生物信息学: 导论与方法 from Coursera

欢迎选修北京大学MOOC课程“生物信息学：导论与方法”。

近三十年来，生命科学与计算科学飞速发展。生物信息学是一门生命科学与计算科学的前沿交叉学科。生物信息学产生和迅猛发展的主要推动力来自于新一代测序等高通量技术在生命科学领域越来越广泛的应用。目前，人和很多动植物的基因组已经被测序出来。已知DNA序列的数量已超过20兆亿碱基，每五个月翻一番。这些前所未有的大数据中蕴藏着很多尚不为人知的新发现、新知识，给生命科学研究带来新的历史机遇。但是同时，这些大数据不仅数量巨大、持续呈现指数增长的趋势，而且噪音高，异构程度高。准确、快速地分析这些数据需要先进的计算方法。

生物信息学是一门强大的新技术，是用来分析、存储、搜索海量生物医学数据的信息技术和计算技术。另一方面，生物信息学是一种研究生命科学问题的新方法、新思路，是一种从全基因组出发、从系统水平出发、基于数据整合，提出新假说、发现新规律的研究方法。在这门“生物信息学：导论与方法”网上课程中，我们将向您系统地讲授生物信息学主要概念及方法。课程内容从基础的序列比对开始，循序渐进，围绕深度测序数据分析、计算基因组学、分子通路鉴定等当前研究的前沿热点内容进行介绍与讨论。进一步地，我们会以我们实验室自己开发的算法、软件及数据库为例，告诉您如何开发新的生物信息学技术。我们将用具体实例展示给您，如何用生物信息学的方法及研究思路来解决生命科学里的实际问题。我们也邀请到几位生命科学领域资深教授介绍相关的生物信息学重要工作及生物信息学在生命科学中的作用。

本课程材料采用 CC BY-NC-SA 协议开放共享。

What's inside

Syllabus

导论与历史

欢迎选学“生物信息学：导论与方法”网上课程！完成本模块的课程后你将可以：熟悉生物信息学的基本概念；了解生物信息这一年轻领域的历史；体会生物信息学的迅猛发展。课程补充材料可以加深你对课程讲座内容的理解，虽然小测和考试对这些内容不作要求。

序列比对

完成本模块的课程后你将可以：掌握基于动态规划编程思想的序列比对算法；区分Needleman-Wunsch全局比对算法和Smith-Waterman局部比对算法；了解空位罚分背后的原理和计算算法的复杂度将帮助你在你自己的研究中应用现有的生物信息学工具；你还可以一睹Smith-Waterman算法的发明人Michael Waterman博士的风采。

序列数据库搜索

完成本模块的课程后你将可以：熟悉序列数据库搜索和最常见的序列数据库；领略BLAST背后算法的奥妙；掌握日后在你自己的科研项目中调节BLAST参数的方法。

马尔可夫模型

完成本模块的课程后你将可以：了解状态转移、马尔科夫链、马尔科夫模型的基本概念；亲手完成一个隐马尔科夫模型；利用隐马尔可夫模型在一个实际的生物学问题中作出预测。

新一代测序NGS：重测序的回帖和变异鉴定

完成本模块的课程后你将可以：描述新一代测序的特点；了解你得到的NGS变异结果是用哪些序列回帖和变异鉴定方法完成的；亲历NGS数据分析流程，体会其中生物信息工具在NGS数据分析中的应用。本模块是模块7的先修模块。

变异的功能预测

完成本模块的课程后你将可以：了解什么是变异功能预测和如何进行变异功能预测；在你得到一些可能的变异位点时学会利用变异数据库解决自己的研究问题；了解变异预测工具（SIFT，Polyphen和SAPRED等）背后的机理差异并会在自己的研究课题中按需应用这些工具。

期中考试

新一代测序NGS：转录组分析RNA-Seq

完成本模块的课程后你将可以：了解转录组数据是如何产生的；掌握转录组分析中的重要计算方法；体验RNA-seq的数据分析流程；本模块是模块9的先修模块。

非编码RNA的预测及分析

完成本模块的课程后你将可以：掌握从转录组数据中分析非编码RNA的方法；掌握从NGS数据中鉴定长非编码RNA（lncRNA）并预测其功能的方法。

本体论、分子通路鉴定

完成本模块的课程后你将可以：了解本体论和基因本体轮等重要定义；了解KEGG通路数据库；了解GO的注释消息；在药物成瘾研究中学会使用KOBAS进行通路分析。

生物信息数据库及软件资源

完成本模块的课程后你将可以：高屋建瓴的去了解最重要的生物信息资源（生物信息数据库和软件工具等）；对NCBI, EBI, UCSC 基因组浏览器这样集中型的生物信息资源与各种独立的生物信息资源的概况有广泛的了解和认识；将你的研究内容和相关生物信息资源联系在一起。

研究案例 I -- 新基因起源

完成本案例模块的课程后你将可以：体验生物信息数据、方法和分析是如何解决一个重要的演化问题的；领略物种特异性新基因的起源、演化、功能研究和分析方法；和享誉全球的新基因研究泰斗——芝加哥大学龙漫远教授一起学习建立系统发育树（选学）。

研究案例II- DNA甲基化酶的演化功能分析

完成本案例模块的课程后你将可以：亲历生物信息学方法对DNA甲基化酶的功能和演化的研究；与中科院院士、同济大学校长裴刚教授一起分享科研经历和对网络开放课程的哲思。

期末考试

Good to know

Know what's good

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, and possible dealbreakers

Develops your understanding of a rapidly growing field that finds widespread applications in biomedicine and health sciences

Covers a diverse range of topics including next-generation sequencing data analysis, computational genomics, molecular pathway identification, and bioinformatics database exploration

Led by renowned instructors from Peking University, Dr. Ge Gao and Dr. Liping Wei, with significant expertise in bioinformatics

Provides a strong foundation for beginners and strengthens an existing foundation for intermediate learners

Offers hands-on exercises and interactive materials to enhance learning

This course may require you to purchase additional software or tools not readily available in a household or library

Reviews summary

Bioinformatics: introductory theory and methods

This course provides a comprehensive overview of the field of bioinformatics, introducing students to its foundational concepts and methods. It is recommended for beginners with some background in biology and mathematics. The course covers a range of topics, including sequence alignment, database searching, Markov models, next-generation sequencing, functional prediction of variants, transcriptome analysis, non-coding RNA prediction and analysis, ontology and molecular pathway identification, bioinformatics databases and software resources, and research case studies on new gene origin and DNA methylation enzyme evolutionary functional analysis. Students appreciate the course's engaging teaching style and clear explanations.

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in 生物信息学: 导论与方法 with these activities:

Review the basics of molecular biology

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Reviewing the basics of molecular biology will help you understand the biological context of bioinformatics.

Browse courses on Molecular Biology

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Read a review article on molecular biology.
Watch a tutorial on molecular biology.
Take a quiz on molecular biology.

Review basic sequence analysis concepts

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Reviewing basic sequence analysis concepts will help you understand the advanced topics covered in this course.

Browse courses on Sequence Analysis

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Read a review article on sequence analysis.
Watch a tutorial on sequence alignment.
Practice sequence alignment using a software tool.

Practice sequence alignment using a software tool

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Practicing sequence alignment using a software tool will help you develop the skills necessary to analyze biological data.

Browse courses on Sequence Alignment

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Choose a sequence alignment software tool.
Load a pair of sequences into the software tool.
Align the sequences using the software tool.
Interpret the results of the sequence alignment.

Ten other activities

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Guided Tutorial: Using BLAST

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This tutorial will introduce you to the basics of BLAST, an essential tool for searching biological sequences.

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Watch the tutorial video on BLAST.
Follow the step-by-step instructions to perform a BLAST search.
Interpret the results of your BLAST search.

Watch a tutorial on RNA-Seq data analysis

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Watching a tutorial on RNA-Seq data analysis will help you understand the process of analyzing RNA-Seq data.

Browse courses on RNA-seq

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Find a tutorial on RNA-Seq data analysis.
Watch the tutorial.
Take notes on the key steps of RNA-Seq data analysis.

参加生物信息学会议

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参加会议可以帮助你与其他生物信息学家建立联系，了解该领域的最新进展。

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寻找即将举行的生物信息学会议。
提交一篇摘要或海报。
参加会议并与其他与会者交流。

Attend a bioinformatics workshop

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Attending a bioinformatics workshop will help you learn about the latest advances in the field and network with other professionals.

Browse courses on Bioinformatics

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Find a bioinformatics workshop.
Register for the workshop.
Attend the workshop.
Network with other professionals at the workshop.

Create a collection of bioinformatics resources

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Creating a collection of bioinformatics resources will help you organize and access the information you need to succeed in the field.

Browse courses on Bioinformatics

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Identify the types of resources you need.
Search for and collect resources.
Organize the resources in a way that makes sense to you.

撰写变异功能预测综述

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撰写综述可以帮助你深入了解变异功能预测的方法及其在生物信息学中的应用。

Browse courses on SIFT

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查阅相关文献，了解变异功能预测的原理和方法。
比较不同变异数据库和预测工具的优缺点。
撰写综述，总结你的研究成果，并提出未来的研究方向。

Create a presentation on a bioinformatics topic

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Creating a presentation on a bioinformatics topic will help you synthesize your knowledge of the field and communicate it to others.

Browse courses on Bioinformatics

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Choose a bioinformatics topic.
Research the topic.
Create a presentation outline.
Develop the presentation slides.
Practice presenting the presentation.

Participate in a bioinformatics competition

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Participating in a bioinformatics competition will help you test your skills and knowledge of the field.

Browse courses on Bioinformatics

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Find a bioinformatics competition.
Register for the competition.
Prepare for the competition.
Participate in the competition.

开发一个NGS数据分析工具

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开发一个NGS数据分析工具可以帮助你应用所学知识，并深入了解NGS数据分析的实际应用。

Browse courses on Python

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确定你想开发的工具的功能。
选择合适的编程语言和开发环境。
编写代码并测试你的工具。
将你的工具发布到一个代码仓库中，以便其他人可以访问和使用它。

Mentor a peer in bioinformatics

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Mentoring a peer in bioinformatics will help you solidify your understanding of the field and help others learn.

Browse courses on Bioinformatics

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Find a peer who is interested in learning about bioinformatics.
Meet with your peer regularly to discuss bioinformatics concepts.
Help your peer with bioinformatics projects.

Career center

Learners who complete 生物信息学: 导论与方法 will develop knowledge and skills that may be useful to these careers:

Computational Biologist

Computational biologists use computational methods to study biological systems. This course provides a solid foundation in the principles and methods of bioinformatics, which are essential for computational biologists who need to develop and apply computational models to understand and predict biological phenomena.

See salaries and explore the career path for Computational Biologist

Bioinformatician

Bioinformaticians analyze biological data using computational tools and techniques to solve biological problems. This course provides a strong foundation in the fundamental concepts and methods of bioinformatics, including sequence alignment, sequence database searching, and statistical modeling. This knowledge is essential for bioinformaticians who need to develop and apply computational methods to analyze large-scale biological data.

See salaries and explore the career path for Bioinformatician

Data Scientist

Data scientists use data analysis techniques to extract insights from large datasets. This course provides a strong foundation in the statistical and computational methods used in bioinformatics, which are essential for data scientists who need to analyze large-scale biological data.

See salaries and explore the career path for Data Scientist

Machine Learning Engineer

Machine learning engineers develop and apply machine learning algorithms to solve real-world problems. This course provides a strong foundation in the principles and methods of machine learning, which are essential for machine learning engineers who need to develop and apply machine learning algorithms to analyze biological data.

See salaries and explore the career path for Machine Learning Engineer

Software Engineer

Software engineers design, develop, and maintain software systems. This course provides a strong foundation in the principles and methods of software engineering, which are essential for software engineers who need to develop and maintain bioinformatics software.

See salaries and explore the career path for Software Engineer

Statistician

Statisticians use statistical methods to analyze data. This course provides a strong foundation in the statistical methods used in bioinformatics, which are essential for statisticians who need to analyze large-scale biological data.

See salaries and explore the career path for Statistician

Research Scientist

Research scientists conduct research in a variety of scientific fields. This course provides a strong foundation in the principles and methods of bioinformatics, which are essential for research scientists who need to analyze large-scale biological data.

See salaries and explore the career path for Research Scientist

Biology Teacher

Biology teachers teach biology to students at the secondary or post-secondary level. This course provides a strong foundation in the principles and methods of bioinformatics, which can be helpful for biology teachers who want to incorporate bioinformatics into their teaching.

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Biomedical Engineer

Biomedical engineers apply engineering principles to solve problems in the biomedical field. This course may be helpful for biomedical engineers who want to use bioinformatics to develop new medical devices or treatments.

See salaries and explore the career path for Biomedical Engineer

Microbiologist

Microbiologists study microorganisms, such as bacteria, viruses, and fungi. This course may be helpful for microbiologists who want to use bioinformatics to analyze microbial data.

See salaries and explore the career path for Microbiologist

Geneticist

Geneticists study the genes and chromosomes of living organisms. This course may be helpful for geneticists who want to use bioinformatics to analyze genetic data.

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Chemist

Chemists study the properties and reactions of matter. This course may be helpful for chemists who want to use bioinformatics to study the structure and function of biological molecules.

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Molecular Biologist

Molecular biologists study the structure and function of biological molecules. This course may be helpful for molecular biologists who want to use bioinformatics to analyze molecular data.

See salaries and explore the career path for Molecular Biologist

Veterinarian

Veterinarians diagnose and treat diseases in animals. This course may be helpful for veterinarians who want to use bioinformatics to analyze animal data or to develop new veterinary treatments.

See salaries and explore the career path for Veterinarian

Physician

Physicians diagnose and treat diseases. This course may be helpful for physicians who want to use bioinformatics to analyze patient data or to develop new medical treatments.

See salaries and explore the career path for Physician