НЕДЕЛЯ 1

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 видео, 2 материалов для самостоятельного изучения

Видео: What is Bioinformatics
Видео: History of Bioinformatics
Видео: Bioinformatics in Mainland China
Видео: About This Course
Reading: Readings
Reading: Slides

Оцениваемый: Introduction and History of Bioinformatics

НЕДЕЛЯ 2

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 видео, 2 материалов для самостоятельного изучения

Видео: Essential Concepts
Видео: Global Alignment by Dynamic Programming
Видео: From Global to Local
Видео: Alignment with Affine Gap Penalty and Calculation of Time Complexity of The Needleman-Wunsch Algorithm
Видео: Interview with M. S. Waterman Waterman
Видео: Supplement on Homology & Similarity, Similarity Matrix and Dot Matrix (English Subtitles)
Видео: Student Presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Sequence Alignment

НЕДЕЛЯ 3

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 видео, 2 материалов для самостоятельного изучения

Видео: Sequence Databases
Видео: BLAST Algorithm: A Primer
Видео: Student Presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Sequence Database Search

НЕДЕЛЯ 4

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 видео, 2 материалов для самостоятельного изучения

Видео: From States to Markov Chain
Видео: Hidden Markov Model
Видео: Predict with Hidden Markov Model
Видео: Student Presentation
Reading: Readings
Reading: Slides

Оцениваемый: Markov Model

НЕДЕЛЯ 5

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 видео, 2 материалов для самостоятельного изучения

Видео: From Sequencing to NGS
Видео: Reads Mapping and Variants Calling
Видео: Computer Lab: Reads mapping and variant calling (English Subtitles)
Видео: Supplement on reads mapping and variant calling (English Subtitles)
Видео: Supplement on genotyping (English Subtitles)
Видео: A quick tour to sequencer 1 - Ion Torrent PGM (English Subtitles)
Видео: A quick tour to sequencer 2 - 3730 Sanger sequencing (English Subtitles)
Видео: Student presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Next Generation Sequencing (NGS)

НЕДЕЛЯ 6

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 видео, 2 материалов для самостоятельного изучения

Видео: Overview of the Problem
Видео: Variant Databases
Видео: Conservation-Based and Rule-Based Methods: SIFT & PolyPhen
Видео: Classifier-Based Methods: SAPRED
Видео: Introduction to Support Vector Machine(SVM) (English Subtitles)
Видео: Student presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Functional Prediction of Genetic Variants

НЕДЕЛЯ 7

Mid-term Exam

The description goes here

Оцениваемый: Mid-term Review

НЕДЕЛЯ 8

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 видео, 2 материалов для самостоятельного изучения

Видео: Transcriptome: An Overview
Видео: RNA-Seq: Mapping & Assembling
Видео: Computer Lab: RNA-seq Data Analysis RNA-seq (English Subtitles)
Видео: Dr. Maynard Olson Talk
Видео: Student presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq

НЕДЕЛЯ 9

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 видео, 2 материалов для самостоятельного изучения

Видео: From Information to Knowledge
Видео: Data Mining: Identify long ncRNAs
Видео: Data Mining: Differential Expression and Clustering
Видео: Feature selection and Clustering (English Subtitles)
Видео: A quick tour to sequencer - illumina HiSeq & MiSeq (English Subtitles)
Видео: Student Presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Prediction and Analysis of Noncoding RNA

НЕДЕЛЯ 10

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 видео, 2 материалов для самостоятельного изучения

Видео: Ontology and Gene Ontology
Видео: KEGG Pathway Database
Видео: Annotations in Gene Ontology
Видео: Pathway Identification
Видео: An Application: Common Molecular Pathways Underlying Addiction
Видео: Brief Introduction to Database (English Subtitles)
Видео: KOBAS Demo (English Subtitles)
Видео: Student presentation on KOBAS (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Ontology and Identification of Molecular Pathways

НЕДЕЛЯ 11

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 видео, 1 материал для самостоятельного изучения

Видео: Overview of Resources
Видео: National Center for Biotechnology Information
Видео: European Bioinformatics Institute
Видео: UCSC Genome Browser
Видео: Individual Resources
Видео: CBI Resources Review (English Subtitles)
Reading: Slides

Оцениваемый: Bioinformatics Database and Software Resources

НЕДЕЛЯ 12

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 видео, 2 материалов для самостоятельного изучения

Видео: New Gene Evolution Detected by Genomic Computation: Basic Concepts and Examples
Видео: New Gene Evolution Detected by Genomic Computation: A Driver for Human Brain Evolution
Видео: A Human-Specific de novo Gene Associated with Addiction
Видео: Origination of de novo Genes from Noncoding RNAs
Видео: Student Presentation (English Subtitles)
Reading: Readings
Reading: Slides

Оцениваемый: Origination of New Genes

НЕДЕЛЯ 13

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 видео, 1 материал для самостоятельного изучения

Видео: From Dry to Wet, an Evolutionary Story Part 1
Видео: Project background introduction by Dr. Gang Pei
Видео: From Dry to Wet, an Evolutionary Story Part 2
Видео: Talk with Dr. Gang Pei (English Subtitles)
Видео: Student Presentation (English Subtitles)
Reading: Slides

НЕДЕЛЯ 14

Final Exam

The description goes here

Оцениваемый: Final Exam

Выполнение	1-2 hours/week
Язык	English
Как пройти курс	Чтобы пройти курс, выполните все оцениваемые задания.
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Bioinformatics: Introduction and Methods 生物信息学: 导论与方法

Bioinformatics: Introduction and Methods 生物信息学: 导论与方法