地点：文汇路校区7号楼附楼2楼学术研讨室
Class location: Academic Meeting room, the building attaching the 7# Building, Wenhui Road campus. Yangzhou University.
课程：“组学”在家畜育种和遗传学中的应用
Course: Application of ‘OMICS’ to Livestock Breeding and Genetics
教师：澳大利亚联邦科学与工业研究组织（CSIRO）首席科学家 Dr.Toni Reverter
Instructor Name: Toni Reverter, senior principal research scientist of Commonwealth Scientific and Industrial Research Organisation (CSIRO)
组织单位：动物科学技术学院/畜牧学优势学科；教育部国际合作联合实验室
Organization unit: College of Animal Science and Technology/ Animal science preponderant discipline, The Ministry of Joint International Research Laboratory
教学内容与时间安排
Course Arrangement
Unit | Date | Topic |
Unit 1: lecture Monday | Oct. 7 8:00 - 12:00 | 1. Introduction to ‘OMICS”, Course Outline and Transcriptomics Data Analysis 1) PREAMBLE – GENERAL (OPEN) SEMINAR How much Mathematics does a Biologist need, and vice-versa? COURSE OUTLINE 2) REVIEW OF MOLECULAR CELL BIOLOGY i. Prokaryotes vs Eukaryotes ii. Sub-cellular components and organelles iii. Basic cell functions: Replication, Transcription, and Translation iv. Organic compounds: Carbohydrates, Lipids, and Proteins v. The ABC of Metabolism |
Unit 2: lecture Monday | Oct. 7 14:00 - 18:00 | 2. Introduction to ‘OMICS”, Course Outline and Transcriptomics Data Analysis 3) REVIEW OF MOLECULAR ‘OMICS’ DATA i. Genomics ii. Epigenomics iii. Transcriptomics iv. Proteomics v. Metabolomics vi. Metagenomics/Microbiomics 4) INTRODUCTION TO TRANSCRIPTOMICS (RNA-SEQ) DATA ANALYSIS i. Data preparations, Edits, Transformation and Normalization ii. Differential expression and Functional categories of interest iii. Gene Ontology (GO), GO Enrichment and The GOrilla tool iv. Cluster analysis and the PermutMatrix software: 5) HOMEWORK #1 i. PermutMatrix ii. Data from Cánovas et al. (2014): |
Unit 3: lecture Tuesday | Oct. 8 8:00 - 12:00 | 3. Beyond Differential Expression and Gene Co-Expression Networks 1) REVIEW OF HOMEWORK #1 i. Data from Alexandre et al. (2019): 2) BEYOND DIFFERENTIAL EXPRESSION i. The quest for causal mutations ii. eQTL: for the inference of gene networks: Random vs Scale-Free networks. |
Unit 4: lecture Wednesday | Oct. 9 8:00 - 12:00 | 4. Beyond Differential Expression and Gene Co-Expression Networks 3) GENE CO-EXPRESSION NETWORKS i. Basic network metrics: Motifs, connectivity degree and clustering coefficient ii. Algorithms for the inference of gene networks: Random vs Scale-Free networks iii. The Cytoscape software: 4) HOMEWORK #2 i. NetSimul F90 Program: Simulate random and scale-free networks ii. Replicate the network from Alexandre et al. (2019) iii. Scripts for the Co-Authorship network |
Unit 5: lecture Thursday | Oct. 10 8:00 - 12:00 | 5. Analytical Methods for Gene Network Inference 1) REVIEW OF HOMEWORK #2 i. Edge and node attributes to the visualization scheme 2) THE PCIT ALGORITHM AND RIF METRICS i. PCIT – Partial Correlation and Information Theory ii. RIF – Regulatory Impact Factors |
Unit 6: lecture Friday | Oct. 11 14:00 - 18:00 | 6. Analytical Methods for Gene Network Inference 3) GENE CO-ASSOCIATION NETWORKS i. AWM – Association Weight Matrix ii. Fortes et al. 2010. Proc Natl Acad Sci USA 107:13642-13647 iii. Reverter and Fortes. 2013. Methods Mol Biol. 1019:437-447 3) FURTHER RECENT APPLICATIONS TO LIVESTOCK i. Beef meat tenderness: Ramayo-Caldas et al. 2016. Genet Sel Evol 48:37 ii. Broiler feed efficiency: Bottje et al. 2017. BMC Syst Biol. 11:29 iii. Atlantic salmon: Mohamed et al. 2018. Front Genet 9:369 |
教师简介：
Dr. Toni Reverter-Gomez：澳大利亚联邦科学与工业研究组织（CSIRO）首席科学家，博士生导师。1989年于西班牙巴塞罗那大学获得兽医学学士学位，1994年于美国科罗拉多州立大学获得统计学硕士学位和动物科学（数量遗传学方向）博士学位，1994年-1995年于西班牙农业部进行博士后研究。1995年至2002年先后任职于西班牙巴塞罗那大学和澳大利亚新英格兰大学，2002年起任职于澳大利亚联邦科学与工业研究组织。主要从事家畜基因组学，转录组学，表观遗传学和代谢组学的大数据分析研究，在国际家畜数量遗传研究领域上享有极高的知名度。在Bioinformatics，Physiological Genomics ，BMC Genomics等17个国际知名杂志担任编委，截至2018年已培养博士后6名。先后在Animal Production Science , J Anim Sci，BMC Genomics，BMC Syst Biol，等国际知名期刊上发表论文134篇，累计影响因子300以上，论文被引次数近3000次。先后主持或参与澳大利亚国家资助、州立资助、学校等部门科研项目12项，累计获科研经费近700万澳元，。
Dr. Toni Reverter-Gomez, senior principal research scientist of Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia, a global well-known scientist in livestock quantity genetic research field, with over 100 refereed publications and been cited more than 2,900 times, as well as invited and contributed papers to international meetings, book chapters, patents and reports. Dr. Toni’s research interest focuses on livestock genomic, transcriptomic, epigenetic and metabolomics, especially Big data analysis in animal science, constantly committed to develop creative analytical methods and capabilities in this area.
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