دورية أكاديمية
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OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing.

التفاصيل البيبلوغرافية
العنوان: OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing.
المؤلفون: Zeng Z; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China. starlitnightly@gmail.com.; Daxing Research Institute, University of Science and Technology Beijing, Beijing, China. starlitnightly@gmail.com., Ma Y; Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China.; Institute of Biopharmaceutics and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province, China., Hu L; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China., Tan B; Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.; School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, China., Liu P; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China., Wang Y; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China., Xing C; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China. cencanxing@ustb.edu.cn.; Daxing Research Institute, University of Science and Technology Beijing, Beijing, China. cencanxing@ustb.edu.cn., Xiong Y; Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-Sen University, Guangzhou, Guangdong, China. xyyan@mail.sysu.edu.cn., Du H; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China. hongwudu@ustb.edu.cn.; Daxing Research Institute, University of Science and Technology Beijing, Beijing, China. hongwudu@ustb.edu.cn.
المصدر: Nature communications [Nat Commun] 2024 Jul 16; Vol. 15 (1), pp. 5983. Date of Electronic Publication: 2024 Jul 16.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Single-Cell Analysis*/methods , Algorithms* , Sequence Analysis, RNA*/methods, Humans ; Computational Biology/methods ; RNA-Seq/methods ; Neural Networks, Computer ; Software ; High-Throughput Nucleotide Sequencing/methods
مستخلص: Single-cell sequencing is frequently affected by "omission" due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly "omitted" cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of "omitted" cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.
(© 2024. The Author(s).)
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معلومات مُعتمدة: 32300682 National Natural Science Foundation of China (National Science Foundation of China)
تواريخ الأحداث: Date Created: 20240716 Date Completed: 20240716 Latest Revision: 20240719
رمز التحديث: 20240719
مُعرف محوري في PubMed: PMC11252408
DOI: 10.1038/s41467-024-50194-3
PMID: 39013860
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-50194-3