生物信息学: 导论与方法

北京大学

课程信息

27,856 次近期查看

A big welcome to “Bioinformatics: Introduction and Methods” from Peking University! In this MOOC you will become familiar with the concepts and computational methods in the exciting interdisciplinary field of bioinformatics and their applications in biology, the knowledge and skills in bioinformatics you acquired will help you in your future study and research.
Course materials are available under the CC BY-NC-SA License.

学生职业成果

40%

通过此课程获得实实在在的工作福利

25%

加薪或升职

可分享的证书

完成后获得证书

100% 在线

立即开始，按照自己的计划学习。

可灵活调整截止日期

根据您的日程表重置截止日期。

完成时间大约为25 小时

英语（English）

字幕：法语（French）, 巴西葡萄牙语, 俄语（Russian）, 英语（English）, 西班牙语（Spanish）

讲师

授课教师评分

4/5 （11 个评分）

Ge Gao 高歌, Ph.D.

Assistant Professor, Principle Investigator

Center for Bioinformatics, School of Life Science

33,832 个学生

2 门课程

Liping Wei 魏丽萍, Ph.D.

Professor, Director

Center for Bioinformatics, School of Life Sciences

33,832 个学生

2 门课程

学生职业成果

40%

通过此课程获得实实在在的工作福利

25%

加薪或升职

可分享的证书

完成后获得证书

100% 在线

立即开始，按照自己的计划学习。

可灵活调整截止日期

根据您的日程表重置截止日期。

完成时间大约为25 小时

英语（English）

字幕：法语（French）, 巴西葡萄牙语, 俄语（Russian）, 英语（English）, 西班牙语（Spanish）

提供方

北京大学

Peking University is determined to make its education openly accessible to students in China and around the world. With over 3000 faculty members, Peking University offers excellence in teaching and learning.

教学大纲 - 您将从这门课程中学到什么

内容评分94%（1,725 个评分）

周

周 1

完成时间为 2 小时

Introduction and History of Bioinformatics

Welcome to “Bioinformatics: Introduction and Methods! Upon completion of this module you will be able to: become familiar with the essential concepts of bioinformatics; explore the history of this young area; experience how rapidly bioinformatics is growing. Our supplementary materials will give you a better understanding of the course lectures through they are not required in quizzes or exams

完成时间为 2 小时

4 个视频（总计 69 分钟）, 2 个阅读材料, 1 个测验

4 个视频

What is Bioinformatics19分钟

History of Bioinformatics30分钟

Bioinformatics in Mainland China8分钟

About This Course9分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Introduction and History of Bioinformatics30分钟

周

周 2

完成时间为 2 小时

Sequence Alignment

Upon completion of this module, you will be able to: describe dynamic programming based sequence alignment algorithms; differentiate between the Needleman-Wunsch algorithm for global alignment and the Smith-Waterman algorithm for local alignment; examine the principles behind gap penalty and time complexity calculation which is crucial for you to apply current bioinformatic tools in your research; experience the discovery of Smith-Waterman algorithm with Dr. Michael Waterman himself.

完成时间为 2 小时

7 个视频（总计 99 分钟）, 2 个阅读材料, 1 个测验

7 个视频

Essential Concepts13分钟

Global Alignment by Dynamic Programming14分钟

From Global to Local6分钟

Alignment with Affine Gap Penalty and Calculation of Time Complexity of The Needleman-Wunsch Algorithm6分钟

Interview with M. S. Waterman Waterman29分钟

Supplement on Homology & Similarity, Similarity Matrix and Dot Matrix (English Subtitles)10分钟

Student Presentation (English Subtitles)18分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Sequence Alignment30分钟

周

周 3

完成时间为 2 小时

Sequence Database Search

Upon completion of this module, you will be able to: become familiar with sequence databse search and most common databases; explore the algoritm behind BLAST and the evaluation of BLAST results; ajdust BLAST parameters base on your own research project.

完成时间为 2 小时

3 个视频（总计 41 分钟）, 2 个阅读材料, 1 个测验

3 个视频

Sequence Databases12分钟

BLAST Algorithm: A Primer13分钟

Student Presentation (English Subtitles)15分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Sequence Database Search30分钟

周

周 4

完成时间为 2 小时

Markov Model

Upon completion of this module, you will be able to: recognize state transitions, Markov chain and Markov models; create a hidden Markov model by yourself; make predictuions in a real biological problem with hidden Markov model.

完成时间为 2 小时

4 个视频（总计 47 分钟）, 2 个阅读材料, 1 个测验

4 个视频

From States to Markov Chain8分钟

Hidden Markov Model11分钟

Predict with Hidden Markov Model10分钟

Student Presentation16分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Markov Model 30分钟

周

周 5

完成时间为 2 小时

Next Generation Sequencing (NGS): Mapping of Reads From Resequencing and Calling of Genetic Variants

Upon completion of this module, you will be able to: describe the features of NGS; associate NGS results you get with the methods for reads mapping and models for variant calling; examine pipelines in NGS data analysis; experience how real NGS data were analyzed using bioinformatic tools. This module is required before entering Module 8.

完成时间为 2 小时

8 个视频（总计 85 分钟）, 2 个阅读材料, 1 个测验

8 个视频

From Sequencing to NGS10分钟

Reads Mapping and Variants Calling14分钟

Computer Lab: Reads mapping and variant calling (English Subtitles)7分钟

Supplement on reads mapping and variant calling (English Subtitles)9分钟

Supplement on genotyping (English Subtitles)18分钟

A quick tour to sequencer 1 - Ion Torrent PGM (English Subtitles)10分钟

A quick tour to sequencer 2 - 3730 Sanger sequencing (English Subtitles)3分钟

Student presentation (English Subtitles)9分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Next Generation Sequencing (NGS)30分钟

周

周 6

完成时间为 2 小时

Functional Prediction of Genetic Variants

Upon completion of this module you will able to: describe what is variant prediction and how to carry out variant predictions; associate variant databases with your own research projects after you get a list of variants; recognize different principles behind prediction tools and know how to use tools such as SIFT, Polyphen and SAPRED according to your won scientific problem.

完成时间为 2 小时

6 个视频（总计 92 分钟）, 2 个阅读材料, 1 个测验

6 个视频

Overview of the Problem 17分钟

Variant Databases 10分钟

Conservation-Based and Rule-Based Methods: SIFT & PolyPhen17分钟

Classifier-Based Methods: SAPRED13分钟

Introduction to Support Vector Machine(SVM) (English Subtitles)18分钟

Student presentation (English Subtitles)14分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Functional Prediction of Genetic Variants30分钟

周

周 7

完成时间为 1 小时

Mid-term Exam

The description goes here

完成时间为 1 小时

1 个练习

Mid-term Review30分钟

周

周 8

完成时间为 2 小时

Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq

Upon completion of this module, you will be able to: describe how transcriptome data were generated; master the algorithm used in transcriptome analysis; explore how the RNA-seq data were analyzed. This module is required before entering Module 9.

完成时间为 2 小时

5 个视频（总计 67 分钟）, 2 个阅读材料, 1 个测验

5 个视频

Transcriptome: An Overview12分钟

RNA-Seq: Mapping & Assembling11分钟

Computer Lab: RNA-seq Data Analysis RNA-seq (English Subtitles)22分钟

Dr. Maynard Olson Talk9分钟

Student presentation (English Subtitles)11分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq30分钟

周

周 9

完成时间为 2 小时

Prediction and Analysis of Noncoding RNA

Upon completion of this module, you will be able to: Analyze non-coding RNAs from transcriptome data; identify long noncoding RNA (lncRNA) from NGS data and predict their functions.

完成时间为 2 小时

6 个视频（总计 74 分钟）, 2 个阅读材料, 1 个测验

6 个视频

From Information to Knowledge10分钟

Data Mining: Identify long ncRNAs10分钟

Data Mining: Differential Expression and Clustering12分钟

Feature selection and Clustering (English Subtitles)14分钟

A quick tour to sequencer - illumina HiSeq & MiSeq (English Subtitles)13分钟

Student Presentation (English Subtitles)10分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Prediction and Analysis of Noncoding RNA30分钟

周

周 10

完成时间为 2 小时

Ontology and Identification of Molecular Pathways

Upon completion of this module, you will be able to: define ontology and gene ontology, explore KEGG pathway databses; examine annotations in Gene Ontology; identify pathways with KOBAS and apply the pipeline to drug addition study.

完成时间为 2 小时

8 个视频（总计 95 分钟）, 2 个阅读材料, 1 个测验

8 个视频

Ontology and Gene Ontology20分钟

KEGG Pathway Database 10分钟

Annotations in Gene Ontology 10分钟

Pathway Identification 22分钟

An Application: Common Molecular Pathways Underlying Addiction7分钟

Brief Introduction to Database (English Subtitles)5分钟

KOBAS Demo (English Subtitles)7分钟

Student presentation on KOBAS (English Subtitles)9分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Ontology and Identification of Molecular Pathways30分钟

周

周 11

完成时间为 2 小时

Bioinformatics Database and Software Resources

Upon completion of this module, you will be able to describe the most important bioinformatic resources including databases and software tools; explore both centralized resources such as NCBI, EBI, UCSC genome browser and lots of individual resources; associate all your bioinformatic problems with certain resources to refer to.

完成时间为 2 小时

6 个视频（总计 71 分钟）, 1 个阅读材料, 1 个测验

6 个视频

Overview of Resources19分钟

National Center for Biotechnology Information13分钟

European Bioinformatics Institute 9分钟

UCSC Genome Browser7分钟

Individual Resources12分钟

CBI Resources Review (English Subtitles)8分钟

1 个阅读材料

Slides10分钟

1 个练习

Bioinformatics Database and Software Resources30分钟

周

周 12

完成时间为 2 小时

Origination of New Genes

Upon completion of this case study module, you will be able to: experience how to apply bioinformatic data, methods and analyses to study an important problem in evolutionary biology; examine how to detect and study the origination, evolution and function of species-specific new genes; create phylogenetic trees with your own data (not required) with Dr. Manyuan Long, a world-renowned pioneer and expert on new genes from University of Chicago.

完成时间为 2 小时

5 个视频（总计 60 分钟）, 2 个阅读材料, 1 个测验

5 个视频

New Gene Evolution Detected by Genomic Computation: Basic Concepts and Examples20分钟

New Gene Evolution Detected by Genomic Computation: A Driver for Human Brain Evolution7分钟

A Human-Specific de novo Gene Associated with Addiction8分钟

Origination of de novo Genes from Noncoding RNAs11分钟

Student Presentation (English Subtitles)12分钟

2 个阅读材料

Readings10分钟

Slides10分钟

1 个练习

Origination of New Genes30分钟

周

周 13

完成时间为 1 小时

Evolution function analysis of DNA methyltransferase

Upon completion of this case study module, you will be able to: experience how to use bioinformatic methods to study the function and evolution of DNA methylases; share with Dr. Gang Pei, president of Tongji University and member of the Chinese Academy of Science, the experiences in scientific research and thought about MOOC.

完成时间为 1 小时

5 个视频（总计 71 分钟）, 1 个阅读材料

5 个视频

From Dry to Wet, an Evolutionary Story Part 16分钟

Project background introduction by Dr. Gang Pei25分钟

From Dry to Wet, an Evolutionary Story Part 28分钟

Talk with Dr. Gang Pei (English Subtitles)20分钟

Student Presentation (English Subtitles)10分钟

1 个阅读材料

Slides10分钟

周

周 14

完成时间为 1 小时

Final Exam

The description goes here

完成时间为 1 小时

1 个练习

Final Exam30分钟

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生物信息学: 导论与方法