Fundamentals of Biomedical Statistics (2 credit hr)
Medical Bioinformatics (2 credit hr)
Scientific English Writing and Presentation (2 credit hr)
Ethics in Research and Writing (1 credit hr)
医学生物信息学 (研究生专业基础课程， 本硕博贯通) 回页首
Medical Bioinformatics Back to top
课程号码: BI052(本科课程代码), BE26031(研究生课程代码)
时间: 秋季 每周四 10:00AM-11:40AM
地点: 上海交通大学闵行校区东上院 311
授课老师: 林关宁, 邮箱: nickgnlin@sjtu.edu.cn
授课语言: 中英双语 (英文为主，中文为辅)
助教: 赵晶晶, 邮箱: 296589025@qq.com
Course number: BI052(Undergraduate), BE26031(Graduate)
Time: Fall, Thur 10:00AM-11:40AM
Location: 311 Dong Shang Yuan
Instructor: Dr. Guan Ning Lin, Email: nickgnlin@sjtu.edu.cn
Language of instruction: English and Chinese (mainly in English, supplemented by Chinese)
Teaching assistant: Jingjing Zhao, Email: 296589025@qq.com
本课程讲授以解决临床医学问题为主导的生物信息学主要概念和基本计算技术。是一门融合了临床医学问题，
疾病生物学概念与计算科学技术的前沿交叉知识的课程。内容主要包括基因、蛋白序列比对，马可夫模型，新一代测序以及转录组测序与分析，
疾病突变原理以及其功能预测，精准医学与临床基因检测等，以及R编程语言入门和实验上机数据处理与分析等。
通过本课程的学习，学生将能系统地掌握医学生物信息学的基本理论、基本知识；掌握医学生物信息学的基本技术；
了解精准医学以及其临床应用的应用。通过本课程的理论介绍和实际数据上机操作，将让学生掌握如何应用医学生物信息学和计算科学手段解决生命和医学，
特别在大数据和精准医疗等领域的科学问题。
This course teaches the main concepts and basic computational techniques of bioinformatics that address clinical and medical problems.
It is an interdisciplinary course that combines clinical/medical issues, disease biology concepts and computational science and technology.
The course covers sequence alignment, Markov model, next generation sequencing, functional prediction of disease variants, precision medicine
and clinical genetic testing, as well as some R programming in-course practices. Students will gain the fundamental knowledge of medical bioinformatics,
the design of the computational biology problems and necessary applications and tools, latest advances in modern genomic technology,
big data and precision medicine. This course’s teaching in fundamental concepts and in-class programming practices, will allow students
to understand how to apply bioinformatics and computational science to solve scientific problems in life and medicine, especially
in the area of big data procession and analysis and the precision medicine.
课程打分 Course grading
出勤率10%，课堂互动 5%，功课20%，课堂PPT汇报25%（讨论医学生物信息学的不同技术和应用），期末考试40%
Attendance rate（10%），class participation（5%），programming practice/homework（20%）, oral presentation (25%), final exam (40%)
Week1: 导论与历史 (Introduction and history)
Week2: 序列比对 (Sequence alignment)
Week3: 马可夫模型 (Markov model)
Week4: 待定: 国定假日 (TDB: Holiday)
Week5: DNA新一代测序分析 (DNA NGS Analysis)
Week6: 基因变异的功能预测 (Functional prediction of genetic variants)
Week7: RNA新一代测序分析 (RNA NGS Analysis)
Week8: 孟德尔遗传病与临床基因检测 (Mendelian disease, NGS, Genetic testing)
Week9: 复杂性疾病, GWAS，临床预测性检测 (Complex disease, GWAS, predictive testing)
Week10: 药物基因组学，癌症基因组学 (Pharmacogenomics, Cancer geneomics)
Week11: R 数据分析实验上机1：生物统计背景及基础数据操作 (R programming 1: Statistic background and basic data manipulation)
Week12: R 数据分析实验上机2：探索性数据分析以及聚类分析(R programming 2: exploratory data analysis and clustering)
Week13: R 数据分析实验上机3：数据预处理和基础统计建模 (R programming 3: Preprocessing and data modeling )
Week14: R 数据分析实验上机4：统计学意义和多重检测 (R programming 4: Statistical significance and multiple testing)
Week15: 学生课堂口头PPT报告 (Student Oral presentation)
Week16: 期末考 (Final Exam)
Supplemental videos: Install R on Mac [ Download Video]
Supplemental videos: Install RStudio on Mac [ Download Video]
Supplemental videos: Setting Your Working Directory and Editing R Code (Windows) [ Download Video]
Supplemental videos: Setting Your Working Directory and Editing R Code (Mac) [ Download Video]
Supplemental videos: Getting started with R and RStudio [ Download Video]
科技英语写作与交流 (研究生公共基础课，博士生课程) 回页首
Scientific English Writing and Presentation Back to top
课程号码:
时间: 夏季小学期, 7月(共4周), 周二和周四, 8:00AM-11:40AM
地点: 上海交通大学徐汇校区工程馆
授课老师: 大课(John B Troy); 小课(林关宁等), 邮箱: nickgnlin@sjtu.edu.cn
授课语言: 中英双语 (大课英文，小课中文)
本课程目的在于教授学生用英语撰写学术论文并将其发表在国际学术期刊、以及用英语在国际学术会议上作口头报告和墙报展示的技巧。
本课程采用海外教授讲授大课与本校教师小班讲授相结合的模式。大课教学将围绕一些高影响因子杂志文章和相关专业学术期刊文章的
思维逻辑和写作技巧进行授课。小班辅导则为学生提供更具细节的写作练习和文章解读，以及墙报展示和口头交流的练习。
通过这个课程，学生将在如何在学术杂志上发表论文、以及如何在学术会议上报告他们的研究成果等方面得到训练和提高。
The objective of this course is to teach students how to write a paper in English for publication in a scientific journal
and to teach students the oral presentation and poster presentation skills needed to present their results at an international
scientific conference. The course includes large-class lectures taught by international professor and small-class tutorials
taught by SJTU tutors. For the large-class teaching, consideration is made of the differences in style of very high impact
journals and journals of a specific discipline. For the small-class tutorials, there will be a number of in-class writing
exercises and discussion of good and not-so-good writing practices. There will also be in-class poster presentation with
oral discussion. Students who complete this course will learn what to do to get their research published and how best to
present their work at a scientific conference.
课程打分 Course grading
摘要写作(20); 摘要修稿(20)
墙报制作(故事逻辑+图/表细节+整体布局) (10 + 10 + 10)
期末墙报汇报及讨论 (10)
出勤率(10)，课堂互动 (10)
abstract drafting + revising (20 + 20)
Poster making (story logic + figure/table details + overall layout) (10 + 10 + 10)
Poster discussion (10)
In-class participation + discussion/interaction (10 + 10)
Week1 day1 small-class Warm up and introduction to the writing course
Week1 day1 large-class Organization of a scientific paper. When to start the writing process
Week1 day2 small-class Overall structure of a good impact scientific paper
Week1 day2 large-class Writing style. Telling a story. Winning the hearts of reviewers
Week2 day1 small-class Tutorial on vocabulary and terminology, sentence writing and grammar; In class commenting Thesis Abstracts
Week2 day1 large-class Use of tables and figures. Good caption writing. Use of statistics
Week2 day2 small-class Explaining tables/figures/captions/statistics following Paper; How to make a poster
Week2 day2 large-class Staying concise. Use of writing tools. Good sentence construction. Use of paragraphs and subheadings. Increasing vocabulary. Clarity.
Week3 day1 small-class In-class commenting on the student written Paper Abstract
Week3 day1 large-class Introduction and Discussion. Submitting a manuscript and dealing with the editor. Citations
Week3 day2 small-class In-class writing practice and analyses; Poster commenting
Week3 day2 large-class The reader. The paper. Grammar. Style. Vocabulary. Figures. Chinese and English sentence.
Week4 day1 small-class In-class commenting the revised abstract
Week4 day1 large-class Good practice for oral presentation.
Week4 day2 large-class Write your paper based on a story
Week4 day2 small-class Student Poster Presentation and Discussion
