GigaScience最新文献

{"title":"Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing.","authors":"Jingmin Kang, Qingsong Li, Jie Liu, Lin Du, Peng Liu, Fuyan Liu, Yue Wang, Xunan Shen, Xujiao Luo, Ninghe Wang, Renhua Wu, Lei Song, Jizheng Wang, Xin Liu","doi":"10.1093/gigascience/giaf012","DOIUrl":"10.1093/gigascience/giaf012","url":null,"abstract":"<p><strong>Background: </strong>Spatial transcriptomics is a powerful tool that integrates molecular data with spatial information, thereby facilitating a deeper comprehension of tissue morphology and cellular interactions. In our study, we utilized cutting-edge spatial transcriptome sequencing technology to explore the development of the mouse heart and construct a comprehensive spatiotemporal cell atlas of early murine cardiac development.</p><p><strong>Results: </strong>Through the analysis of this atlas, we elucidated the spatial organization of cardiac cellular lineages and their interactions during the developmental process. Notably, we observed dynamic changes in gene expression within fibroblasts and cardiomyocytes. Moreover, we identified critical genes, such as Igf2, H19, and Tcap, as well as transcription factors Tcf12 and Plagl1, which may be associated with the loss of myocardial regeneration ability during early heart development. In addition, we successfully identified marker genes, like Adamts8 and Bmp10, that can distinguish between the left and right atria.</p><p><strong>Conclusion: </strong>Our study provides novel insights into murine cardiac development and offers a valuable resource for future investigations in the field of heart research, highlighting the significance of spatial transcriptomics in understanding the complex processes of organ development.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11831923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"xRead: a coverage-guided approach for scalable construction of read overlapping graph.","authors":"Tangchao Kong, Yadong Wang, Bo Liu","doi":"10.1093/gigascience/giaf007","DOIUrl":"10.1093/gigascience/giaf007","url":null,"abstract":"<p><strong>Background: </strong>The development of long-read sequencing is promising for the high-quality and comprehensive de novo assembly for various species around the world. However, it is still challenging for assemblers to handle thousands of genomes, tens of gigabase-level assembly sizes, and terabase-level datasets efficiently, which is a bottleneck to large-scale de novo sequencing studies. A major cause is the read overlapping graph construction that state-of-the-art tools usually have to cost terabyte-level RAM space and tens of days for large genomes. Such lower performance and scalability are not suited to handle the numerous samples being sequenced.</p><p><strong>Findings: </strong>Herein, we propose xRead, a novel iterative overlapping graph construction approach that achieves high performance, scalability, and yield simultaneously. Under the guidance of its coverage-based model, xRead converts read-overlapping to heuristic read-mapping and incremental graph construction tasks with highly controllable RAM space and faster speed. It enables the processing of very large datasets (such as the 1.28 Tb Ambystoma mexicanum dataset) with less than 64 GB RAM and obviously lower time costs. Moreover, benchmarks suggest that it can produce highly accurate and well-connected overlapping graphs, which are also supportive of various kinds of downstream assembly strategies.</p><p><strong>Conclusions: </strong>xRead is able to break through the major bottleneck to graph construction and lays a new foundation for de novo assembly. This tool is suited to handle a large number of datasets from large genomes and may play important roles in many de novo sequencing studies.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11831799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses.","authors":"Yanshuo Liang, Kuidong Xu, Junyuan Li, Jingyuan Shi, Jiehong Wei, Xiaoyu Zheng, Wanying He, Xin Zhang","doi":"10.1093/gigascience/giaf031","DOIUrl":"10.1093/gigascience/giaf031","url":null,"abstract":"<p><p>The ability of octocorals and stony corals to deposit calcium carbonate (CaCO3) has contributed to their ecological success. Whereas stony corals possess a homogeneous aragonite skeleton, octocorals have developed distinct skeletal structures composed of different CaCO3 polymorphs and a skeletal organic matrix. Nevertheless, the molecular basis of skeletal structure formation in octocorals remains inadequately understood. Here, we sequenced the genomes and skeletal proteomes of two calcite-forming octocorals, namely Paragorgia papillata and Chrysogorgia sp. The assembled genomes sizes were 618.13 Mb and 781.04 Mb for P. papillata and Chrysogorgia sp., respectively, with contig N50s of 2.67 Mb and 2.61 Mb. Comparative genomic analyses identified 162 and 285 significantly expanded gene families in the genomes of P. papillata and Chrysogorgia sp., respectively, which are primarily associated with biomineralization and immune response. Furthermore, comparative analyses of skeletal proteomes demonstrated that corals with different CaCO3 polymorphs share a fundamental toolkit comprising cadherin, von Willebrand factor type A, and carbonic anhydrase domains for calcified skeleton deposition. In contrast, collagen is abundant in the calcite-forming octocoral skeletons but occurs rarely in aragonitic stony corals. Additionally, certain collagens have developed domains related to matrix adhesion and immunity, which may confer novel genetic functions in octocoral calcification. These findings enhance our understanding of the diverse forms of coral biomineralization processes and offer preliminary insights into the formation and evolution of the octocoral skeleton.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation.","authors":"Chun Liu, Jianyu Zhang, Ranran Xu, Jinhui Lv, Zhu Qiao, Mingzhou Bai, Shancen Zhao, Lijuan Luo, Guodao Liu, Pandao Liu","doi":"10.1093/gigascience/giae118","DOIUrl":"10.1093/gigascience/giae118","url":null,"abstract":"<p><strong>Background: </strong>Drought is a major limiting factor for plant survival and crop productivity. Stylosanthes angustifolia, a pioneer plant, exhibits remarkable drought tolerance, yet the molecular mechanisms driving its drought resistance remain largely unexplored.</p><p><strong>Results: </strong>We present a chromosome-scale reference genome of S. angustifolia, which provides insights into its genome evolution and drought tolerance mechanisms. The assembled genome is 645.88 Mb in size, containing 319.98 Mb of repetitive sequences and 36,857 protein-coding genes. The high quality of this genome assembly is demonstrated by the presence of 99.26% BUSCO and a 19.49 long terminal repeat assembly index. Evolutionary analyses revealed that S. angustifolia shares a whole-genome duplication (WGD) event with other legumes but lacks recent WGD. Additionally, S. angustifolia has undergone gene expansion through tandem duplication approximately 12.31 million years ago. Through integrative multiomics analyses, we identified 4 gene families-namely, xanthoxin dehydrogenase, 2-hydroxyisoflavanone dehydratase, patatin-related phospholipase A, and stachyose synthetase-that underwent tandem duplication and were significantly upregulated under drought stress. These gene families contribute to the biosynthesis of abscisic acid, genistein, daidzein, jasmonic acid, and stachyose, thereby enhancing drought tolerance.</p><p><strong>Conclusions: </strong>The genome assembly of S. angustifolia represents a significant advancement in understanding the genetic mechanisms underlying drought tolerance in this pioneer plant species. This genomic resource provides critical insights into the evolution of drought resistance and offers valuable genetic information for breeding programs aimed at improving drought resistance in crops.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143032998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis.","authors":"Yanfeng Zhou, Chenhe Wang, Binhu Wang, Dongpo Xu, Xizhao Zhang, You Ge, Shulun Jiang, Fujiang Tang, Chunhai Chen, Xuemei Li, Jianbo Jian, Yang You","doi":"10.1093/gigascience/giae115","DOIUrl":"10.1093/gigascience/giae115","url":null,"abstract":"<p><p>The Asian icefish, Protosalanx chinensis, has undergone extensive colonization in various waters across China for decades due to its ecological and physiological significance as well as its economic importance in the fishery resource. Here, we decoded a telomere-to-telomere (T2T) genome for P. chinensis combining PacBio HiFi long reads and ultra-long ONT (nanopore) reads and Hi-C data. The telomere was identified in both ends of the contig/chromosome. The expanded gene associated with circadian entrainment suggests that P. chinensis may exhibit a high sensitivity to photoperiod. The contracted genes' immune-related families and DNA repair associated with positive selection in P. chinensis suggested the selection pressure during adaptive evolution. The population genetic analysis reported the genetic diversity and genomic footprints in 254 individuals from 8 different locations. The natural seawater samples can be the highest diversity and different from other freshwater and introduced populations. The divergent regions' associated genes were found to be related to the osmotic pressure system, suggesting adaptations to alkalinity and salinity. Thus, the T2T genome and genetic variation can be valuable resources for genomic footprints in P. chinensis, shedding light on its evolution, comparative genomics, and the genetic differences between natural and introduced populations.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Data reuse in agricultural genomics research: challenges and recommendations.","authors":"Alenka Hafner, Victoria DeLeo, Cecilia H Deng, Christine G Elsik, Damarius S Fleming, Peter W Harrison, Theodore S Kalbfleisch, Bruna Petry, Boas Pucker, Elsa H Quezada-Rodríguez, Christopher K Tuggle, James E Koltes","doi":"10.1093/gigascience/giae106","DOIUrl":"10.1093/gigascience/giae106","url":null,"abstract":"<p><p>The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Here, we identify the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research. We propose possible solutions stakeholders could implement to mitigate and overcome these challenges and provide an optimistic perspective on the future of genomics and transcriptomics data reuse.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11727710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142978043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl.","authors":"Gang Wang, Xinye Zhang, Xiurong Zhao, Xufang Ren, Anqi Chen, Wenting Dai, Li Zhang, Yan Lu, Zhihua Jiang, Huie Wang, Yong Liu, Xiaoyu Zhao, Junhui Wen, Xue Cheng, Yalan Zhang, Zhonghua Ning, Liping Ban, Lujiang Qu","doi":"10.1093/gigascience/giae124","DOIUrl":"10.1093/gigascience/giae124","url":null,"abstract":"<p><strong>Introduction: </strong>The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation that causes the leucistic plumage of the blue peafowl (also called white peafowl) remains unknown.</p><p><strong>Results: </strong>In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, and a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes, and 33 peafowl W chromosomes genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found 3 hybrid green peafowls in zoo samples rather than in the wild samples, with a blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that 2 of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in 4 zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP3 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for leucistic plumage of blue peafowl, preventing melanocytes from being transported into plumage, thereby inhibiting melanin deposition.</p><p><strong>Conclusion: </strong>Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide a valuable resource for blue peafowl genomics-assisted breeding.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143448878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.","authors":"Hongwoo Lee, Pil Joon Seo","doi":"10.1093/gigascience/giaf020","DOIUrl":"10.1093/gigascience/giaf020","url":null,"abstract":"<p><strong>Background: </strong>Three-dimensional (3D) chromatin organization is emerging as a key factor in gene regulation in eukaryotes. Recent studies using high-resolution Hi-C analysis have explored fine-scale local chromatin contact domains in plants, as exemplified by the basic contact domains established at accessible gene border regions in Arabidopsis (Arabidopsis thaliana). However, we lack effective tools to identify these contact domains and examine their structural dynamics.</p><p><strong>Results: </strong>We developed the Hi-C-based 3D Gene Domain analysis Tool (Hi-GDT) to identify fine-scale local chromatin contact domains in plants, with a particular focus on gene borders. Hi-GDT successfully identifies local contact domains, including single-gene and multigene domains, with high reproducibility. Hi-GDT can also be used to discover local contact domains that are differentially organized in association with differences in gene expression between tissue types, genotypes, or in response to environmental stimuli.</p><p><strong>Conclusions: </strong>Hi-GDT is a valuable tool for identifying genes regulated by dynamic 3D conformational changes, expanding our understanding of the structural and functional relevance of local 3D chromatin organization in plants. Hi-GDT is publicly available at https://github.com/CDL-HongwooLee/Hi-GDT.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phased high-quality genome of the gymnosperm Himalayan Yew assists in paclitaxel pathway exploration.","authors":"Zhenzhu Li, Hang Zong, Xiaonan Liu, Xiao Wang, Shimeng Liu, Xi Jiao, Xianqing Chen, Hao Wu, Zhuoya Liu, Zhongkai Wang, Yongqiang Wang, Yi Liu, Botong Zhou, Zihe Li, Qiuhui Du, Jing Li, Jian Cheng, Jie Bai, Xiaoxi Zhu, Yue Yang, Guichun Liu, Li Zhang, Huifeng Jiang, Wen Wang","doi":"10.1093/gigascience/giaf026","DOIUrl":"10.1093/gigascience/giaf026","url":null,"abstract":"<p><strong>Background: </strong>Taxus wallichiana is an important species for paclitaxel production. Previous genome versions for Taxus spp. have been limited by extensive gaps, hindering the complete annotation and mining of paclitaxel (known as Taxol commercially) synthesis pathway-related genes.</p><p><strong>Results: </strong>Here, we present the first phased high-quality reference genome of T. wallichiana, which significantly improves assembly quality and corrects large-scale assembly errors present in previous versions. The 2 haplotypes are 9.87 Gb and 9.98 Gb in length, respectively, and all 24 chromosomes were assembled with telomeres at both ends. Based on this high-quality genome (TWv1), we inferred that the candidate sex chromosome of T. wallichiana is chr12, and its sex determination system may follow a ZW model. Particularly, we identified and experimentally validated a batch of 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODDs), which may be key C4β-C20 epoxidases in the paclitaxel synthesis pathway.</p><p><strong>Conclusions: </strong>This study not only provides a valuable data resource for gene mining in the biosynthetic pathways of secondary metabolites, such as paclitaxel, but also offers the highest-quality reference genome of gymnosperms to date for the identification of sex chromosomes, facilitating comparative genomic studies among gymnosperms.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Network-based anomaly detection algorithm reveals proteins with major roles in human tissues.","authors":"Dima Kagan, Juman Jubran, Esti Yeger-Lotem, Michael Fire","doi":"10.1093/gigascience/giaf034","DOIUrl":"10.1093/gigascience/giaf034","url":null,"abstract":"<p><strong>Background: </strong>Proteins act through physical interactions with other molecules to maintain organismal health. Protein-protein interaction (PPI) networks have proved to be a powerful framework for obtaining insight into protein functions, cellular organization, response to signals, and disease states. In multicellular organisms, protein content varies between tissues, influencing tissue morphology and function. Weighted PPI networks, reflecting the likelihood of interactions in specific tissues, offer insights into tissue-specific processes and disease mechanisms. We hypothesized that detecting anomalous nodes in these networks could reveal proteins with key tissue-specific functions.</p><p><strong>Results: </strong>Here, we introduce Weighted Graph Anomalous Node Detection (WGAND), a novel machine-learning algorithm to identify anomalous nodes in weighted graphs. WGAND estimates expected edge weights and uses deviations to generate anomaly detection features, which are then used to score network nodes. We applied WGAND to weighted PPI networks of 17 human tissues. High-ranking anomalous nodes were enriched for proteins associated with tissue-specific diseases and tissue-specific biological processes, such as neuron signaling in the brain and spermatogenesis in the testis. WGAND outperformed other methods in terms of area under the ROC curve and precision at K, highlighting its effectiveness in uncovering biologically meaningful anomalies.</p><p><strong>Conclusions: </strong>Our findings demonstrate WGAND's potential as a powerful tool for detecting anomalous proteins with significant biological roles. By identifying proteins involved in critical tissue-specific processes and diseases, WGAND offers valuable insights for discovering novel biomarkers and therapeutic targets. Its versatile algorithm is suitable for any weighted graph and is broadly applicable across various fields. The WGAND algorithm is available as an open-source Python library at https://github.com/data4goodlab/wgand.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}