CellBranch : a toolset for exploring Stem Cell Differentiation and Pluripotency with Branching Process Theory

CellBranch：利用分支过程理论探索干细胞分化和多能性的工具集

• 批准号: BB/L018705/1
• 负责人: Susan Stepney
• 金额: $ 18.65万
• 依托单位: University of York
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL018705%2F1
• 关键词: CellBranch; toolset; exploring; Stem; Cell

One important biological application area is stem cell differentiation. Embryonic stem (ES) cells have the potential to produce all an animal's cell types: this is called pluripotency. In theory, stem cells could be directed to differentiate into any cell type, for therapeutic purposes. However, we cannot yet reliably direct their behaviour, and so cannot yet fully exploit this potential.To further our understanding of such biological systems, we need sophisticated tools to analyse the system's complexity and the vast amounts of data available. Computational tools provide an important route to gaining such understanding. Here we will build computational models and simulation tools based on Branching Process Theory, targeted to research questions in the domain of embryonic stem cell differentiation, as informed by high volumes of data. We will validate the tool, to ensure that it is working as desired, by application to specific existing biological datasets. Tools need to be usable and accessible to benefit the wider community. We will make the fully documented tools available to the wider research community through York's HEFCE-funded YouShare "Software as a Service" portal.

干细胞分化是一个重要的生物学应用领域。胚胎干细胞具有产生所有动物细胞类型的潜力：这被称为多能性。从理论上讲，干细胞可以被引导分化为任何类型的细胞，用于治疗目的。然而，我们还不能可靠地指导它们的行为，因此还不能充分开发这一潜力。为了加深我们对此类生物系统的理解，我们需要先进的工具来分析系统的复杂性和可用的大量数据。计算工具提供了获得这种理解的重要途径。在这里，我们将建立基于分支过程理论的计算模型和模拟工具，目标是研究大量数据提供的胚胎干细胞分化领域的问题。我们将通过将该工具应用于特定的现有生物数据集来验证该工具，以确保其按预期工作。工具必须是可用的和可访问的，才能使更广泛的社区受益。我们将通过约克大学由HEFCE资助的YouShare“软件即服务”门户网站向更广泛的研究社区提供完整的文档工具。

项目成果

A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells.

• DOI: 10.1371/journal.pcbi.1005713
• 发表时间: 2017-09
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Greaves RB;Dietmann S;Smith A;Stepney S;Halley JD
• 通讯作者: Halley JD

Genome-wide embryonic stem cell regulatory network self-organisation: a big data CoSMoS computational modelling approach

全基因组胚胎干细胞调控网络自组织：大数据CoSMoS计算建模方法

• 发表时间: 2016
• 作者: Richard B. Greaves

CellBranch CoSMoS model : increments 1, 2 and 3

CellBranch CoSMoS 模型：增量 1、2 和 3

• 发表时间: 2016
• 作者: Richard B. Greaves