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Cis-regulatory control of transcriptional timing and noise in response to estrogen. 顺式调节控制转录时间和噪音对雌激素的反应
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-04-24 DOI: 10.1016/j.xgen.2024.100542
Matthew Ginley-Hidinger, Hosiana Abewe, Kyle Osborne, Alexandra Richey, Noel Kitchen, Katelyn L Mortenson, Erin M Wissink, John Lis, Xiaoyang Zhang, Jason Gertz

Cis-regulatory elements control transcription levels, temporal dynamics, and cell-cell variation or transcriptional noise. However, the combination of regulatory features that control these different attributes is not fully understood. Here, we used single-cell RNA-seq during an estrogen treatment time course and machine learning to identify predictors of expression timing and noise. We found that genes with multiple active enhancers exhibit faster temporal responses. We verified this finding by showing that manipulation of enhancer activity changes the temporal response of estrogen target genes. Analysis of transcriptional noise uncovered a relationship between promoter and enhancer activity, with active promoters associated with low noise and active enhancers linked to high noise. Finally, we observed that co-expression across single cells is an emergent property associated with chromatin looping, timing, and noise. Overall, our results indicate a fundamental tradeoff between a gene's ability to quickly respond to incoming signals and maintain low variation across cells.

顺式调控元件控制着转录水平、时间动态、细胞间差异或转录噪音。然而,控制这些不同属性的调控特征的组合还不完全清楚。在这里,我们利用雌激素治疗时间过程中的单细胞 RNA-seq和机器学习来识别表达时间和噪音的预测因子。我们发现,具有多个活跃增强子的基因表现出更快的时间反应。我们通过研究发现,增强子的活性会改变雌激素靶基因的时间反应,从而验证了这一发现。对转录噪音的分析发现了启动子和增强子活性之间的关系,活跃的启动子与低噪音相关,而活跃的增强子与高噪音相关。最后,我们观察到,单细胞间的共表达是一种与染色质循环、时间和噪声相关的新兴特性。总之,我们的研究结果表明,在基因快速响应传入信号的能力与保持跨细胞低变异的能力之间存在着根本性的权衡。
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引用次数: 0
Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts. 基于血液表观基因组的全人群慢性低度炎症分析。
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-04-30 DOI: 10.1016/j.xgen.2024.100544
Robert F Hillary, Hong Kiat Ng, Daniel L McCartney, Hannah R Elliott, Rosie M Walker, Archie Campbell, Felicia Huang, Kenan Direk, Paul Welsh, Naveed Sattar, Janie Corley, Caroline Hayward, Andrew M McIntosh, Cathie Sudlow, Kathryn L Evans, Simon R Cox, John C Chambers, Marie Loh, Caroline L Relton, Riccardo E Marioni, Paul D Yousefi, Matthew Suderman

Chronic inflammation is a hallmark of age-related disease states. The effectiveness of inflammatory proteins including C-reactive protein (CRP) in assessing long-term inflammation is hindered by their phasic nature. DNA methylation (DNAm) signatures of CRP may act as more reliable markers of chronic inflammation. We show that inter-individual differences in DNAm capture 50% of the variance in circulating CRP (N = 17,936, Generation Scotland). We develop a series of DNAm predictors of CRP using state-of-the-art algorithms. An elastic-net-regression-based predictor outperformed competing methods and explained 18% of phenotypic variance in the Lothian Birth Cohort of 1936 (LBC1936) cohort, doubling that of existing DNAm predictors. DNAm predictors performed comparably in four additional test cohorts (Avon Longitudinal Study of Parents and Children, Health for Life in Singapore, Southall and Brent Revisited, and LBC1921), including for individuals of diverse genetic ancestry and different age groups. The best-performing predictor surpassed assay-measured CRP and a genetic score in its associations with 26 health outcomes. Our findings forge new avenues for assessing chronic low-grade inflammation in diverse populations.

慢性炎症是与年龄有关的疾病的标志。包括 C 反应蛋白(CRP)在内的炎症蛋白在评估长期炎症方面的有效性因其阶段性而受到阻碍。CRP的DNA甲基化(DNAm)特征可作为慢性炎症的更可靠标记。我们的研究表明,DNAm 的个体间差异可捕捉到循环 CRP 变异的 50%(N = 17936,苏格兰一代)。我们使用最先进的算法开发了一系列 CRP 的 DNAm 预测因子。在 1936 年洛锡安出生队列(LBC1936)队列中,基于弹性网回归的预测方法优于其他竞争方法,解释了 18% 的表型变异,是现有 DNAm 预测方法的两倍。DNAm 预测方法在另外四个测试队列(雅芳父母与子女纵向研究、新加坡生命健康研究、Southall 和 Brent Revisited 以及 LBC1921)中的表现不相上下,其中包括不同基因血统和不同年龄段的个体。在与 26 种健康结果的关联方面,表现最佳的预测因子超过了化验测定的 CRP 和基因评分。我们的研究结果为评估不同人群的慢性低度炎症开辟了新的途径。
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引用次数: 0
Rare-variant association study unveils the Achilles' heel for HCC. 罕见变异关联研究揭示了 HCC 的致命弱点。
Q1 CELL BIOLOGY Pub Date : 2024-05-08 DOI: 10.1016/j.xgen.2024.100558
Yin Wang, Ying Wai Chan

In this issue of Cell Genomics, Wang, Liu, Zuo, Wang, et al.1 investigate rare variants in hepatocellular carcinoma (HCC) by performing the first rare-variant association study (RVAS) in a Chinese population cohort. It uncovers BRCAness phenotypes associated with the NRDE2-p.N377I variant, suggesting PARP inhibitors as a promising therapeutic approach for certain HCC patients.

在本期《细胞基因组学》(Cell Genomics)杂志上,Wang、Liu、Zuo、Wang 等人1 首次在中国人群队列中开展了罕见变异关联研究(RVAS),研究了肝细胞癌(HCC)中的罕见变异。该研究发现了与 NRDE2-p.N377I 变异相关的 BRCAness 表型,提示 PARP 抑制剂是治疗某些 HCC 患者的有效方法。
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引用次数: 0
The broken Alzheimer's disease genome. 破碎的阿尔茨海默病基因组
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-05-01 DOI: 10.1016/j.xgen.2024.100555
Cláudio Gouveia Roque, Hemali Phatnani, Ulrich Hengst

The complex pathobiology of late-onset Alzheimer's disease (AD) poses significant challenges to therapeutic and preventative interventions. Despite these difficulties, genomics and related disciplines are allowing fundamental mechanistic insights to emerge with clarity, particularly with the introduction of high-resolution sequencing technologies. After all, the disrupted processes at the interface between DNA and gene expression, which we call the broken AD genome, offer detailed quantitative evidence unrestrained by preconceived notions about the disease. In addition to highlighting biological pathways beyond the classical pathology hallmarks, these advances have revitalized drug discovery efforts and are driving improvements in clinical tools. We review genetic, epigenomic, and gene expression findings related to AD pathogenesis and explore how their integration enables a better understanding of the multicellular imbalances contributing to this heterogeneous condition. The frontiers opening on the back of these research milestones promise a future of AD care that is both more personalized and predictive.

晚发性阿尔茨海默病(AD)的病理生物学非常复杂,给治疗和预防干预带来了巨大挑战。尽管存在这些困难,但基因组学和相关学科,尤其是高分辨率测序技术的引入,使基本的机理认识得以清晰呈现。毕竟,DNA 与基因表达界面的中断过程(我们称之为 "破碎的 AD 基因组")提供了详细的定量证据,不受对该疾病先入为主的观念的限制。除了强调经典病理学特征之外的生物学途径之外,这些进展还为药物发现工作注入了新的活力,并推动了临床工具的改进。我们回顾了与多发性硬化症发病机制相关的遗传学、表观基因组学和基因表达研究成果,并探讨了如何通过整合这些研究成果更好地理解导致这种异质性疾病的多细胞失衡。这些具有里程碑意义的研究成果所开辟的前沿领域有望为未来的注意力缺失症治疗提供更加个性化和更具预测性的服务。
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引用次数: 0
NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors. NRDE2 缺乏会损害同源重组修复,并使肝癌对 PARP 抑制剂敏感。
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-05-01 DOI: 10.1016/j.xgen.2024.100550
Yahui Wang, Xinyi Liu, Xianbo Zuo, Cuiling Wang, Zheng Zhang, Haitao Zhang, Tao Zeng, Shunqi Chen, Mengyu Liu, Hongxia Chen, Qingfeng Song, Qi Li, Chenning Yang, Yi Le, Jinliang Xing, Hongxin Zhang, Jiaze An, Weihua Jia, Longli Kang, Hongxing Zhang, Hui Xie, Jiazhou Ye, Tianzhun Wu, Fuchu He, Xuejun Zhang, Yuanfeng Li, Gangqiao Zhou

To identify novel susceptibility genes for hepatocellular carcinoma (HCC), we performed a rare-variant association study in Chinese populations consisting of 2,750 cases and 4,153 controls. We identified four HCC-associated genes, including NRDE2, RANBP17, RTEL1, and STEAP3. Using NRDE2 (index rs199890497 [p.N377I], p = 1.19 × 10-9) as an exemplary candidate, we demonstrated that it promotes homologous recombination (HR) repair and suppresses HCC. Mechanistically, NRDE2 binds to the subunits of casein kinase 2 (CK2) and facilitates the assembly and activity of the CK2 holoenzyme. This NRDE2-mediated enhancement of CK2 activity increases the phosphorylation of MDC1 and then facilitates the HR repair. These functions are eliminated almost completely by the NRDE2-p.N377I variant, which sensitizes the HCC cells to poly(ADP-ribose) polymerase (PARP) inhibitors, especially when combined with chemotherapy. Collectively, our findings highlight the relevance of the rare variants to genetic susceptibility to HCC, which would be helpful for the precise treatment of this malignancy.

为了确定肝细胞癌(HCC)的新型易感基因,我们在中国人群中进行了一项罕见变异关联研究,其中包括 2,750 例病例和 4,153 例对照。我们发现了四个 HCC 相关基因,包括 NRDE2、RANBP17、RTEL1 和 STEAP3。我们以 NRDE2(指标 rs199890497 [p.N377I], p = 1.19 × 10-9)为例,证明它能促进同源重组(HR)修复并抑制 HCC。从机理上讲,NRDE2 与酪蛋白激酶 2(CK2)的亚基结合,促进了 CK2 全酶的组装和活性。NRDE2 介导的 CK2 活性增强会增加 MDC1 的磷酸化,进而促进 HR 修复。NRDE2-p.N377I变体几乎完全消除了这些功能,它使HCC细胞对多(ADP-核糖)聚合酶(PARP)抑制剂敏感,尤其是在与化疗联合使用时。总之,我们的研究结果凸显了罕见变异与 HCC 遗传易感性的相关性,这将有助于这种恶性肿瘤的精确治疗。
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引用次数: 0
Increasing equity in science requires better ethics training: A course by trainees, for trainees. 提高科学领域的公平性需要更好的伦理培训:学员为学员开设的课程。
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-05-01 DOI: 10.1016/j.xgen.2024.100554
Roshni A Patel, Rachel A Ungar, Alanna L Pyke, Alvina Adimoelja, Meenakshi Chakraborty, Daniel J Cotter, Malika Freund, Pagé Goddard, Justin Gomez-Stafford, Emily Greenwald, Emily Higgs, Naiomi Hunter, Tim M G MacKenzie, Anjali Narain, Tamara Gjorgjieva, Daphne O Martschenko

Despite the profound impacts of scientific research, few scientists have received the necessary training to productively discuss the ethical and societal implications of their work. To address this critical gap, we-a group of predominantly human genetics trainees-developed a course on genetics, ethics, and society. We intend for this course to serve as a template for other institutions and scientific disciplines. Our curriculum positions human genetics within its historical and societal context and encourages students to evaluate how societal norms and structures impact the conduct of scientific research. We demonstrate the utility of this course via surveys of enrolled students and provide resources and strategies for others hoping to teach a similar course. We conclude by arguing that if we are to work toward rectifying the inequities and injustices produced by our field, we must first learn to view our own research as impacting and being impacted by society.

尽管科学研究影响深远,但很少有科学家接受过必要的培训,以富有成效地讨论其工作的伦理和社会影响。为了弥补这一重大差距,我们--一群主要由人类遗传学学员组成的团队--开发了一门关于遗传学、伦理学和社会的课程。我们打算将这门课程作为其他机构和科学学科的模板。我们的课程将人类遗传学置于历史和社会背景之中,鼓励学生评估社会规范和结构如何影响科学研究的开展。我们通过对注册学生的调查证明了这门课程的实用性,并为其他希望教授类似课程的人提供了资源和策略。最后,我们认为,如果我们要努力纠正我们的领域所产生的不公平和不公正现象,我们必须首先学会将我们自己的研究视为影响社会和被社会影响的研究。
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引用次数: 0
Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. 儿童肥胖症 chr12q13 位点的变异到功能分析显示,rs7132908 是 FAIM2 3' UTR 中的一个因果变异。
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-05-01 DOI: 10.1016/j.xgen.2024.100556
Sheridan H Littleton, Khanh B Trang, Christina M Volpe, Kieona Cook, Nicole DeBruyne, Jean Ann Maguire, Mary Ann Weidekamp, Kenyaita M Hodge, Keith Boehm, Sumei Lu, Alessandra Chesi, Jonathan P Bradfield, James A Pippin, Stewart A Anderson, Andrew D Wells, Matthew C Pahl, Struan F A Grant

The ch12q13 locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via cis-regulation. We implicated rs7132908 as a putative causal variant by leveraging our in-house 3D genomic data and public domain datasets. Using a luciferase reporter assay, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. We generated isogenic human embryonic stem cell lines homozygous for either rs7132908 allele to assess changes in gene expression and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. The rs7132908 obesity risk allele influenced expression of FAIM2 and other genes and decreased the proportion of neurons produced by differentiation. We have functionally validated rs7132908 as a causal obesity variant that temporally regulates nearby effector genes and influences neurodevelopment and survival.

ch12q13位点是全基因组关联研究中发现的最重要的儿童肥胖位点之一。该位点位于 FAIM2 中的非编码区;因此,潜在的因果变异可能通过顺式调控影响疾病易感性。我们利用内部三维基因组数据和公共领域数据集,将 rs7132908 推测为一个因果变异体。通过荧光素酶报告实验,我们观察到了携带 rs7132908 的直接区域的等位基因特异性顺式调节活性。我们生成了rs7132908等位基因同源的人类胚胎干细胞系,以评估在向下丘脑神经元分化的整个过程中基因表达和染色质可及性的变化,下丘脑神经元是已知调节进食行为的关键细胞类型。rs7132908肥胖风险等位基因影响了FAIM2和其他基因的表达,并降低了分化产生的神经元比例。我们从功能上验证了 rs7132908 是肥胖症的因果变异基因,它能在时间上调节附近的效应基因,影响神经发育和存活。
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引用次数: 0
Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning. 通过低资源感知表征学习对 T 细胞受体和 T 细胞转录组进行统一的跨模态整合与分析。
Q1 CELL BIOLOGY Pub Date : 2024-05-08 Epub Date: 2024-04-29 DOI: 10.1016/j.xgen.2024.100553
Yicheng Gao, Kejing Dong, Yuli Gao, Xuan Jin, Jingya Yang, Gang Yan, Qi Liu

Single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (TCR-seq) are pivotal for investigating T cell heterogeneity. Integrating these modalities, which is expected to uncover profound insights in immunology that might otherwise go unnoticed with a single modality, faces computational challenges due to the low-resource characteristics of the multimodal data. Herein, we present UniTCR, a novel low-resource-aware multimodal representation learning framework designed for the unified cross-modality integration, enabling comprehensive T cell analysis. By designing a dual-modality contrastive learning module and a single-modality preservation module to effectively embed each modality into a common latent space, UniTCR demonstrates versatility in connecting TCR sequences with T cell transcriptomes across various tasks, including single-modality analysis, modality gap analysis, epitope-TCR binding prediction, and TCR profile cross-modality generation, in a low-resource-aware way. Extensive evaluations conducted on multiple scRNA-seq/TCR-seq paired datasets showed the superior performance of UniTCR, exhibiting the ability of exploring the complexity of immune system.

单细胞 RNA 测序(scRNA-seq)和 T 细胞受体测序(TCR-seq)是研究 T 细胞异质性的关键。由于多模态数据的低资源特性,将这些模态整合在一起面临着计算上的挑战。在此,我们提出了 UniTCR,这是一种新型的低资源感知多模态表征学习框架,旨在进行统一的跨模态整合,从而实现全面的 T 细胞分析。UniTCR 设计了双模态对比学习模块和单模态保存模块,将每种模态有效地嵌入到一个共同的潜在空间中,从而以一种低资源感知的方式在各种任务中展示了连接 TCR 序列和 T 细胞转录组的多功能性,包括单模态分析、模态差距分析、表位-TCR 结合预测和 TCR 图谱跨模态生成。在多个scRNA-seq/TCR-seq配对数据集上进行的广泛评估表明,UniTCR性能优越,具有探索免疫系统复杂性的能力。
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引用次数: 0
MUSSEL: Enhanced Bayesian polygenic risk prediction leveraging information across multiple ancestry groups. MUSSEL:利用多个祖先群体信息的增强型贝叶斯多基因风险预测。
Q1 CELL BIOLOGY Pub Date : 2024-04-10 DOI: 10.1016/j.xgen.2024.100539
Jin Jin, Jianan Zhan, Jingning Zhang, Ruzhang Zhao, Jared O'Connell, Yunxuan Jiang, Steven Buyske, Christopher Gignoux, Christopher Haiman, Eimear E Kenny, Charles Kooperberg, Kari North, Bertram L Koelsch, Genevieve Wojcik, Haoyu Zhang, Nilanjan Chatterjee

Polygenic risk scores (PRSs) are now showing promising predictive performance on a wide variety of complex traits and diseases, but there exists a substantial performance gap across populations. We propose MUSSEL, a method for ancestry-specific polygenic prediction that borrows information in summary statistics from genome-wide association studies (GWASs) across multiple ancestry groups via Bayesian hierarchical modeling and ensemble learning. In our simulation studies and data analyses across four distinct studies, totaling 5.7 million participants with a substantial ancestral diversity, MUSSEL shows promising performance compared to alternatives. For example, MUSSEL has an average gain in prediction R2 across 11 continuous traits of 40.2% and 49.3% compared to PRS-CSx and CT-SLEB, respectively, in the African ancestry population. The best-performing method, however, varies by GWAS sample size, target ancestry, trait architecture, and linkage disequilibrium reference samples; thus, ultimately a combination of methods may be needed to generate the most robust PRSs across diverse populations.

目前,多基因风险评分(PRSs)在各种复杂性状和疾病方面显示出了良好的预测性能,但在不同人群之间还存在很大的性能差距。我们提出的 MUSSEL 是一种针对特定祖先的多基因预测方法,它通过贝叶斯分层建模和集合学习,从多个祖先群体的全基因组关联研究(GWAS)中借用汇总统计信息。在我们的模拟研究和四项不同研究的数据分析中,与其他替代方案相比,MUSSEL 表现出了良好的性能,这些研究的参与者总计 570 万人,其祖先具有很大的多样性。例如,在非洲血统人群中,与 PRS-CSx 和 CT-SLEB 相比,MUSSEL 在 11 个连续性状上的预测 R2 平均增益分别为 40.2% 和 49.3%。然而,表现最好的方法因 GWAS 样本大小、目标祖先、性状结构和连锁不平衡参考样本而异;因此,最终可能需要结合多种方法才能在不同人群中生成最稳健的 PRS。
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引用次数: 0
Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases. 综合多基因风险评分提高了复杂性状和疾病的预测准确性。
Q1 CELL BIOLOGY Pub Date : 2024-04-10 Epub Date: 2024-03-19 DOI: 10.1016/j.xgen.2024.100523
Buu Truong, Leland E Hull, Yunfeng Ruan, Qin Qin Huang, Whitney Hornsby, Hilary Martin, David A van Heel, Ying Wang, Alicia R Martin, S Hong Lee, Pradeep Natarajan

Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p = 9.17 × 10-5) and 1.19-fold (95% CI, [1.11; 1.27]; p = 1.92 × 10-6), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p = 7.58 × 10-6) and 1.42-fold (95% CI, [1.25; 1.59]; p = 8.01 × 10-7) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction = 2.6 × 10-4). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.

多基因风险评分(PRS)是预测个体临床表型和结果的新兴工具。我们提出了 PRSmix 和 PRSmix+,前者是一个利用目标性状的 PRS 语料库来提高预测准确性的框架,后者则纳入了遗传相关性状,以更好地捕捉欧洲和南亚血统中分别为 47 种和 32 种疾病/性状的人类遗传结构。PRSmix 的平均预测准确率提高了 1.20 倍(95% 置信区间 [CI],[1.10; 1.3];p = 9.17 × 10-5)和 1.19 倍(95% 置信区间 [CI],[1.11; 1.27];p = 1.92 × 10-6),PRSmix+则将欧洲血统和南亚血统的预测准确率分别提高了 1.72 倍(95% CI,[1.40; 2.04];p = 7.58 × 10-6)和 1.42 倍(95% CI,[1.25; 1.59];p = 8.01 × 10-7)。与之前使用预先定义的相关性状得分的交叉性状组合方法相比,我们的方法提高了冠心病的预测准确率达 3.27 倍(95% CI,[2.1; 4.44];经错误发现率 (FDR) 校正后的 p 值 = 2.6 × 10-4)。我们的方法提供了一个全面的框架,可对 PRS 的综合能力进行基准测试和利用,从而在所需的目标人群中实现最高性能。
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引用次数: 0
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Cell genomics
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