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Module Catalogue

LF319-15 Advanced Computational Genomics

Department
Life Sciences
Level
Undergraduate Level 3
Module leader
Sascha Ott
Credit value
15
Module duration
7 weeks
Assessment
Multiple
Study location
University of Warwick main campus, Coventry

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Introductory description

This module aims to build hands on skills to handle and analyse genomic and transcriptomic data sets through a set of lectures and workshops. It introduces a range of genomic technologies and statistical and computational foundations required to analyse high-throughput data types that are produced by these technologies. This module is a destination for students studying genetics and would suite those who wish to pursue research or industry work in the fields of genomics and analysis of big data.

Computational Biology (LF132) is the prerequisite for this module.

Module aims

  • learn to appraise the use of different sequencing technologies for specific purposes
  • extract insights from annotated genomes
  • learn to compute genome assemblies
  • fundamental aspects of statistics in genomics
  • beyond DNA sequencing: advanced genomic technologies
  • comparative genomics
  • analysis of single-cell sequencing data
  • use of the command line
  • calling single nucleotide polymorphisms
  • identifying differentially expressed genes

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

This module covers sequencing technologies, advanced genomic protocols, genomic data visualisation and extraction, genome assembly, frequent statistical issues in genomics, comparative genomics, single-cell analyses, command line use, calling single nucleotide polymorphisms, and differential expression analyses.

Learning outcomes

By the end of the module, students should be able to:

  • appraise the use of different sequencing technologies for specific purposes
  • extract insights from annotated genomes
  • compute genome assemblies
  • understand fundamental aspects of statistics in genomics
  • understand the possibilities of advanced genomic technologies
  • understand the fundamentals of comparative genomics
  • analyse single-cell sequencing data
  • make basic use of the command line
  • call single nucleotide polymorphisms
  • identify differentially expressed genes

Interdisciplinary

See above.

Subject specific skills

  • appraise use of different sequencing technologies for specific purposes
  • extracting insights from annotated genomes
  • genome assemblies
  • fundamental aspects of statistics in genomics
  • beyond DNA sequencing: advanced genomic technologies
  • comparative genomics
  • analysis of single-cell sequencing data
  • use of the command line
  • calling single nucleotide polymorphisms
  • identifying differentially expressed genes

Transferable skills

  1. Critical analysis of complex workflows consisting of experimental and computational components, in relation to scientific objectives.
  2. Basic programming skills for the command line.
  3. Integrating concepts from multiple scientific disciplines into a single coherent line of reasoning.

Study time

Type Required
Lectures 7 sessions of 1 hour (5%)
Practical classes 7 sessions of 3 hours (14%)
Assessment 122 hours (81%)
Total 150 hours

Private study description

No private study requirements defined for this module.

Costs

No further costs have been identified for this module.

You do not need to pass all assessment components to pass the module.

Assessment group C
Weighting Study time Eligible for self-certification
Genomic exercises 50% 61 hours Yes (extension)

Computational exercises for which solutions can be derived based on materials taught in lectures and workshops.
Advanced Computational Genomics Viva 50% 61 hours No

Essential opportunity to develop oral examination skills crucial for most career paths. Questions are drawn from learning materials of lectures and workshops.
Assessment group R
Weighting Study time Eligible for self-certification
Genomic exercises 100% No

Computational exercises for which solutions can be derived based on materials taught in lectures and workshops.
Feedback on assessment

Final examination feedback is given to returning students as generalised feedback on what constituted a good answer to question types; common mistakes/misconceptions and good practise are identified and shared.

Past exam papers for LF319

Pre-requisites

Having taken Genetics and Genomics in Year 2 is advantagous, but not a hard requirement.

To take this module, you must have passed:

Courses

This module is Optional for:

  • UBSA-C700 Undergraduate Biochemistry
    • Year 3 of C700 Biochemistry
    • Year 3 of C700 Biochemistry
  • ULFA-C1A2 Undergraduate Biochemistry (MBio)
    • Year 3 of C1A2 Biochemistry
    • Year 3 of C700 Biochemistry
  • Year 3 of ULFA-C702 Undergraduate Biochemistry (with Placement Year)
  • Year 3 of ULFA-C1A6 Undergraduate Biochemistry with Industrial Placement (MBio)
  • UBSA-3 Undergraduate Biological Sciences
    • Year 3 of C100 Biological Sciences
    • Year 3 of C100 Biological Sciences
    • Year 3 of C102 Biological Sciences with Cell Biology
    • Year 3 of C103 Biological Sciences with Environmental Resources
    • Year 3 of C104 Biological Sciences with Microbiology
    • Year 3 of C105 Biological Sciences with Molecular Genetics
    • Year 3 of C107 Biological Sciences with Virology
  • Year 3 of ULFA-C1A1 Undergraduate Biological Sciences (MBio)
  • Year 3 of ULFA-C113 Undergraduate Biological Sciences (with Placement Year)
  • Year 3 of ULFA-C1A5 Undergraduate Biological Sciences with Industrial Placement (MBio)
  • UBSA-C1B9 Undergraduate Biomedical Science
    • Year 3 of C1B9 Biomedical Science
    • Year 3 of C1B9 Biomedical Science
    • Year 3 of C1B9 Biomedical Science
  • ULFA-C1A3 Undergraduate Biomedical Science (MBio)
    • Year 3 of C1A3 Biomedical Science
    • Year 3 of C1B9 Biomedical Science
  • Year 3 of ULFA-C1A7 Undergraduate Biomedical Science with Industrial Placement (MBio)
  • ULFA-CB18 Undergraduate Biomedical Science with Placement Year
    • Year 3 of CB18 Biomedical Science with Placement Year
    • Year 3 of CB18 Biomedical Science with Placement Year
    • Year 3 of CB18 Biomedical Science with Placement Year
  • Year 3 of ULFA-B140 Undergraduate Neuroscience (BSc)
  • Year 3 of ULFA-B142 Undergraduate Neuroscience (MBio)
  • Year 3 of ULFA-B143 Undergraduate Neuroscience (with Industrial Placement) (MBio)
  • Year 3 of ULFA-B141 Undergraduate Neuroscience (with Placement Year) (BSc)