Genomics, Proteomics & Bioinformatics最新文献_第4页

Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma gondii 人畜共患病寄生虫弓形虫的蛋白质乳化和代谢调节。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 Epub Date: 2022-10-07 DOI: 10.1016/j.gpb.2022.09.010

Deqi Yin , Ning Jiang , Chang Cheng , Xiaoyu Sang , Ying Feng , Ran Chen , Qijun Chen

The biology of Toxoplasma gondii, the causative pathogen of one of the most widespread parasitic diseases (toxoplasmosis), remains poorly understood. Lactate, which is derived from glucose metabolism, is not only an energy source in a variety of organisms, including T. gondii, but also a regulatory molecule that participates in gene activation and protein function. Lysine lactylation (Kla) is a type of post-translational modifications (PTMs) that has been recently associated with chromatin remodeling; however, Kla of histone and non-histone proteins has not yet been studied in T. gondii. To examine the prevalence and function of lactylation in T. gondii parasites, we mapped the lactylome of proliferating tachyzoite cells and identified 1964 Kla sites on 955 proteins in the T. gondii RH strain. Lactylated proteins were distributed in multiple subcellular compartments and were closely related to a wide variety of biological processes, including mRNA splicing, glycolysis, aminoacyl-tRNA biosynthesis, RNA transport, and many signaling pathways. We also performed a chromatin immunoprecipitation sequencing (ChIP-seq) analysis using a lactylation-specific antibody and found that the histones H4K12la and H3K14la were enriched in the promoter and exon regions of T. gondii associated with microtubule-based movement and cell invasion. We further confirmed the delactylase activity of histone deacetylases TgHDAC2–4, and found that treatment with anti-histone acetyltransferase (TgMYST-A) antibodies profoundly reduced protein lactylation in T. gondii. This study offers the first dataset of the global lactylation proteome and provides a basis for further dissecting the functional biology of T. gondii.

弓形虫是最普遍的寄生虫病之一（弓形虫病）的致病病原体，但人们对弓形虫的生物学特性仍然知之甚少。葡萄糖代谢产生的乳酸不仅是包括弓形虫在内的多种生物的能量来源，也是参与基因激活和蛋白质功能的调节分子。赖氨酸乳化（Kla）是一种翻译后修饰（PTM），最近被认为与染色质重塑有关。为了研究乳化作用在淋病双球菌寄生虫中的普遍性和功能，我们绘制了增殖速虫细胞的乳化组图谱，并在淋病双球菌 RH 株的 955 个蛋白质上鉴定出了 1964 个乳化位点。乳化蛋白分布在多个亚细胞区，与多种生物过程密切相关，包括 mRNA 剪接、糖酵解、氨基酰-tRNA 生物合成、RNA 运输和许多信号通路。我们还使用乳化特异性抗体进行了染色质免疫沉淀测序（ChIP-seq）分析，发现组蛋白H4K12la和H3K14la富集在与微管运动和细胞侵袭相关的淋球菌启动子和外显子区域。我们进一步证实了组蛋白去乙酰化酶 TgHDACs 2、3 和 4 的脱乳活性，并发现用抗组蛋白乙酰转移酶（TgMYST-A）抗体处理能显著减少淋病双球菌的蛋白乳化。这项研究首次提供了全球乳化蛋白质组的数据集，为进一步剖析淋球菌的功能生物学提供了基础。

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引用次数: 0

A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction 蛋白质磷酸化位点预测的机器学习和算法方法综述。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 Epub Date: 2023-10-19 DOI: 10.1016/j.gpb.2023.03.007

Farzaneh Esmaili , Mahdi Pourmirzaei , Shahin Ramazi , Seyedehsamaneh Shojaeilangari , Elham Yavari

Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related databases and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and machine learning (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end deep learning methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.

翻译后修饰（PTMs）在扩展蛋白质的功能多样性方面发挥着关键作用，从而调节原核生物和真核生物的不同细胞过程。磷酸化修饰是一种重要的PTM，发生在大多数蛋白质中，在许多生物过程中发挥着重要作用。磷酸化过程中的障碍会导致多种疾病，包括神经系统疾病和癌症。这篇综述论文的目的是组织与磷酸化位点（p-位点）预测相关的知识体系，以促进该领域的未来研究。首先，我们全面回顾了所有相关数据库，并介绍了p位点预测中数据集创建、数据预处理和方法评估的所有步骤。接下来，我们研究了p位点预测方法，这些方法分为两组：算法和机器学习（ML）。此外，研究表明，ML预测p位点基本上有两种主要方法：传统的和端到端的深度学习方法，并对这两种方法进行了概述。此外，本研究还介绍了最重要的特征提取技术，这些技术主要用于p位点预测。最后，我们根据普通物种和人类物种，从与2022年发布的dbPTM数据库版本相关的新蛋白质中创建了三个测试集。评估dbPTM 2022版本中引入的新添加蛋白质的在线p位点预测工具，与dbPTM 2019版本中的工具不同，揭示了它们的局限性。换句话说，这些在线p位点预测工具对看不见的蛋白质的实际性能明显低于其各自研究论文中报告的结果。

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引用次数: 0

Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces 多组学数据揭示丁酸钠对链霉菌基因表达和蛋白质修饰的影响

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-12-01 Epub Date: 2022-09-15 DOI: 10.1016/j.gpb.2022.09.002

Jiazhen Zheng , Yue Li , Ning Liu , Jihui Zhang , Shuangjiang Liu , Huarong Tan

Streptomycetes possess numerous gene clusters and the potential to produce a large amount of natural products. Histone deacetylase (HDAC) inhibitors play an important role in the regulation of histone modifications in fungi, but their roles in prokaryotes remain poorly understood. Here, we investigated the global effects of the HDAC inhibitor, sodium butyrate (SB), on marine-derived Streptomyces olivaceus FXJ 8.021, particularly focusing on the activation of secondary metabolite biosynthesis. The antiSMASH analysis revealed 33 secondary metabolite biosynthetic gene clusters (BGCs) in strain FXJ 8.021, among which the silent lobophorin BGC was activated by SB. Transcriptomic data showed that the expression of genes involved in lobophorin biosynthesis (ge00097–ge00139) and CoA-ester formation (e.g., ge02824), as well as the glycolysis/gluconeogenesis pathway (e.g., ge01661), was significantly up-regulated in the presence of SB. Intracellular CoA-ester analysis confirmed that SB triggered the biosynthesis of CoA-ester, thereby increasing the precursor supply for lobophorin biosynthesis. Further acetylomic analysis revealed that the acetylation levels on 218 sites of 190 proteins were up-regulated and those on 411 sites of 310 proteins were down-regulated. These acetylated proteins were particularly enriched in transcriptional and translational machinery components (e.g., elongation factor GE04399), and their correlations with the proteins involved in lobophorin biosynthesis were established by protein–protein interaction network analysis, suggesting that SB might function via a complex hierarchical regulation to activate the expression of lobophorin BGC. These findings provide solid evidence that acetylated proteins triggered by SB could affect the expression of genes involved in the biosynthesis of primary and secondary metabolites in prokaryotes.

链霉菌拥有众多的基因簇，并具有生产大量天然产品的潜力。组蛋白去乙酰化酶（HDAC）抑制剂在调节真菌中的组蛋白修饰方面发挥着重要作用，但人们对 HDAC 在原核生物中的作用知之甚少。在这里，我们描述了 HDAC 抑制剂丁酸钠（SB）对海洋来源的橄榄链霉菌 FXJ 8.021 的整体影响，尤其是对次生代谢物生物合成的激活作用。反SMASH 分析发现，在菌株 FXJ 8.021 中有 33 个次生代谢物生物合成基因簇（BGC），其中沉默的叶鞘素 BGC 被 SB 激活。转录组数据显示，在 SB 存在的情况下，参与叶鞘素生物合成（ge00097-ge00139）、CoA-酯形成（如 ge02824）以及糖酵解/糖酮生成途径（如 ge01661）的基因表达主要上调。细胞内 CoA-酯分析证实，SB 触发了 CoA-酯的生物合成，从而增加了叶绿素生物合成的前体供应。进一步的乙酰化组分析显示，190 个蛋白质的 218 个乙酰化位点的乙酰化水平上调，310 个蛋白质的 411 个位点的乙酰化水平下调。这些被乙酰化的蛋白质尤其富集于转录和翻译机制成分（如延伸因子 GE04399）中，并且通过蛋白质-蛋白质相互作用网络分析确定了它们与参与小叶花青素生物合成的蛋白质之间的相关性，这表明 SB 可能通过复杂的分级调控来激活小叶花青素 BGC 的表达。这些发现提供了确凿的证据，证明 SB 触发的乙酰化蛋白可影响原核生物中初级和次级代谢产物生物合成基因的表达。

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引用次数: 0

Revolutionizing Antibody Discovery: An Innovative AI Model for Generating Robust Libraries 革命性的抗体发现:一种用于生成鲁棒库的创新AI模型。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2023-06-22 DOI: 10.1016/j.gpb.2023.06.001

Yaojun Wang , Shiwei Sun

引用次数: 0

MicroRNA–disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice 微RNA-疾病网络分析将甲氨蝶呤重新用于治疗小鼠腹主动脉瘤

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2022-08-24 DOI: 10.1016/j.gpb.2022.08.002

Yicong Shen , Yuanxu Gao , Jiangcheng Shi , Zhou Huang , Rongbo Dai , Yi Fu , Yuan Zhou , Wei Kong , Qinghua Cui

Abdominal aortic aneurysm (AAA) is a permanent dilatation of the abdominal aorta and is highly lethal. The main purpose of the current study is to search for noninvasive medical therapies for AAA, for which there is currently no effective drug therapy. Network medicine represents a cutting-edge technology, as analysis and modeling of disease networks can provide critical clues regarding the etiology of specific diseases and therapeutics that may be effective. Here, we proposed a novel algorithm to quantify disease relations based on a large accumulated microRNA–disease association dataset and then built a disease network covering 15 disease classes and 304 diseases. Analysis revealed some patterns for these diseases. For instance, diseases tended to be clustered and coherent in the network. Surprisingly, we found that AAA showed the strongest similarity with rheumatoid arthritis and systemic lupus erythematosus, both of which are autoimmune diseases, suggesting that AAA could be one type of autoimmune diseases in etiology. Based on this observation, we further hypothesized that drugs for autoimmune diseases could be repurposed for the prevention and therapy of AAA. Finally, animal experiments confirmed that methotrexate, a drug for autoimmune diseases, was able to alleviate the formation and development of AAA.

腹主动脉瘤（AAA）是腹主动脉的永久性扩张，致死率极高。目前这项研究的主要目的是寻找治疗 AAA 的非侵入性医疗方法，因为目前还没有有效的药物疗法。网络医学是一项前沿技术，因为对疾病网络的分析和建模可以为特定疾病的病因学以及哪些疗法可能有效提供重要线索。在这里，我们提出了一种基于大量累积的 microRNA-疾病关联数据集的量化疾病关系的新型算法，然后构建了一个涵盖 15 种疾病类别和 304 种疾病的疾病网络。分析揭示了这些疾病的一些模式。例如，疾病在网络中趋于集群和一致。令人惊讶的是，我们发现 AAA 与类风湿性关节炎和系统性红斑狼疮的相似性最强，而这两种疾病都是自身免疫性疾病，这表明 AAA 在病因学上可能是自身免疫性疾病的一种。基于这一观察结果，我们进一步假设，治疗自身免疫性疾病的药物可以重新用于预防和治疗 AAA。最后，动物实验证实，治疗自身免疫性疾病的药物甲氨蝶呤能够缓解 AAA 的形成和发展。

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引用次数: 0

Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development Omics 对哺乳动物早期发育中细胞命运决定机制的看法。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2023-04-17 DOI: 10.1016/j.gpb.2023.03.001

Lin-Fang Ju , Heng-Ji Xu , Yun-Gui Yang , Ying Yang

During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination, ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation, several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages, including the 2- and 4-cell stages. The underlying mechanisms of early cell fate determination have long been an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis, as well as the current understanding of their regulatory roles in cell fate decisions. Moreover, as powerful tools for early embryogenesis research, single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators. Here, we summarize their applications in the research of preimplantation embryos, and provide new insights and perspectives on cell fate regulation.

在哺乳动物胚胎植入前的发育过程中，一个全能的合子要经历数次细胞裂解和两轮细胞命运决定，最终形成一个成熟的囊胚。在压实的同时，顶基底细胞极性的建立打破了胚胎的对称性，并指导后续的细胞命运选择。虽然内细胞团（ICM）和滋养外胚层（TE）的细胞系分离是细胞分化的第一个标志，但在更早的阶段，包括 2 细胞和 4 细胞阶段，有几种分子已被证明能通过其细胞间的变化偏向早期细胞命运。长期以来，早期细胞命运决定的内在机制一直是一个重要的研究课题。在这篇综述中，我们总结了早期胚胎发生过程中发生的分子事件，以及目前对它们在细胞命运决定中的调控作用的理解。此外，作为早期胚胎发生研究的有力工具，单细胞全息技术已被应用于小鼠和人类植入前胚胎，并为发现细胞命运调控因子做出了贡献。在此，我们总结了这些技术在植入前胚胎研究中的应用，并为细胞命运调控提供了新的见解和视角。

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引用次数: 0

Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency 基于同源重组修复缺陷的患者评估和治疗计划

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2023-02-14 DOI: 10.1016/j.gpb.2023.02.004

Wenbin Li , Lin Gao , Xin Yi , Shuangfeng Shi , Jie Huang , Leming Shi , Xiaoyan Zhou , Lingying Wu , Jianming Ying

Defects in genes involved in the DNA damage response cause homologous recombination repair deficiency (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Accumulating evidence has identified HRD as a biomarker for assessing the therapeutic response of tumor cells to poly(ADP-ribose) polymerase inhibitors and platinum-based chemotherapies. Nevertheless, the biology of HRD is complex, and its applications and the benefits of different HRD biomarker assays are controversial. This is primarily due to inconsistencies in HRD assessments and definitions (gene-level tests, genomic scars, mutational signatures, or a combination of these methods) and difficulties in assessing the contribution of each genomic event. Therefore, we aim to review the biological rationale and clinical evidence of HRD as a biomarker. This review provides a blueprint for the standardization and harmonization of HRD assessments.

参与 DNA 损伤反应的基因缺陷会导致同源重组修复缺陷（HRD）。HRD在多种肿瘤类型的癌症患者中都有发现，在癌症预防和治疗中具有临床意义。越来越多的证据表明，HRD 是评估肿瘤细胞对聚（ADP 核糖）聚合酶抑制剂和铂类化疗药物治疗反应的生物标志物。然而，HRD 的生物学特性十分复杂，其应用和不同 HRD 生物标志物检测方法的益处也存在争议。这主要是由于 HRD 评估和定义（基因水平测试、基因组疤痕、突变特征或这些方法的组合）不一致，以及难以评估每个基因组事件的贡献。因此，我们旨在回顾将 HRD 作为生物标记物的生物学原理和临床证据。这篇综述为 HRD 评估的标准化和统一化提供了一个蓝图。

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引用次数: 0

HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes HPC图谱：计算构建人类蛋白质复合物的综合图谱。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2023-09-18 DOI: 10.1016/j.gpb.2023.05.001

Yuliang Pan , Ruiyi Li , Wengen Li , Liuzhenghao Lv , Jihong Guan , Shuigeng Zhou

A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells. For a complete understanding of human cellular functions, it is crucial to have a comprehensive atlas of human protein complexes. Unfortunately, we still lack such a comprehensive atlas of experimentally validated protein complexes, which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes, as well as the underlying biological mechanisms. To fill this gap, we built Human Protein Complexes Atlas (HPC-Atlas), as far as we know, the most accurate and comprehensive atlas of human protein complexes available to date. We integrated two latest protein interaction networks, and developed a novel computational method to identify nearly 9000 protein complexes, including many previously uncharacterized complexes. Compared with the existing methods, our method achieved outstanding performance on both testing and independent datasets. Furthermore, with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-affected human protein complexes, and 456 multifunctional proteins that contain many potential moonlighting proteins. These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources, but also a valuable resource for exploring new biological findings. The HPC-Atlas webserver is freely available at http://www.yulpan.top/HPC-Atlas.

生物学的一个基本原理是，蛋白质往往会形成复合体，在细胞的核心功能中发挥重要作用。为了全面了解人类细胞功能，拥有一个全面的人类蛋白质复合物图谱至关重要。不幸的是，我们仍然缺乏如此全面的实验验证的蛋白质复合物图谱，这使我们无法完全了解人类蛋白质复合物的组成和功能以及生物学机制。为了填补这一空白，我们建立了人类蛋白质复合体图谱（HPC图谱），据我们所知，这是迄今为止最准确、最全面的人类蛋白质复合体图集。我们整合了两个最新的蛋白质相互作用网络，并开发了一种新的计算方法来识别近9000个蛋白质复合物，包括许多以前未表征的复合物。与现有的工作相比，我们的方法在测试集和独立集上都取得了突出的性能。此外，通过HPC Atlas，我们鉴定了751种严重急性呼吸综合征冠状病毒2型（严重急性呼吸系统综合征冠状病毒冠状病毒2型）影响的人类蛋白质复合物，以及456种含有许多潜在兼职蛋白质的多功能蛋白质。这些结果表明，HPC Atlas不仅可以作为一个计算框架，通过整合多个蛋白质数据源来有效识别具有生物学意义的蛋白质复合物，而且可以作为探索新的生物学发现的宝贵资源。HPC Atlas Web服务器可在http://www.yulpan.top/HPC-Atlas.

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引用次数: 0

OBIA: An Open Biomedical Imaging Archive OBIA：一个开放的生物医学成像档案。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2023-10-06 DOI: 10.1016/j.gpb.2023.09.003

Enhui Jin , Dongli Zhao , Gangao Wu , Junwei Zhu , Zhonghuang Wang , Zhiyao Wei , Sisi Zhang , Anke Wang , Bixia Tang , Xu Chen , Yanling Sun , Zhe Zhang , Wenming Zhao , Yuanguang Meng

With the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, and accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified de-identification and quality control process. In addition, OBIA provides friendly and intuitive web interfaces for data submission, browsing, and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed at https://ngdc.cncb.ac.cn/obia.

随着人工智能技术的发展，生物医学成像数据在科学研究和临床应用中发挥着重要作用，但可用资源有限。在这里，我们介绍了开放式生物医学成像档案（OBIA），一个用于存档生物医学成像和相关临床数据的存储库。OBIA采用五个数据对象（采集、个体、研究、系列和图像）进行数据组织，接受多种模式、器官和疾病的生物医学图像提交。为了保护个人隐私，海外建筑信息管理局制定了统一的身份识别和质量控制流程。此外，OBIA为数据提交、浏览和检索以及图像检索提供了友好直观的网络界面。截至2023年9月，OBIA共收集了937个个体、4136项研究、24701个系列和1938309张图像的数据，涵盖9种模式和30个解剖部位。总之，OBIA为生物医学成像数据管理提供了一个可靠的平台，并提供了对所有公开可用数据的免费开放访问，以支持世界各地的研究活动。OBIA可访问https://ngdc.cncb.ac.cn/obia.

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引用次数: 0

From BIG Data Center to China National Center for Bioinformation 从BIG数据中心到中国生物信息中心。

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics

Pub Date : 2023-10-01 Epub Date: 2023-10-12 DOI: 10.1016/j.gpb.2023.10.001

Yiming Bao , Yongbiao Xue

引用次数: 0