journal
https://read.qxmd.com/read/38770419/cd-loop-a-chromatin-loop-detection-method-based-on-the-diffusion-model
#21
JOURNAL ARTICLE
Jiquan Shen, Yang Wang, Junwei Luo
MOTIVATION: In recent years, there have been significant advances in various chromatin conformation capture techniques, and annotating the topological structure from Hi-C contact maps has become crucial for studying the three-dimensional structure of chromosomes. However, the structure and function of chromatin loops are highly dynamic and diverse, influenced by multiple factors. Therefore, obtaining the three-dimensional structure of the genome remains a challenging task. Among many chromatin loop prediction methods, it is difficult to fully extract features from the contact map and make accurate predictions at low sequencing depths...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38770418/mifam-dti-a-drug-target-interactions-predicting-model-based-on-multi-source-information-fusion-and-attention-mechanism
#22
JOURNAL ARTICLE
Jianwei Li, Lianwei Sun, Lingbo Liu, Ziyu Li
Accurate identification of potential drug-target pairs is a crucial step in drug development and drug repositioning, which is characterized by the ability of the drug to bind to and modulate the activity of the target molecule, resulting in the desired therapeutic effect. As machine learning and deep learning technologies advance, an increasing number of models are being engaged for the prediction of drug-target interactions. However, there is still a great challenge to improve the accuracy and efficiency of predicting...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38770417/causal-associations-of-birth-body-size-and-adult-body-size-with-systemic-lupus-erythematosus-a-bidirectional-mendelian-randomization-study
#23
JOURNAL ARTICLE
Juan Peng, Huizi Wang, Yanjuan Li, Xudong Dong
OBJECTIVE: Body size is associated with the onset of systemic lupus erythematosus (SLE). However, the evidence for this association is inconclusive. In this study, we aimed to investigate the causal relationship between body size and SLE. METHOD: We performed a bidirectional Mendelian randomization (MR) analysis that utilized summary statistics sourced from genome-wide association study (GWAS) data obtained from the IEU Open GWAS project website. The inverse variance weighting (IVW) method was used to evaluate the causality, and four additional MR methods were used to supplement the IVW results...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38764599/corrigendum-expression-profiling-of-alog-family-genes-during-inflorescence-development-and-abiotic-stress-responses-in-rice-oryza-sativa-l
#24
Zhiyuan Liu, Zhenjiang Fan, Lei Wang, Siyue Zhang, Weichen Xu, Sijie Zhao, Sijia Fang, Mei Liu, Sackitey Mark Kofi, Shuangxi Zhang, Ningning Kang, Hao Ai, Ruining Li, Tingting Feng, Shuya Wei, Heming Zhao
[This corrects the article DOI: 10.3389/fgene.2024.1381690.].
2024: Frontiers in Genetics
https://read.qxmd.com/read/38756451/association-between-migraine-and-venous-thromboembolism-a-mendelian-randomization-and-genetic-correlation-study
#25
JOURNAL ARTICLE
Xu-Peng Wu, Peng-Peng Niu, Hong Liu
OBJECTIVE: Previous observational studies have reported an increased risk of venous thromboembolism (VTE) among individuals with migraine. This study aimed to investigate the causal effect of migraine on the development of VTE, as well as explore the genetic correlation between them. METHODS: We conducted a two-sample Mendelian randomization (MR) study using publicly available summary statistics from large-scale genome-wide association studies for migraine and VTE...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38756450/associations-of-dietary-factors-with-gastric-cancer-risk-insights-from-nhanes-2003-2016-and-mendelian-randomization-analyses
#26
JOURNAL ARTICLE
Yigang Zhang, Sen Wang, Qingya Li, Hongda Liu, Zhe Xuan, Fengyuan Li, Zheng Li, Yiwen Xia, Tianlu Jiang, Penghui Xu, Lang Fang, Linjun Wang, Diancai Zhang, Hao Xu, Li Yang, Zekuan Xu
Background: Gastric cancer (GC) continues to be one of the leading causes of cancer-related deaths globally. Diet significantly influences the incidence and progression of GC. However, the relationship between dietary intake and GC is inconsistent. Methods: A study was conducted with adults who participated in the National Health and Nutrition Examination Survey (NHANES) from 2003 to 2016 to investigate possible associations between 32 dietary factors and GC. To further detect potential causal relationships between these dietary factors and the risk of GC, a two-sample Mendelian randomization (MR) analysis was conducted...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38756449/association-analysis-between-acetyl-coenzyme-a-acyltransferase-1-gene-polymorphism-and-growth-traits-in-xiangsu-pigs
#27
JOURNAL ARTICLE
Meimei Xiao, Yong Ruan, Jiajin Huang, Lingang Dai, Jiali Xu, Houqiang Xu
INTRODUCTION: Acetyl-Coenzyme A Acyltransferase-1 ( ACAA1 ) is a peroxisomal acyltransferase involved in fatty acid metabolism. Current evidence does not precisely reveal the effect of the ACAA1 gene on pig growth performance. METHODS: The present study assessed the mRNA expression levels of the ACAA1 gene in the heart, liver, spleen, lung, kidney of 6-month-old Xiangsu pigs and in the longissimus dorsi muscle at different growth stages (newborn, 6 months and 12 months of age) using RT-qPCR...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38756448/a-leading-edge-scenario-in-the-phylogeography-and-evolutionary-history-of-east-asian-insular-taxus-in-taiwan-and-the-philippines
#28
JOURNAL ARTICLE
Hao-Chih Kuo, Travis Schoneman, Lian-Ming Gao, William Sm Gruezo, Victor B Amoroso, Yang Yang, Kuo-Cheng Yang, Ching-Te Chien, Michael Möller, Chun-Neng Wang
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii , have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38756447/deciphering-the-role-of-apoptosis-signature-on-the-immune-dynamics-and-therapeutic-prognosis-in-breast-cancer-implication-for-immunotherapy
#29
JOURNAL ARTICLE
Yunfang Yu, Xueyuan Jia, Sunyu Chen, Zijia Lai, Heran Deng, Yuqian Mo, Xinxin Xie, Zehua Wang, Ruichong Lin, Wenhao Ouyang, Herui Yao, Jiannan Wu
Background: In breast cancer oncogenesis, the precise role of cell apoptosis holds untapped potential for prognostic and therapeutic insights. Thus, it is important to develop a model predicated for breast cancer patients' prognosis and immunotherapy response based on apoptosis-related signature. Methods: Our approach involved leveraging a training dataset from The Cancer Genome Atlas (TCGA) to construct an apoptosis-related gene prognostic model. The model's validity was then tested across several cohorts, including METABRIC, Sun Yat-sen Memorial Hospital Sun Yat-sen University (SYSMH), and IMvigor210, to ensure its applicability and robustness across different patient demographics and treatment scenarios...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38752183/editorial-application-of-genomics-and-epigenetics-in-disease-and-syndrome-classification
#30
EDITORIAL
Yanqi Dang, Wei Wang, Aiping Lyu, Lisheng Wang, Guang Ji
No abstract text is available yet for this article.
2024: Frontiers in Genetics
https://read.qxmd.com/read/38746057/in-search-of-the-ratio-of-mirna-expression-as-robust-biomarkers-for-constructing-stable-diagnostic-models-among-multi-center-data
#31
JOURNAL ARTICLE
Cuidie Ma, Yonghao Zhang, Rui Ding, Han Chen, Xudong Wu, Lida Xu, Changyuan Yu
MicroRNAs (miRNAs) are promising biomarkers for the early detection of disease, and many miRNA-based diagnostic models have been constructed to distinguish patients and healthy individuals. To thoroughly utilize the miRNA-profiling data across different sequencing platforms or multiple centers, the models accounting the batch effects were demanded for the generalization of medical application. We conducted transcription factor (TF)-mediated miRNA-miRNA interaction network analysis and adopted the within-sample expression ratios of miRNA pairs as predictive markers...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38746056/characterization-biogenesis-model-and-current-bioinformatics-of-human-extrachromosomal-circular-dna
#32
Lina Zhou, Wenyi Tang, Bo Ye, Lingyun Zou
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38746055/exploring-the-evolution-of-chs-gene-family-in-plants
#33
JOURNAL ARTICLE
Li Yang, Shuai Zhang, Dake Chu, Xumei Wang
Chalcone synthase ( CHS ) is a key enzyme that catalyzes the first committed step of flavonoid biosynthetic pathway. It plays a vital role not only in maintaining plant growth and development, but also in regulating plant response to environmental hazards. However, the systematic phylogenomic analysis of CHS gene family in a wide range of plant species has not been reported yet. To fill this knowledge gap, a large-scale investigation of CHS genes was performed in 178 plant species covering green algae to dicotyledons...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38746054/analysis-of-immunogenetics-interlaboratory-comparisons-success-rates-external-quality-assurance-system-of-the-spanish-society-for-immunology-geclid-sei
#34
JOURNAL ARTICLE
M Carmen Martín
BACKGROUND: For many years, transplantation outcomes were uncertain and not hopeful, until histocompatibility testing spread. Common criteria for histocompatibility assays and communications' improvement allowed an efficient organ sharing system. The possibility of organ exchanges is closely linked to the importance of interlaboratory comparisons for histocompatibility and immunogenetics methods. The external proficiency testing (EPT) systems are the most powerful quality assurance tools...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38742167/transcriptome-analysis-revealed-potential-mechanisms-of-channel-catfish-growth-advantage-over-blue-catfish-in-a-tank-culture-environment
#35
JOURNAL ARTICLE
Haolong Wang, Baofeng Su, Ying Zhang, Mei Shang, Jinhai Wang, Andrew Johnson, Hamza Dilawar, Timothy J Bruce, Rex A Dunham, Xu Wang
Channel catfish ( Ictalurus punctatus ) and blue catfish ( Ictalurus furcatus ) are two economically important freshwater aquaculture species in the United States, with channel catfish contributing to nearly half of the country's aquaculture production. While differences in economic traits such as growth rate and disease resistance have been noted, the extent of transcriptomic variance across various tissues between these species remains largely unexplored. The hybridization of female channel catfish with male blue catfish has led to the development of superior hybrid catfish breeds that exhibit enhanced growth rates and improved disease resistance, which dominate more than half of the total US catfish production...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38742166/corrigendum-novel-foxl2-variants-in-two-chinese-families-with-blepharophimosis-ptosis-and-epicanthus-inversus-syndrome
#36
Mingyu Zhao, Xiaolu Meng, Jiaqi Wang, Tailing Wang
[This corrects the article DOI: 10.3389/fgene.2024.1343411.].
2024: Frontiers in Genetics
https://read.qxmd.com/read/38737126/genomic-prediction-based-on-a-joint-reference-population-for-the-xinjiang-brown-cattle
#37
JOURNAL ARTICLE
Menghua Zhang, Lei Xu, Haibo Lu, Hanpeng Luo, Jinghang Zhou, Dan Wang, Xiaoxue Zhang, Xixia Huang, Yachun Wang
Introduction: Xinjiang Brown cattle constitute the largest breed of cattle in Xinjiang. Therefore, it is crucial to establish a genomic evaluation system, especially for those with low levels of breed improvement. Methods: This study aimed to establish a cross breed joint reference population by analyzing the genetic structure of 485 Xinjiang Brown cattle and 2,633 Chinese Holstein cattle (Illumina GeneSeek GGP bovine 150 K chip). The Bayes method single-step genome-wide best linear unbiased prediction was used to conduct a genomic evaluation of the joint reference population for the milk traits of Xinjiang Brown cattle...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38737125/predict-lncrna-drug-associations-based-on-graph-neural-network
#38
JOURNAL ARTICLE
Peng Xu, Chuchu Li, Jiaqi Yuan, Zhenshen Bao, Wenbin Liu
LncRNAs are an essential type of non-coding RNAs, which have been reported to be involved in various human pathological conditions. Increasing evidence suggests that drugs can regulate lncRNAs expression, which makes it possible to develop lncRNAs as therapeutic targets. Thus, developing in-silico methods to predict lncRNA-drug associations (LDAs) is a critical step for developing lncRNA-based therapies. In this study, we predict LDAs by using graph convolutional networks (GCN) and graph attention networks (GAT) based on lncRNA and drug similarity networks...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38737124/editorial-ehlers-danlos-syndrome-from-bedside-to-bench
#39
EDITORIAL
Tomoki Kosho, Shujiro Hayashi, Ken-Ichi Matsumoto, Delfien Syx, Anupriya Kaur
No abstract text is available yet for this article.
2024: Frontiers in Genetics
https://read.qxmd.com/read/38725485/bayesian-hidden-mark-interaction-model-for-detecting-spatially-variable-genes-in-imaging-based-spatially-resolved-transcriptomics-data
#40
JOURNAL ARTICLE
Jie Yang, Xi Jiang, Kevin Wang Jin, Sunyoung Shin, Qiwei Li
Recent technology breakthroughs in spatially resolved transcriptomics (SRT) have enabled the comprehensive molecular characterization of cells whilst preserving their spatial and gene expression contexts. One of the fundamental questions in analyzing SRT data is the identification of spatially variable genes whose expressions display spatially correlated patterns. Existing approaches are built upon either the Gaussian process-based model, which relies on ad hoc kernels, or the energy-based Ising model, which requires gene expression to be measured on a lattice grid...
2024: Frontiers in Genetics
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