Understanding molecular variations of cattle genome by machine learning

本博士项目将利用大规模的组学数据，培养一名具有新时代信息学与动物遗传和基因组研究相结合的创新思想的博士研究人员。学生将整合遗传学和机器学习方法，以识别牛基因组的分子变异，并评估分子变异与复杂表型的关联（例如，健康、生产、效率、健身）。成功的候选人将有机会使用大规模的牛组学数据，包括全基因组序列，RNA序列，英国牛群的复杂表型。除了数据，学生将有机会获得方法，软件和高性能的计算资源（例如，Nvidia DGX工作站，集群，笔记本电脑），我们已经建立了很好的解决研究问题。将对数据进行联合分析，以确定牛基因组的分子变异（例如，eQTL）使用序列数据和机器/深度学习方法。将鉴定出的具有功能意义的变异体与牛复杂表型相关联，以研究功能变异体与牛健康、健身、生产和效率之间的联系。博士项目提供跨学科研究，该项目通过交叉监督在SRUC和爱丁堡大学之间进行了强有力的合作。学生将从SRUC和爱丁堡大学获得关于定量遗传学，统计建模和机器学习的富有成效的研究培训。学生还将获得科学写作，项目管理技能和职业发展技能方面的宝贵培训。学生是EASTBIO培训计划的一部分，将进行增强的特定学科，核心生物科学和通用技能培训以及3个月的专业实习（PIPS）。学生将在4年内提交博士论文。

With large-scale omics data available, this PhD project will train a PhD researcher with innovative ideas of integrating informatics into animal genetic and genomic research in the new era. The student will integrate genetics and machine learning methods to identify molecular variations of the cattle genome and assess the association of molecular variants with complex phenotypes (e.g., health, production, efficiency, fitness). The successful candidate will have the opportunity to work with large-scale cattle omics data including whole-genome sequence, RNA-sequence, complex phenotypes of UK cattle population. In addition to the data, the student will have access to methodology, software, and high-performance computational resources (e.g., Nvidia DGX Workstation, clusters, Jupyter Notebook) that have been well-established by us to address the research questions. The data will be jointly analyzed to identify molecular variations of cattle genome (e.g., eQTL) using sequence data and machine/deep learning methods. The identified variants with functional significance will be associated with cattle complex phenotypes to investigate the links between functional variants and cattle health, fitness, production, and efficiency. The PhD project offers interdisciplinary research and the project has strong collaborative efforts between SRUC and University of Edinburgh through cross-supervision. The student will obtain fruitful research training from both SRUC and University of Edinburgh on quantitative genetics, statistical modelling, and machine learning. The student will also obtain valuable training in scientific writing, project management skills, and career development skills. Students are part of the EASTBIO training programme and will undertake enhanced subject-specific, core bioscience and generic skills training and a 3-month professional internship (PIPS) outwith academia. The students are expected to submit a PhD thesis in 4 years.