Syllabus

UCSD Academic and Administrative Calendar 2018–2019

This graduate course covers various fields of genomic data science, including but not limited to genome assembly, haplotype assembly, analysis of RNA-seq data, computational immunology, and structural genomics. In this course, we will discuss various computational problems arising in these fields, algorithms and the state-of-the-art tools solving them. Students will complete a number of homework assignments involving analysis of real sequencing data and interpretation of the results. Students will also complete a scientific project dedicated to one of discussed topics.

Prerequisites to the course:

• Python or any other programming language
• Confident work with command line
• Knowledge of algorithms
• Knowledge of basic biology
• Access to a server (at least 20Gb RAM)

The detailed syllabus is available here.

Schedule

Week 1.

• Mon, Apr 1st: Introduction to genomic data science
• Wed, Apr 3rd: Sequencing Data. History of immunology

Week 2. Analysis of immunosequencing (Rep-seq) data - 1

• Mon, Apr 8th:
  • Introduction to computational immunology and Rep-seq data.
  • HW #1: Basic analysis of antibody sequences
  • Examples of final projects
• Wed, Apr 10th: Repertoire sequencing data: protocols, artifacts, and error correction. Repertoire construction problem.

Week 3. Analysis of immunosequencing (Rep-seq) data - 2

• Mon, Apr 15th:
  • Population analysis of immunoglobulin genes and immunoglobulin locus
  • HW #2: Finding IGH genes in the reference genome
  • Deadline for submission of final project abstracts

Week 4. Analysis of immunosequencing (Rep-seq) data - 3

• Mon, Apr 22nd:
  • De novo inference of immunoglobulin genes using Rep-seq data
  • HW #3: Clonal analysis of antibody repertoires
• Wed, Apr 24th:
  • Clonal analysis of antibody repertoires
• Sun, Apr 28th, 11:59 pm: Deadline for HW 1 & 2.

Week 5. Analysis of immunosequencing (Rep-seq) data - 4. Midterm 1.

• Mon, Apr 29th:
  • Finding CDRs, types of antibodies, and design of antibody drugs. Application of immunosequencing data to biomedical studies
• Wed, May 1st: Midterm 1
• Sun, May 5th, 11:59 pm: Deadline for HW 3

Week 6. Analysis of immunosequencing (Rep-seq) data - 5.

• Mon, May 6th: Properties of antibodies from various vertebrate species. TCR repertoires.
• Wed, May 8th: Interim presentations of final projects

Week 7. Algorithms and tools for genome assembly (invited lecturer: Anton Bankevich)

• Mon, May 13th: Genome assembly, part I (slides 1 - 39)
• Wed, May 15th:
  • Genome assembly, part II (slides 40 - 46)
  • HW #4: Choose a genome assembler and read the paper describing it. Answer the following questions:
    • How does the assembler perform the main genome assembly steps described on slide 45 (lecture slides)?
    • What steps the assembler does particularly focus on and what innovation does it introduce into these steps?
    • What assumptions does the assembler make to formulate a computational problem?
    • Recommended assemblers: Celera, ARACHNE, Velvet, SPAdes, IDBA-UD, SOAPdenovo, Canu, Flye

Week 8. Haplotype assembly. RNA-seq data.

• Mon, May 20th:
  • Genome assembly, part III (slides 47 - 71).
  • Haplotype assembly, part I (slides 1 - 32)
• Wed, May 22nd:
  • Haplotype assembly, part II (slides 33 - 51).
  • Analysis of RNA-seq data.
  • HW #5: Differential Gene Expression
• Sun, May 26th, 11:59 pm: Deadline for HW 4

Week 9. Analysis of genomic 3D structure using Hi-C data.

• Mod, May 27th: Memorial Day observance
• Wed, May 29th: Analysis of Hi-C data

Week 10. Midterm 2

• Mon, Jun 3rd: Journal club
• Wed, Jun 5th: Midterm 2
• Sun, Jun 9th, 11:59 pm: Deadline for HW 5

Final week. Presentations of student projects

• Mon, Jun 10th: 8:00 am - 11:00 am.