SEMAINE 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 vidéos, 2 lectures

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

Noté: Introduction and History of Bioinformatics

SEMAINE 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 vidéos, 2 lectures

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

Noté: Sequence Alignment

SEMAINE 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 vidéos, 2 lectures

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

Noté: Sequence Database Search

SEMAINE 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 vidéos, 2 lectures

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

Noté: Markov Model

SEMAINE 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 vidéos, 2 lectures

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

Noté: Next Generation Sequencing (NGS)

SEMAINE 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 vidéos, 2 lectures

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

Noté: Functional Prediction of Genetic Variants

SEMAINE 7

Mid-term Exam

The description goes here

Noté: Mid-term Review

SEMAINE 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 vidéos, 2 lectures

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

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

SEMAINE 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 vidéos, 2 lectures

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

Noté: Prediction and Analysis of Noncoding RNA

SEMAINE 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 vidéos, 2 lectures

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

Noté: Ontology and Identification of Molecular Pathways

SEMAINE 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 vidéos, 1 lecture

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

Noté: Bioinformatics Database and Software Resources

SEMAINE 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 vidéos, 2 lectures

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

Noté: Origination of New Genes

SEMAINE 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 vidéos, 1 lecture

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

SEMAINE 14

Final Exam

The description goes here

Noté: Final Exam

Engagement	1-2 hours/week
Langue	English
Comment réussir	Réussissez tous les devoirs notés pour terminer le cours.
Notes des utilisateurs	4.7 étoiles Note moyenne des utilisateurs 4.7Voir ce que disent les étudiants

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