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Peking University extends a warm welcome to “Bioinformatics: Introduction and Methods”! This MOOC will familiarise you 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 will acquire will help you in your future study and research.
Syllabus :
1. Introduction and History of Bioinformatics
- What is Bioinformatics
- History of Bioinformatics
- Bioinformatics in Mainland China
2. 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)
3. Sequence Database Search
- Sequence Databases
- BLAST Algorithm: A Primer
4. Markov Model
- From States to Markov Chain
- Hidden Markov Model
- Predict with Hidden Markov Model
5. 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)
6. 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)
7. 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
8. 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)
9. 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)
10. 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)
11. 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
12. 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)
