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.
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北京大学
教学大纲 - 您将从这门课程中学到什么
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
4 个视频 （总计 69 分钟）, 2 个阅读材料, 1 个测验
4 个视频
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 Bioinformatics20分钟
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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.
7 个视频 （总计 99 分钟）, 2 个阅读材料, 1 个测验
7 个视频
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 Alignment18分钟
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3完成时间为 1 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.
3 个视频 （总计 41 分钟）, 2 个阅读材料, 1 个测验
3 个视频
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 Search10分钟
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4完成时间为 1 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.
4 个视频 （总计 47 分钟）, 2 个阅读材料, 1 个测验
4 个视频
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 14分钟
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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.
8 个视频 （总计 85 分钟）, 2 个阅读材料, 1 个测验
8 个视频
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)10分钟
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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.
6 个视频 （总计 92 分钟）, 2 个阅读材料, 1 个测验
6 个视频
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 Variants14分钟
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7完成时间为 2 小时
Mid-term Exam
The description goes here
1 个测验
1 个练习
Mid-term Review40分钟
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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.
5 个视频 （总计 67 分钟）, 2 个阅读材料, 1 个测验
5 个视频
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-Seq16分钟
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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.
6 个视频 （总计 74 分钟）, 2 个阅读材料, 1 个测验
6 个视频
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 RNA14分钟
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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.
8 个视频 （总计 95 分钟）, 2 个阅读材料, 1 个测验
8 个视频
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 Pathways12分钟
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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.
6 个视频 （总计 71 分钟）, 1 个阅读材料, 1 个测验
6 个视频
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 Resources10分钟
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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.
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: 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 Genes10分钟
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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.
5 个视频 （总计 71 分钟）, 1 个阅读材料
5 个视频
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
14完成时间为 1 小时
Final Exam
The description goes here
1 个测验
1 个练习
Final Exam20分钟
4.7
31 个审阅40%
通过此课程获得实实在在的工作福利
25%
加薪或升职
热门审阅
The course has given me a great way to learn Bioinformatics. I especially loved the mode of teaching and the case studies.
讲师
Ge Gao 高歌, Ph.D.
Assistant Professor, Principle InvestigatorCenter for Bioinformatics, School of Life Science
Liping Wei 魏丽萍, Ph.D.
Professor, DirectorCenter for Bioinformatics, School of Life Sciences
关于 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.
Founded in 1898, Peking University (PKU) was the first national comprehensive university in China. For the past 115 years, with its hundreds of thousands of outstanding alumni, Peking University has made prominent contributions in the humanities and sciences to further China's prosperity and progress.
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