...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00744
更新日期:2019-01-23 00:00:00
abstract::Decreased expression of the fly and worm Indy genes extends longevity. The fly Indy gene and its mammalian homolog are transporters of Krebs cycle intermediates, with the highest rate of uptake for citrate. Cytosolic citrate has a role in energy regulation by affecting fatty acid synthesis and glycolysis. Fly, worm, a...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00047
更新日期:2013-04-08 00:00:00
abstract::For the past several decades, research in understanding the molecular basis of human muscle aging has progressed significantly. However, the development of accessible tissue-specific biomarkers of human muscle aging that may be measured to evaluate the effectiveness of therapeutic interventions is still a major challe...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00242
更新日期:2018-07-12 00:00:00
abstract::Over the last decade, numerous computational methods have been developed in order to infer and model biological networks. Transcriptional networks in particular have attracted significant attention due to their critical role in cell survival. The majority of network inference methods use genome-wide experimental data ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00110
更新日期:2013-06-20 00:00:00
abstract::Habitat loss and the illegal exploitation of natural resources are among the main drivers of species extinction around the world. These disturbances act at different scales, once changes in the landscape composition and configuration operate at large scales and exploitation of natural resources at local scales. Eviden...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01090
更新日期:2019-11-07 00:00:00
abstract::In this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of both 5' and 3' end small RNAs (5' and 3' sRNAs). 5' and 3' sRNAs alone can be used to annotate nuclear non-coding and mitochondrial genes at 1-bp resolution and identify new steady RNAs, which are usually transcribed from functional gene...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00105
更新日期:2019-02-14 00:00:00
abstract:AIMS/HYPOTHESIS:Genome-wide association studies have identified over 50 new genetic loci for type 2 diabetes (T2D). Several studies conclude that higher dietary heme iron intake increases the risk of T2D. Therefore we assessed whether the relation between genetic loci and T2D is modified by dietary heme iron intake. M...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00007
更新日期:2013-01-30 00:00:00
abstract::Tumorigenesis is a multi-step process, involving the acquisition of multiple oncogenic mutations that transform cells, resulting in systemic dysregulation that enables proliferation, invasion, and other cancer hallmarks. The goal of precision medicine is to identify therapeutically-actionable mutations from large-scal...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00341
更新日期:2015-12-23 00:00:00
abstract::Liver fibrosis resulting from chronic liver damage constitutes a major health care burden worldwide; however, no antifibrogenic agents are currently available. Our previous study reported that the small molecule NPLC0393 extracted from the herb Gynostemma pentaphyllum exerts efficient antifibrotic effects both in vivo...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.594824
更新日期:2020-11-04 00:00:00
abstract::Telomeres are important for maintaining genomic stability. Telomere length has been associated with aging, disease, and mortality and is highly heritable (∼82%). In this study, we aimed to identify rare genetic variants associated with telomere length using whole-exome sequence data. We studied 1,303 participants of t...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00337
更新日期:2020-04-30 00:00:00
abstract::Cellular commitment and differentiation involve highly coordinated mechanisms by which tissue-specific genes are activated while others are repressed. These mechanisms rely on the activity of specific transcription factors, chromatin remodeling enzymes, and higher-order chromatin organization in order to modulate tran...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.578712
更新日期:2020-09-18 00:00:00
abstract::Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not followi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00215
更新日期:2012-10-22 00:00:00
abstract::We evaluated differences in gene expression in pigs from the Porcine Reproductive and Respiratory Syndrome (PRRS) Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. RNA obtained ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00321
更新日期:2013-01-16 00:00:00
abstract::Global microarray gene expression analyses previously demonstrated differences in female and male embryos during neurodevelopment. In particular, before sexual maturation of the gonads, the differences seem to concentrate on the expression of genes encoded on the X- and Y-chromosomes. To investigate genome-wide differ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00891
更新日期:2019-09-24 00:00:00
abstract::RNA binding proteins (RBPs) play a key role in post-transcriptional gene regulation. They have been shown to be dysfunctional in a variety of cancers and are closely related to the occurrence and progression of cancers. However, the biological function and clinical significance of RBPs in clear cell renal carcinoma (c...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.617872
更新日期:2021-01-07 00:00:00
abstract::MicroRNAs are a class of noncoding RNAs that can be involved in the regulation of gene expression in cancers, including lung cancer. Our previous research has shown that miR-486-5p is one of the most downregulated microRNAs in tissue and serum samples of lung cancer as a good diagnostic biomarker. The objective of thi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00688
更新日期:2019-07-26 00:00:00
abstract::Background: Papillary renal cell carcinoma (PRCC), although the second-most common type of renal cell carcinoma, still lacks specific biomarkers for diagnosis, treatment, and prognosis. TopBP1-interacting checkpoint and replication regulator (TICRR) is a DNA replication initiation regulator upregulated in various canc...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.605378
更新日期:2021-01-11 00:00:00
abstract::In spite of the significant advancements in the treatment modalities, 30% of advanced stage ovarian cancer (OC) patients do not respond to the standard chemotherapeutic regimen and most of the responders finally relapse over time due to the escalation of multidrug resistance (MDR) Phenomenon. Our present study evaluat...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00516
更新日期:2020-05-26 00:00:00
abstract::Trauma is a leading cause of morbidity and mortality. It is unclear why some trauma victims follow a complicated clinical course and die, while others, with apparently similar injury characteristics, do not. Interpatient genomic differences, in the form of single nucleotide polymorphisms (SNPs), have been associated p...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01115
更新日期:2019-11-08 00:00:00
abstract::The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00004
更新日期:2014-02-12 00:00:00