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Bioinformatics: Introduction and Methods 生物信息学: 导论与方法
  • Level Foundation
  • Course by Peking University
  • Offered by

About

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.

Modules

What is Bioinformatics

    • 1 Videos
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1 Videos

  • What is Bioinformatics

History of Bioinformatics

    • 1 Videos
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1 Videos

  • History of Bioinformatics

Overview of Bioinformatics in China and About This Course

    • 2 Videos
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2 Videos

  • Bioinformatics in Mainland China
  • About This Course

Review

    • 1 Assignment
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1 Assignment

  • Introduction and History of Bioinformatics

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Sequence Alignment, Part I

    • 2 Videos
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2 Videos

  • Essential Concepts
  • Global Alignment by Dynamic Programming

Sequence Alignment, Part II

    • 2 Videos
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2 Videos

  • 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

    • 1 Videos
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1 Videos

  • Interview with M. S. Waterman Waterman

Supplemental Lectures and Presentations

    • 2 Videos
    • 2 Readings
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2 Videos

  • Supplement on Homology & Similarity, Similarity Matrix and Dot Matrix (English Subtitles)
  • Student Presentation (English Subtitles)

2 Readings

  • Readings
  • Slides

Review

    • 1 Assignment
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1 Assignment

  • Sequence Alignment

Sequence Database Search

    • 2 Videos
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2 Videos

  • Sequence Databases
  • BLAST Algorithm: A Primer

Student Presentation

    • 1 Videos
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1 Videos

  • Student Presentation (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Sequence Database Search

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Markov Model

    • 3 Videos
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3 Videos

  • From States to Markov Chain
  • Hidden Markov Model
  • Predict with Hidden Markov Model

Student Presentation

    • 1 Videos
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1 Videos

  • Student Presentation

Review

    • 1 Assignment
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1 Assignment

  • Markov Model

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Next Generation Sequencing (NGS)

    • 3 Videos
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3 Videos

  • From Sequencing to NGS
  • Reads Mapping and Variants Calling
  • Computer Lab: Reads mapping and variant calling (English Subtitles)

Supplemental Lectures

    • 4 Videos
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4 Videos

  • 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

    • 1 Videos
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1 Videos

  • Student presentation (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Next Generation Sequencing (NGS)

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Variant Databases

    • 2 Videos
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2 Videos

  • Overview of the Problem
  • Variant Databases

Predicting Methods

    • 2 Videos
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2 Videos

  • Conservation-Based and Rule-Based Methods: SIFT & PolyPhen
  • Classifier-Based Methods: SAPRED

Supplemental Lectures

    • 1 Videos
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1 Videos

  • Introduction to Support Vector Machine(SVM) (English Subtitles)

Student Presentation

    • 1 Videos
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1 Videos

  • Student presentation (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Functional Prediction of Genetic Variants

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Mid-term Exam

    • 1 Assignment
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1 Assignment

  • Mid-term Review

Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq

    • 3 Videos
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3 Videos

  • Transcriptome: An Overview
  • RNA-Seq: Mapping & Assembling
  • Computer Lab: RNA-seq Data Analysis RNA-seq (English Subtitles)

Supplemental Lectures

    • 1 Videos
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1 Videos

  • Dr. Maynard Olson Talk

Student Presentation

    • 1 Videos
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1 Videos

  • Student presentation (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

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

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Prediction and Analysis of Noncoding RNA

    • 3 Videos
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3 Videos

  • From Information to Knowledge
  • Data Mining: Identify long ncRNAs
  • Data Mining: Differential Expression and Clustering

Supplemental Lectures

    • 2 Videos
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2 Videos

  • Feature selection and Clustering (English Subtitles)
  • A quick tour to sequencer - illumina HiSeq & MiSeq (English Subtitles)

Student Presentation

    • 1 Videos
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1 Videos

  • Student Presentation (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Prediction and Analysis of Noncoding RNA

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Ontology, Gene Ontology and KEGG Pathway Database

    • 2 Videos
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2 Videos

  • Ontology and Gene Ontology
  • KEGG Pathway Database

Annotations in Gene Ontology and Pathway Identification

    • 3 Videos
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3 Videos

  • Annotations in Gene Ontology
  • Pathway Identification
  • An Application: Common Molecular Pathways Underlying Addiction

Supplemental Lectures

    • 2 Videos
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2 Videos

  • Brief Introduction to Database (English Subtitles)
  • KOBAS Demo (English Subtitles)

Student Presentation

    • 1 Videos
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1 Videos

  • Student presentation on KOBAS (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Ontology and Identification of Molecular Pathways

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Overview and NCBI

    • 2 Videos
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2 Videos

  • Overview of Resources
  • National Center for Biotechnology Information

EBI, UCSC and Individual Resources

    • 3 Videos
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3 Videos

  • European Bioinformatics Institute
  • UCSC Genome Browser
  • Individual Resources

Student Presentation

    • 1 Videos
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1 Videos

  • CBI Resources Review (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Bioinformatics Database and Software Resources

Supplementary

    • 1 Readings
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1 Readings

  • Slides

Origination of New Genes Part I

    • 2 Videos
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2 Videos

  • New Gene Evolution Detected by Genomic Computation: Basic Concepts and Examples
  • New Gene Evolution Detected by Genomic Computation: A Driver for Human Brain Evolution

Origination of New Genes Part II

    • 2 Videos
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2 Videos

  • A Human-Specific de novo Gene Associated with Addiction
  • Origination of de novo Genes from Noncoding RNAs

Student Presentation

    • 1 Videos
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1 Videos

  • Student Presentation (English Subtitles)

Review

    • 1 Assignment
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1 Assignment

  • Origination of New Genes

Supplementary

    • 2 Readings
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2 Readings

  • Readings
  • Slides

Evolution Function Analysis of DNA Methyltransferase

    • 3 Videos
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3 Videos

  • 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

Supplemental Lectures

    • 1 Videos
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1 Videos

  • Talk with Dr. Gang Pei (English Subtitles)

Student Presentation

    • 1 Videos
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1 Videos

  • Student Presentation (English Subtitles)

Supplementary

    • 1 Readings
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1 Readings

  • Slides

Final Exam

    • 1 Assignment
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1 Assignment

  • Final Exam

Auto Summary

"Bioinformatics: Introduction and Methods" is an engaging online course offered by Peking University through Coursera, designed for individuals interested in the intersection of biology and computational science. This foundational course delves into the essential concepts and computational techniques within the dynamic field of bioinformatics, equipping learners with valuable knowledge and skills applicable to both academic study and research. Guided by expert instructors, participants will explore a variety of bioinformatics applications in biology, gaining a comprehensive understanding of this interdisciplinary domain. The course materials are freely available under the CC BY-NC-SA License, ensuring open access to learning resources. Ideal for beginners, the course offers both Starter and Professional subscription options, catering to different levels of commitment and professional goals. Whether you're a student, researcher, or simply curious about bioinformatics, this course provides a solid foundation to advance your expertise in this rapidly evolving field.

Ge Gao 高歌, Ph.D.
Instructors

Ge Gao 高歌, Ph.D.

Liping Wei 魏丽萍, Ph.D.
Instructors

Liping Wei 魏丽萍, Ph.D.