Integrative clustering of cells and samples using multi-modal single-cell data

使用多模态单细胞数据对细胞和样本进行综合聚类

• 批准号: 10215623
• 负责人: Joshua D Campbell
• 金额: $ 35.89万
• 依托单位: BOSTON UNIVERSITY MEDICAL CAMPUS
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10215623
• 关键词: Academic Medical Centers; Address; African; Algorithms; American; Apache; Atlases; Bayesian Modeling; Bioinformatics; Biological; Biological Process; Biology; Biometry; Biopsy; Boston; Brain; Catalogs; Cells; Cellular Assay; Characteristics; Chromatin; Clinical Data; Cloud Computing; Complex; Computational Biology; Data; Data Set; Development; Developmental Process; Devices; Disease; Environment; European; Funding; Gene Cluster; Gene Expression; Genomics; Goals; High Performance Computing; Human; Immunology; Individual; Lesion; Letters; Lung; Lung nodule; Malignant Neoplasms; Malignant neoplasm of prostate; Massachusetts; Measurement; Measures; Messenger RNA; Methods; Microfluidics; Modeling; Molecular; Molecular and Cellular Biology; Nature; Noise; Normal Cell; Nose; Opiate Addiction; Patients; Procedures; Process; Proteins; Protocols documentation; Research Personnel; Running; Sampling; Smoker; Smoking; Speed; Subgroup; Techniques; Technology; Tissues; Visualization; base; cancer heterogeneity; cell type; cloud based; cloud platform; cluster computing; combat; complex biological systems; computer science; digital; discrete data; epigenetic marker; experimental study; genomic data; high risk; human tissue; insight; language processing; large scale data; lung development; multimodal data; multimodality; multiple data types; new technology; novel; premalignant; protein biomarkers; protein expression; single cell analysis; single cell technology; single-cell RNA sequencing; user-friendly; web interface

Single-cell genomic technologies such as single-cell RNA-seq have emerged as powerful techniques to quantify molecular states of individual cells and can be used to elucidate the cellular building blocks of complex tissues and diseases. Given recent rapid advances in single-cell technologies, novel statistical and computational approaches are needed to efficiently analyze large-scale single-cell datasets with multiple data types such as gene and protein expression. Discrete Bayesian hierarchical models have been widely used for unsupervised modeling of discrete data types in fields such as Nature Language Processing (NLP). We have developed a Bayesian hierarchical model called Cellular Latent Dirichlet Allocation (Celda) to perform bi-clustering of genes into modules and cells into subpopulations. We will develop novel models that can perform clustering of cells into subpopulations using multi-modal genomic data or clustering of patients into subgroups using both single- cell data and patient-level characteristics. These novel methods will be made available in a scalable and interpretable cloud-based framework accessible to both computational and non-computational users. The aims of this study are to (1) develop novel models to perform integrative multi-modal and multi-level clustering with single-cell data, (2) develop an R package and cloud-based platform with a web interface for rapid inference and visualization of large-scale datasets, and (3) apply Celda models to single-cell datasets from a variety of biological settings including cancer, lung development, and immunology. Overall, these aims will be accomplished by an interdisciplinary team with strong expertise in computational biology and bioinformatics, biostatistics, computer science, and molecular and cellular biology.

单细胞基因组技术，如单细胞RNA-seq，已经成为量化基因组的强大技术。 单个细胞的分子状态，并可用于阐明复杂组织的细胞构建块 和疾病。考虑到单细胞技术最近的快速发展， 需要有效分析具有多种数据类型的大规模单像元数据集的方法， 基因和蛋白质表达。离散贝叶斯分层模型已被广泛用于无监督 在诸如自然语言处理（NLP）等领域中对离散数据类型进行建模。我们已经开发出一种 贝叶斯层次模型称为细胞潜在狄利克雷分配（Celda），用于执行基因的双聚类 模块和细胞的亚群。我们将开发新的模型，可以执行细胞聚类 使用多模态基因组数据将患者聚类成亚群，或者使用单模态基因组数据和多模态基因组数据将患者聚类成亚群。 细胞数据和患者水平特征。这些新的方法将在可扩展的和 计算和非计算用户都可以访问的可解释的基于云的框架。目标 本研究的目的是（1）开发新的模型来执行综合多模态和多层次聚类， 单细胞数据，（2）开发一个R包和基于云的平台，具有用于快速推理的Web界面， 大规模数据集的可视化，以及（3）将Celda模型应用于各种单细胞数据集 生物环境，包括癌症、肺发育和免疫学。总的来说，这些目标将是 由一个在计算生物学和生物信息学方面具有丰富专业知识的跨学科团队完成， 生物统计学、计算机科学以及分子和细胞生物学。

项目成果

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.

使用 DecontPro 对基于液滴的单细胞蛋白质表达数据中的背景噪声进行表征和净化。

• DOI: 10.1101/2023.01.27.525964
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Yin,Yuan;Yajima,Masanao;Campbell,JoshuaD
• 通讯作者: Campbell,JoshuaD

Machine learning enables design automation of microfluidic flow-focusing droplet generation.

• DOI: 10.1038/s41467-020-20284-z
• 发表时间: 2021-01-04
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Lashkaripour A;Rodriguez C;Mehdipour N;Mardian R;McIntyre D;Ortiz L;Campbell J;Densmore D
• 通讯作者: Densmore D

Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data.

• DOI: 10.1093/nargab/lqac066
• 发表时间: 2022-09
• 期刊: NAR genomics and bioinformatics
• 影响因子: 4.6