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（Peking University）
シラバス - 本コースの学習内容
週
12時間で修了
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件のビデオ （合計69分）, 2 readings, 1 quiz
4件のビデオ
History of Bioinformatics30 分
Bioinformatics in Mainland China8 分
About This Course9 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Introduction and History of Bioinformatics20 分
週
22時間で修了
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件のビデオ （合計99分）, 2 readings, 1 quiz
7件のビデオ
Global Alignment by Dynamic Programming14 分
From Global to Local6 分
Alignment with Affine Gap Penalty and Calculation of Time Complexity of The Needleman-Wunsch Algorithm6 分
Interview with M. S. Waterman Waterman29 分
Supplement on Homology & Similarity, Similarity Matrix and Dot Matrix (English Subtitles)10 分
Student Presentation (English Subtitles)18 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Sequence Alignment18 分
週
31時間で修了
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件のビデオ （合計41分）, 2 readings, 1 quiz
3件のビデオ
BLAST Algorithm: A Primer13 分
Student Presentation (English Subtitles)15 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Sequence Database Search10 分
週
41時間で修了
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件のビデオ （合計47分）, 2 readings, 1 quiz
4件のビデオ
Hidden Markov Model11 分
Predict with Hidden Markov Model10 分
Student Presentation16 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Markov Model 14 分
週
52時間で修了
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件のビデオ （合計85分）, 2 readings, 1 quiz
8件のビデオ
Reads Mapping and Variants Calling14 分
Computer Lab: Reads mapping and variant calling (English Subtitles)7 分
Supplement on reads mapping and variant calling (English Subtitles)9 分
Supplement on genotyping (English Subtitles)18 分
A quick tour to sequencer 1 - Ion Torrent PGM (English Subtitles)10 分
A quick tour to sequencer 2 - 3730 Sanger sequencing (English Subtitles)3 分
Student presentation (English Subtitles)9 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Next Generation Sequencing (NGS)10 分
週
62時間で修了
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件のビデオ （合計92分）, 2 readings, 1 quiz
6件のビデオ
Variant Databases 10 分
Conservation-Based and Rule-Based Methods: SIFT & PolyPhen17 分
Classifier-Based Methods: SAPRED13 分
Introduction to Support Vector Machine(SVM) (English Subtitles)18 分
Student presentation (English Subtitles)14 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Functional Prediction of Genetic Variants14 分
週
72時間で修了
Mid-term Exam
The description goes here
1 quiz
1の練習問題
Mid-term Review40 分
週
82時間で修了
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件のビデオ （合計67分）, 2 readings, 1 quiz
5件のビデオ
RNA-Seq: Mapping & Assembling11 分
Computer Lab: RNA-seq Data Analysis RNA-seq (English Subtitles)22 分
Dr. Maynard Olson Talk9 分
Student presentation (English Subtitles)11 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq16 分
週
92時間で修了
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件のビデオ （合計74分）, 2 readings, 1 quiz
6件のビデオ
Data Mining: Identify long ncRNAs10 分
Data Mining: Differential Expression and Clustering12 分
Feature selection and Clustering (English Subtitles)14 分
A quick tour to sequencer - illumina HiSeq & MiSeq (English Subtitles)13 分
Student Presentation (English Subtitles)10 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Prediction and Analysis of Noncoding RNA14 分
週
102時間で修了
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件のビデオ （合計95分）, 2 readings, 1 quiz
8件のビデオ
KEGG Pathway Database 10 分
Annotations in Gene Ontology 10 分
Pathway Identification 22 分
An Application: Common Molecular Pathways Underlying Addiction7 分
Brief Introduction to Database (English Subtitles)5 分
KOBAS Demo (English Subtitles)7 分
Student presentation on KOBAS (English Subtitles)9 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Ontology and Identification of Molecular Pathways12 分
週
112時間で修了
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件のビデオ （合計71分）, 1 reading, 1 quiz
6件のビデオ
National Center for Biotechnology Information13 分
European Bioinformatics Institute 9 分
UCSC Genome Browser7 分
Individual Resources12 分
CBI Resources Review (English Subtitles)8 分
1件の学習用教材
Slides10 分
1の練習問題
Bioinformatics Database and Software Resources10 分
週
122時間で修了
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件のビデオ （合計60分）, 2 readings, 1 quiz
5件のビデオ
New Gene Evolution Detected by Genomic Computation: A Driver for Human Brain Evolution7 分
A Human-Specific de novo Gene Associated with Addiction8 分
Origination of de novo Genes from Noncoding RNAs11 分
Student Presentation (English Subtitles)12 分
2件の学習用教材
Readings10 分
Slides10 分
1の練習問題
Origination of New Genes10 分
週
131時間で修了
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件のビデオ （合計71分）, 1 reading
5件のビデオ
Project background introduction by Dr. Gang Pei25 分
From Dry to Wet, an Evolutionary Story Part 28 分
Talk with Dr. Gang Pei (English Subtitles)20 分
Student Presentation (English Subtitles)10 分
1件の学習用教材
Slides10 分
週
141時間で修了
Final Exam
The description goes here
1 quiz
1の練習問題
Final Exam20 分
4.7
31件のレビュー40%
コースが具体的なキャリアアップにつながった
25%
昇給や昇進につながった
人気のレビュー
The course has given me a great way to learn Bioinformatics. I especially loved the mode of teaching and the case studies.
講師
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
北京大学（Peking University）について
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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