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

Approx. 25 hours to complete

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Course Summary

Explore the application of computational tools in analyzing biological data with this bioinformatics course from Peking University.

Key Learning Points

Understand the basics of bioinformatics and its applications in life sciences
Learn how to use popular bioinformatics tools and databases
Apply bioinformatics methods to solve real-world problems

Learning Outcomes

Ability to apply bioinformatics methods to analyze biological data
Understanding of popular bioinformatics tools and databases
Skills to solve real-world problems using bioinformatics

Prerequisites or good to have knowledge before taking this course

Basic knowledge of biology and genetics
Familiarity with programming concepts

Course Difficulty Level

Intermediate

Course Format

Self-paced
Online
Video Lectures
Assignments and Quizzes

Similar Courses

Data Science in Genomics
Introduction to Bioinformatics

Related Education Paths

Bioinformatics Certification

Notable People in This Field

Ewan Birney
Bonnie Berger

Related Books

Description

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.

Outline

Introduction and History of Bioinformatics
What is Bioinformatics
History of Bioinformatics
Bioinformatics in Mainland China
About This Course
Readings
Slides
Introduction and History of Bioinformatics

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

Sequence Database Search
Sequence Databases
BLAST Algorithm: A Primer
Student Presentation (English Subtitles)
Readings
Slides
Sequence Database Search

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

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

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

Mid-term Exam
Mid-term Review

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

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

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

Bioinformatics Database and Software Resources
Overview of Resources
National Center for Biotechnology Information
European Bioinformatics Institute
UCSC Genome Browser
Individual Resources
CBI Resources Review (English Subtitles)
Slides
Bioinformatics Database and Software Resources

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

Evolution function analysis of DNA methyltransferase
From Dry to Wet, an Evolutionary Story Part 1
Project background introduction by Dr. Gang Pei
From Dry to Wet, an Evolutionary Story Part 2
Talk with Dr. Gang Pei (English Subtitles)
Student Presentation (English Subtitles)
Slides

Final Exam
Final Exam

Summary of User Reviews

The Bioinformatics course from Peking University on Coursera has received positive reviews from many users. The course covers a wide range of topics in bioinformatics, from sequence analysis to structural biology. One key aspect that users thought was good is the comprehensive nature of the course, which provides a strong foundation in the subject.

Pros from User Reviews

Comprehensive coverage of bioinformatics topics
Well-structured course with clear explanations and examples
Engaging lectures and helpful assignments
Access to a supportive online community of learners

Cons from User Reviews

Some users found the course content too difficult or technical
The course may require a significant time commitment to complete
Some users felt that the course could benefit from more interactive elements or hands-on practice

Recommended for you

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

Course materials are available under the CC BY-NC-SA License. Introduction and History of Bioinformatics What is Bioinformatics History of Bioinformatics Bioinformatics in Mainland China...

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