检索结果-南通市图书馆

SpaGRA:Graph augmentation facilitates domain identification for spatially resolved transcriptomics

在线全文

学校读者我要写书评

暂无评论

Journal of Genetics and genomics 2025年第1期52卷 93-104页

作者： Xue Sun Wei Zhang Wenrui Li Na Yu Daoliang Zhang Qi Zou Qiongye Dong Xianglin Zhang Zhiping Liu Zhiyuan Yuan Rui Gao Center of Intelligent Medicine School of Control Science and EngineeringShandong UniversityJinanShandong 250061China MOE Key Lab of bioinformatics and bioinformatics Division of BNRIST Department of AutomationTsinghua UniversityBeijing 100084China Institute of Precision Medicine Peking University Shenzhen HospitalShenzhenGuangdong 518036China department of Clinical Laboratory The Second HospitalCheeloo College of MedicineShandong UniversityJinanShandong 250033China Institute of Science and Technology for Brain-Inspired Intelligence Center for Medical Research and InnovationShanghai Pudong HospitalFudan University Pudong Medical CenterFudan UniversityShanghai 200433China

Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various ***-based geometric deep learning has gained widespread adoption for spatial domain identification ***,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain *** tackle this challenge,we propose a novel method,SpaGRA(https://***/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph *** uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive ***,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random *** results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different *** SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD ***,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.

关键词： Spatial domain identification Spatially resolved transcriptomics Multi-head graph attention networks Graph augmentation Geometric contrastive learning

Single-cell technologies: current and near future

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Science China(Life Sciences) 2025年第1期68卷 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi KeyLaboratory of Spine and Spinal CordInjury Repairand Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchoolofLifeSciencesandTechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Key Laboratory of Advanced Theory and Application in Statistics and Data Science(MOE) School of StatisticsEast China Normal UniversityShanghai 200062China

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity,tissue organization,and overall organism function(Sun et al.,2024).In 2009,single-cell RNA sequencing(scRNA-seq)was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology,single-cell approaches have expanded to encompass other omics,such as genomics,epigenomics,proteomics,and ***,multimodal technologies including spatially resolved transcriptomics and clustered regularly interspaced short palindromic repeats(CRISPR)screening at the single-cell level further advanced our ability to comprehensively understand cellular ***-cell methods provide deeper insights into disease mechanisms across various conditions,including cancer,developmental disorders,and aging-associated *** this issue,we focus on topics related to single-cell methods,covering the following four aspects:(i)single-cell multi-omic sequencing technology;(ii)single-cell spatial technology;(iii)singlecell CRISPR screening technology;(iv)applications of single-cell technology.

关键词： expanded enable insight

同方期刊数据库

Impact of Seed Halopriming on Germination,Morphological Traits,and Cry1Ac Gene Expression in Bt Cotton(Gossypium hirsutum)

在线全文

学校读者我要写书评

暂无评论

Phyton-International Journal of Experimental Botany 2025年第1期94卷 229-241页

作者： Wenqi Shi Binyameen Bin Shafqat Muhammad Arif Ayesha Fazal Nawaz Muhammad Amir Zia Xu Ling Dingli Hong Ruhong Xu Luhua Li College of Agriculture Guizhou UniversityGuiyang550025China Faculty of Medicine and Health Technology Tampere UniversityTampere33720Finland department of Life Sciences University of TriesteVia Licio Giorgieri 5Trieste34127Italy National Institute for genomics and Advanced Biotechnology(NIGAB) National Agricultural Research Centre(NARC)Islamabad45500Pakistan

Seed priming is an effective seed pretreatment technology that enhances germination and overall crop performance by optimizing seed hydration and metabolic processes before *** quality is a critical determinant of cotton(Gossypium hirsutum)crop performance,influencing germination,plant vigor,and *** study evaluates the effects of seed priming with potassium salts(1%and 2%KCl and K2SO4)on germination,morphological traits,and Cry1Ac gene expression in three Bt cotton cultivars(IUB-2013,NIAB-878B,FH-142)as Cry1Ac enhance the pest resistance in Bt cotton and reduce the plant’s dependence on chemical *** were primed for six hours,air-dried,and sown in the *** rates,plant height,number of bolls per plant,boll weight,seed cotton yield,and ginning outturn(GOT)were assessed at crop ***1Ac gene expression was quantified to explore the influence of priming treatments on transgene *** demonstrated that 1%K2SO4 priming significantly enhanced germination and yield-related traits,with Cry1Ac expression peaking in the IUB-2013 cultivar under 1%K2SO4 *** findings suggest that potassium-based halopriming improves cotton seedling establishment and Bt gene *** study addresses the critical gaps in understanding the effects of seed halopriming on morphological traits,germination,and expression of the Cry1Ac gene in Bt cotton while providing a novel eco-friendly and cost-effective halopriming approach,offering the potential to improve cotton production.

关键词： Cotton seed priming halopriming Cry1Ac Bt cotton germination yield traits

Structure-Based Prediction of Transcription Factor Binding Sites

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Tsinghua Science and Technology 2014年第6期19卷 568-577页

作者： Jun-tao Guo Shane Lofgren Alvin Farrel department of bioinformatics and genomics University of North Carolina at Charlotte Charlotte NC 28223 USA

Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many *** of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.

关键词： transcription factor binding site structure-based predictions knowledge-based potential physics-based potential

Natural variants and editing events provide insights into routes for spike architecture modification in common wheat

在线全文

学校读者我要写书评

暂无评论

The crop Journal 2023年第1期11卷 148-156页

作者： Min Fan Xiaoyu Zhang Ragupathi Nagarajan Wenxuan Zhai Yahya Rauf Haiyan Jia Zhengqiang Ma Liuling Yan crop genomics and bioinformatics Center and National Key Laboratory of crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityJiangsuNanjing 210095JiangsuChina department of Plant and Soil Sciences Oklahoma State UniversityStillwaterOK 74078USA

Spike architecture is an indicative trait of grain yield in common wheat(Triticum aestivum).A segregating population was generated for mapping genes contributing to spike morphometric traits by crossing the two common wheat cultivars'CItr 17600'with branching spikes and'Yangmai 18'with normal spikes.A major quantitative trait locus for spike length was mapped to the Q5A region of chromosome ***18 carried a Q5Ab allele for short spikes,which harbored one SNP in the last intron,and a 1-bp InDel in the 720-bp fragment from the start codon,compared to Q5Aa in Chinese *** 17600 harbored a q5Ab allele for long spikes,which has a 6-bp deletion compared to the reported q5Aa allele that was involved in the binding site of microRNA 172(miR172).This 6-bp deletion in immediately upstream of this binding site was involved in changes of four amino *** natural q5A allele appeared to be rare in common wheat but frequent in tetraploid *** accessions with branching *** CRISPR/Cas9 technology was used to edit the upstream region involving in the miR172 binding site in Yangmai 18 and identified two independent editing events,one with a 1-bp insertion in Q5A and the other with a 2-bp deletion in Q5D,resulting in several shapes of spikes in the transgenic *** addition to the effects of natural q5A allele and the edited Q5A genes,this study indicated the regeneratability and transformability of Yangmai 18 as an elite ***,this study provides insight into future modification and engineering of spike architecture in common wheat.

关键词： Q gene Spike shape miR172 Gene editing Wheat

A haplotype block associated with thousand-kernel weight on chromosome 5DS in common wheat(Triticum aestivum L.)

在线全文

学校读者我要写书评

暂无评论

Journal of Integrative Plant Biology 2015年第8期57卷 662-672页

作者： Yuquan Wang Chenyang Hao Jun Zheng Hongmei Ge Yang Zhou Zhengqiang Ma Xueyong Zhang crop genomics and bioinformatics Center and National Key Lab of crop Genetics and Germplasm Enhancement College of Agricultural SciencesNanjing Agricultural University Key Laboratory of crop Gene Resources and Germplasm Enhancement Ministry of Agriculture/Institute of Crop Science the Chinese Academy of Agricultural Sciences

Spike number per unit area, number of grains per spike, and thousand-kernel weight（TKW） are important yield components for wheat（Triticum aestivum L.）. TKW has the highest heritability among the three components. We validated 27 simple sequence repeat（SSR） loci associated with TKW in an F2：5breeding population grown in four environments. A cfd78265 bpmarker on chromosome 5DS showed the strongest association with TKW and had a significantly positive effect on TKW compared to allele cfd78259 bp, with mean increases of 5.17, 3.63, 4.11, and 5.16 g in the four environments. Markers cfd67 and cfd40 flanking cfd78 also showed significantly positive associations with TKW with increases of 5.11, 3.29, 4.31, and 4.50 g for cfd67205, and4.98, 3.49, 4.06, and 4.84 g for cfd40187 compared with cfd67203 and cfd40190in the four environments, respectively. A major quantitative trait locus for TKW spanning 2.94 c M on chromosome 5DS was detected by association *** linkage disequilibrium（LD）（r2〉 0.2） was detected Resear among the three linked markers, which formed three haplotype blocks in the F2：5breeding population. Mean TKW differences between Hap B-I and Hap B-II were 5.80, 4.41, 4.02,and 5.06 g in the four environments, respectively. Moreover,significant LD was detected only between cfd78 and cfd67 and between cfd67 and cfd40 in a germplasm collection. This study provides a base for cloning genes related to TKW on chromosome 5DS.

关键词： Association mapping haplotype thousand-kernel weight Triticum oestivum

Identification and fine mapping of PmNJ3946 for powdery mildew resistance in einkorn wheat

在线全文

学校读者我要写书评

暂无评论

The crop Journal 2023年第6期11卷 1846-1851页

作者： Peisi Wang Jun Huang Na Li Jie Zhang Caimei Gu Yang Yuan Ziruo Wen Haiyan Jia Zhongxin Kong Zhengqiang Ma crop genomics and bioinformatics Center and National Key Laboratory of crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095JiangsuChina Zhongshan Biological Breeding Laboratory Nanjing 210014JiangsuChina

Powdery mildew caused by Blumeria graminis ***(Bgt)is a destructive wheat *** it can be easily overcome by deployment of resistance genes,the resistance is often quickly compromised by pathogen ***,exploration and characterization of new resistance genes is always *** NJ3946 derived from a cross of einkorn wheat accessions TA2032 and M389 showed resistance to powdery *** analysis of an F2 population derived from a cross of NJ3946 and M389 suggested that the resistance was conferred by a dominant *** polymorphic markers identified through bulked segregant analysis(BSA),this gene was mapped to a novel locus on chromosome 3A,and was designated as *** segregant RNA-seq analysis(BSR-seq)was conducted to obtain more closely linked markers,which allowed delimitation of the PMNJ3946 locus to a 0.9 cM interval covering a physical distance of less than 1 ***3946 was flanked by Xwgrc5153 and SNP-derived marker CHS21_3A008915069,and co-segregated with SNP-derived markers CHS21_3A008939814 and CHS21_*** PmNJ3946 discovery expands the diversity of powdery mildew resistance genes and is useful for wheat breeding.

关键词： Powdery mildew Disease resistance Genetic mapping Triticum monococcum PmNJ3946

Methods for Population-Based eQTL Analysis in Human Genetics

在线全文

学校读者我要写书评

暂无评论

Tsinghua Science and Technology 2014年第6期19卷 624-634页

作者： Lu Tian Andrew Quitadamo Frederick Lin Xinghua Shi department of bioinformatics and genomics College of Computing and Informatics University of North Carolina at Charlotte NC 28223 USA

Gene expression is a critical process in biological system that is influenced and modulated by many factors including genetic variation. Expression Quantitative Trait Loci（e QTL） analysis provides a powerful way to understand how genetic variants affect gene expression. For genome wide e QTL analysis, the number of genetic variants and that of genes are large and thus the search space is tremendous. Therefore, e QTL analysis brings about computational and statistical challenges. In this paper, we provide a comprehensive review of recent advances in methods for e QTL analysis in population-based studies. We first present traditional pairwise association methods, which are widely used in human genetics. To account for expression heterogeneity, we investigate the methods for correcting confounding factors. Next, we discuss newly developed statistical learning methods including Lasso-based models. In the conclusion, we provide an overview of future method development in analyzing e QTL associations. Although we focus on human genetics in this review, the methods are applicable to many other organisms.

关键词： expression Quantitative Trait Loci(e QTL) analysis confounding factors sparse learning models Lasso

The evolutionarily diverged single-stranded DNA-binding proteins SSB1/SSB2 differentially affect the replication,recombination and mutation of organellar genomes in Arabidopsis thaliana

在线全文

学校读者我要写书评

暂无评论

Plant Diversity 2025年第1期47卷 127-135页

作者： Weidong Zhu Jie Qian Yingke Hou Luke R.Tembrock Liyun Nie Yi-Feng Hsu Yong Xiang Yi Zou Zhiqiang Wu Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Guangdong Laboratory for Lingnan Modern Agriculture College of Life SciencesSouth China Agricultural UniversityGuangzhou 510642China School of Life Sciences Southwest UniversityChongqing 400715China department of Biology Colorado State UniversityFort CollinsCO 80523USA School of Medical Molecular and Forensic SciencesMurdoch UniversityMurdochWA 6149Australia State Key Laboratory of crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Shenzhen Research Institute of Henan University Shenzhen 518000China

Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA *** Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still *** this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed *** on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both *** findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.

关键词： SSB Organellar genomes Replication Recombination Mutation