22 episodes

This course is an introduction to computational biology emphasizing the fundamentals of nucleic acid and protein sequence and structural analysis; it also includes an introduction to the analysis of complex biological systems.

Foundations of Computational and Systems Biology MIT

    • Science

This course is an introduction to computational biology emphasizing the fundamentals of nucleic acid and protein sequence and structural analysis; it also includes an introduction to the analysis of complex biological systems.

    • video
    Lecture 1: Introduction to Computational and Systems Biology

    Lecture 1: Introduction to Computational and Systems Biology

    In this lecture, Professors Burge, Gifford, and Fraenkel give an historical overview of the field of computational and systems biology, as well as outline the material they plan to cover throughout the semester.

    • 1 hr 6 min
    • video
    Lecture 2: Local Alignment (BLAST) and Statistics

    Lecture 2: Local Alignment (BLAST) and Statistics

    In this lecture, Professor Burge reviews classical and next-generation sequencing. He then introduces local alignment (BLAST) and some of the associated statistics.

    • 1 hr 16 min
    • video
    Lecture 3: Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)

    Lecture 3: Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)

    In this lecture, Prof. Burge discusses global sequence alignment and gapped local sequence alignment. He later talks about substitution matrices for protein comparison.

    • 1 hr 20 min
    • video
    Lecture 4: Comparative Genomic Analysis of Gene Regulation

    Lecture 4: Comparative Genomic Analysis of Gene Regulation

    Prof. Burge discusses comparative genomics. He begins with a review of global alignment of protein sequences, then talks about Markov models, the Jukes-Cantor model, and Kimura models. He discusses types of selection: natural, negative, and positive.

    • 1 hr 22 min
    • video
    Lecture 5: Library Complexity and Short Read Alignment (Mapping)

    Lecture 5: Library Complexity and Short Read Alignment (Mapping)

    Prof. Gifford talks about library complexity as it relates to genome sequencing. He explains how to create a full-text minute-size (FM) index, which involves a Burrows-Wheeler transform (BWT). He ends with how to deal with the problem of mismatching.

    • 1 hr 20 min
    • video
    Lecture 6: Genome Assembly

    Lecture 6: Genome Assembly

    Prof. Gifford talks about two different ways to assemble a genome de novo. The first approach is overlap layout consensus assemblers, as exemplified by string graph assemblers. The second approach is de Bruijn graph-based assemblers.

    • 1 hr 8 min

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