Research Initiation Award: Uncovering and Extracting Biological Information from Nanopore Long-read Sequencing Data with Machine Learning and Mathematical Approaches

HBCU-UP的研究启动奖为STEM教师提供支持，以开展研究活动，进一步提高他们的研究能力和有效性，并帮助加强HBCU的研究和教学。授予Tougaloo College的这一奖项旨在揭示基因表达和细胞分化的关键见解。它将通过利用创新技术和计算工具推进基因组学领域。通过使用长读测序，该项目旨在为理解基因表达的一般控制做出贡献，并在特定应用中理解疾病。此外，它通过提供本科生，特别是那些来自历史上被边缘化的社区，通过宝贵的研究经验，促进教育和多样性。通过将这项研究融入课程，Tougaloo College旨在改变STEM学科，丰富学生在各个学科的学习。这个项目的潜在好处是广泛的。它不仅将提高教师的研究能力，还将促进未来STEM专业人员的发展。通过让学生参与真实的研究，它将为他们成功的职业生涯做好准备，并有助于他们在STEM领域的保留。该项目的总体目标是利用高通量基因组和转录组数据集，主要基于Nanopore长读测序，研究DNA甲基化对不同生物系统和疾病中RNA速度轨迹的影响。该项目将开发创新的计算工具，以准确估计RNA速度并检测DNA甲基化模式，包括罕见或新颖的修饰。利用Nanopore长读测序的独特优势，例如丰富的信号水平信息，该项目将通过提供对DNA甲基化和RNA速度之间相互作用的全面理解来推进该领域。该研究的技术方法涉及开发用于RNA速度估计的计算工具箱和用于直接DNA甲基化检测的基于transformer的机器学习工具。通过整合RNA速度和DNA甲基化数据，该项目将揭示基因表达和细胞分化的调控机制。预期的成果有可能影响各个部门，包括医疗保健，通过实现更准确的诊断，个性化的治疗，并在基因组医学的变革性进步。这个奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响力审查标准进行评估的支持。

HBCU-UP’s Research Initiation Awards provide support for STEM faculty to pursue research activities to further their research capabilities and effectiveness and help enhance research and teaching at HBCUs. This award to Tougaloo College seeks to uncover crucial insights into gene expression and cellular differentiation. It will advance the field of genomics by utilizing innovative technology and computational tools. Through the use of long-read sequencing, the project aims to make contributions in understanding the control of gene expression in general, with specific application understanding diseases. Additionally, it promotes education and diversity by providing undergraduate students, particularly those from historically marginalized communities, through valuable research experiences. By integrating this research into the curriculum, Tougaloo College aims to transform STEM pedagogies and enrich the learning of students in various disciplines. The potential benefits of this project are wide-reaching. It will not only enhance the research capabilities of faculty members, but also foster the development of future STEM professionals. By engaging students in authentic research, it will prepare them for successful careers and contributes to their retention in STEM fields. The overarching goal of this project is to utilize high-throughput genomic and transcriptome data sets, primarily based on Nanopore long-read sequencing, to investigate the influence of DNA methylation on RNA velocity trajectories in diverse biological systems and diseases. The project will develop innovative computational tools to accurately estimate RNA velocity and detect DNA methylation patterns, including rare or novel modifications. Leveraging the unique advantages of Nanopore long-read sequencing, such as rich signal-level information, the project will advance the field by providing a comprehensive understanding of the interplay between DNA methylation and RNA velocity. This research's technical approach involves the development of a computational toolbox for RNA velocity estimation and a transformer-based machine learning tool for direct DNA methylation detection. Through the integration of RNA velocity and DNA methylation data, the project will shed light on the regulatory mechanisms underlying gene expression and cellular differentiation. The anticipated outcomes have the potential to impact various sectors, including healthcare, by enabling more accurate diagnostics, personalized therapies, and transformative advancements in genomic medicine.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.