Genome Biology最新文献_第5页

Genomics will forever reshape forensic science and criminal justice 基因组学将永远重塑法医科学和刑事司法

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03798-x

Bruce Budowle, Kristen Mittelman, David Mittelman

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KEGNI: knowledge graph enhanced framework for gene regulatory network inference KEGNI：基因调控网络推理的知识图谱增强框架

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03780-7

Pengxiao Li, Lin Li, Jingminjie Nan, Jiahuan Chen, Jielin Sun, Yanan Cao

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Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning 利用深度学习技术破解植物基因组转录起始调控的序列基础及应用

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03782-5

Pengfei Gao, Lijie Lian, Wanjie Feng, Yuxue Ma, Jieni Lin, Liya Qin, Shanmeng Hao, Haonan Zhao, Xuantong Liu, Jing Yuan, Zongcheng Lin, Xia Li, Yuefeng Guan, Xutong Wang

{"title":"Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning","authors":"Pengfei Gao, Lijie Lian, Wanjie Feng, Yuxue Ma, Jieni Lin, Liya Qin, Shanmeng Hao, Haonan Zhao, Xuantong Liu, Jing Yuan, Zongcheng Lin, Xia Li, Yuefeng Guan, Xutong Wang","doi":"10.1186/s13059-025-03782-5","DOIUrl":"https://doi.org/10.1186/s13059-025-03782-5","url":null,"abstract":"Transcription initiation is a key checkpoint in plant gene regulation, yet the DNA features that determine where and the frequency of the genes start transcription remain unclear. We develop GenoRetriever, an interpretable deep learning model trained on base pair resolution STRIPE-seq data from multiple crop genomes, to systematically reveal and quantify the sequence code that governs transcription start sites (TSSs). Using TSS profiles from 16 soybean tissues and six additional crops, GenoRetriever identifies 27 core promoter motifs, including canonical TATA box and initiator elements, that together dictate TSS choice and activity. Model interpretation shows how each motif modulates both initiation frequency and precise start site position; these effects are confirmed by in silico motif edits, saturation mutagenesis, and targeted promoter assays. A new telomere-to-telomere assembly of wild soybean, Glycine soja, reveals that 31.85% of natural promoter variants shift dominant motifs relative to cultivated soybean, explaining domestication-driven changes in transcriptional regulation. Cross-species comparisons further indicate that, although many motif functions are conserved, monocots and dicots display distinct motif frequencies and positional preferences. GenoRetriever provides an interpretable, cross species framework for decoding transcription initiation in plants. By linking specific sequence motifs to quantitative transcriptional outcomes and validating these links experimentally, our study advances fundamental knowledge of promoter architecture and supplies a practical platform for rational engineering of gene expression in crop improvement and functional genomics.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"32 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MHCquant2 refines immunopeptidomics tumor antigen discovery MHCquant2改进免疫肽组学肿瘤抗原发现

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03763-8

Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann, Lennart Martens, Marissa L. Dubbelaar, Sven Nahnsen, Juliane S. Walz

引用次数: 0

Regulation of heterosis-associated gene expression complementation in maize hybrids 玉米杂种优势相关基因表达互补的调控

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03768-3

Marion Pitz, Jutta A. Baldauf, Hans-Peter Piepho, Peng Yu, Heiko Schoof, Annaliese S. Mason, Guoliang Li, Frank Hochholdinger

{"title":"Regulation of heterosis-associated gene expression complementation in maize hybrids","authors":"Marion Pitz, Jutta A. Baldauf, Hans-Peter Piepho, Peng Yu, Heiko Schoof, Annaliese S. Mason, Guoliang Li, Frank Hochholdinger","doi":"10.1186/s13059-025-03768-3","DOIUrl":"https://doi.org/10.1186/s13059-025-03768-3","url":null,"abstract":"Classical genetic concepts to explain heterosis attribute the superiority of F1-hybrids over their homozygous parents to the complementation of unfavorable by beneficial alleles (dominance) or to heterozygote advantage (overdominance). Here we analyze 112 intermated B73xMo17 recombinant inbred lines of maize and their backcrosses to their original parents B73 and Mo17 to obtain hybrids with an average heterozygosity of ~ 50%. This genetic architecture allows studying the influence of homozygous and heterozygous genomic regions on gene expression in hybrids. We demonstrate that single parent expression (SPE) complementation explains between − 8% and 29% of the mid-parent heterotic variance in these hybrids. In this expression pattern, consistent with dominance, genes are active in only one parent and in the hybrid, thus increasing the number of expressed genes in hybrids. Furthermore, we establish that eQTL regulating SPE genes are predominantly located in heterozygous regions of the genome. Finally, we identify an SPE gene that regulates lateral root density in hybrids. Remarkably, the activity of this gene depends on the presence of a Mo17 allele in an eQTL that regulates this gene. Here we show that dominance of SPE genes influences the number of active genes in hybrids, while heterozygosity is instrumental for the regulation of these genes. This finding supports the notion that the genetic constitution of distant regulatory elements is instrumental for the activity of heterosis-associated genes. In summary, our results connect genetic variation at regulatory loci and the degree of heterozygosity with phenotypic variation of heterosis via SPE complementation.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"195 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis SIGEL：用于空间基因组分析的上下文感知基因组表示学习框架

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03748-7

Wenlin Li, Maocheng Zhu, Yucheng Xu, Mengqian Huang, Ziyi Wang, Jing Chen, Hao Wu, Xiaobo Sun

引用次数: 0

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data 从全基因组长读测序数据估计端粒长度的方法

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03783-4

Linh Nguyen, Jae Young Choi

引用次数: 0

GeneRAIN: multifaceted representation of genes via deep learning of gene expression networks GeneRAIN：通过基因表达网络的深度学习实现基因的多面表示

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03749-6

Zheng Su, Mingyan Fang, Andrei Smolnikov, Marcel E. Dinger, Emily C. Oates, Fatemeh Vafaee

引用次数: 0

ScIsoX: a multidimensional framework for measuring isoform-level transcriptomic complexity in single cells ScIsoX：测量单细胞中同种异构体水平转录组复杂性的多维框架

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-22 DOI: 10.1186/s13059-025-03758-5

Siyuan Wu, Ulf Schmitz

引用次数: 0

Systematic benchmarking of computational methods to identify spatially variable genes 系统的基准计算方法，以确定空间可变的基因

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-18 DOI: 10.1186/s13059-025-03731-2

Zhijian Li, Zain M.Patel, Dongyuan Song, Sai Nirmayi Yasa, Robrecht Cannoodt, Guanao Yan, Jingyi Jessica Li, Luca Pinello

{"title":"Systematic benchmarking of computational methods to identify spatially variable genes","authors":"Zhijian Li, Zain M.Patel, Dongyuan Song, Sai Nirmayi Yasa, Robrecht Cannoodt, Guanao Yan, Jingyi Jessica Li, Luca Pinello","doi":"10.1186/s13059-025-03731-2","DOIUrl":"https://doi.org/10.1186/s13059-025-03731-2","url":null,"abstract":"Spatially resolved transcriptomics offers unprecedented insight by enabling the profiling of gene expression within the intact spatial context of cells, effectively adding a new and essential dimension to data interpretation. To efficiently detect spatial structure of interest, an essential step in analyzing such data involves identifying spatially variable genes (SVGs). Despite researchers having developed several computational methods to accomplish this task, the lack of a comprehensive benchmark evaluating their performance remains a considerable gap in the field. Here, we systematically evaluate 14 methods using 96 spatial datasets and 6 metrics. We compare the methods regarding gene ranking and classification based on real spatial variation, statistical calibration, and computation scalability and investigate the impact of identified SVGs on downstream applications such as spatial domain detection. Finally, we explore the applicability of the methods to spatial ATAC-seq data to examine their effectiveness in identifying spatially variable peaks (SVPs). Overall, SPARK-X outperforms other benchmarked methods and Moran’s I achieves a competitive performance, representing a strong baseline for future method development. Moreover, our results reveal that most methods are poorly calibrated, and more specialized algorithms are needed to identify spatially variable peaks. Our benchmarking provides a detailed comparison of SVG detection methods and serves as a reference for both users and method developers.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"18 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145077421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0