SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Introduction and History of Bioinformatics

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Sequence Alignment

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Sequence Database Search

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Markov Model

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Next Generation Sequencing (NGS)

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Functional Prediction of Genetic Variants

SEMANA 7

Mid-term Exam

The description goes here

Nota atribuída: Mid-term Review

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Prediction and Analysis of Noncoding RNA

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Ontology and Identification of Molecular Pathways

SEMANA 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 vídeos, 1 leitura

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

Nota atribuída: Bioinformatics Database and Software Resources

SEMANA 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 vídeos, 2 leituras

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

Nota atribuída: Origination of New Genes

SEMANA 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 vídeos, 1 leitura

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

SEMANA 14

Final Exam

The description goes here

Nota atribuída: Final Exam

Compromisso	1-2 hours/week
Idioma	English
Como ser aprovado	Seja aprovado em todas as tarefas para concluir o curso.
Classificação do usuário	4.7 estrelas Classificação média do usuário 4.7Veja o que os aprendizes disseram

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