Bioinformatics

Module code: BS2040

Module co-ordinators: Dr Richard Badge and Professor Raymond Dalgleish

In this module you will study how computers are used to investigate the organisation and evolution of genes and genomes. We will look at a wide range of genes and genomes including model systems such as yeast, Drosophila and mouse - and of course, humans.

Practical sessions, giving you hands-on experience in some of the techniques used in the computer analysis of genes and genomes, will include:

  • Sequence-database searching — identifying genes and their human homologues
  • Researching human genetic variation in the context of disease genes and populations
  • Construction of phylogenetic trees to determine evolutionary relatedness of genes

Topics covered

  • Introduction to Bioinformatics:
    An introductory overview of the field of bioinformatics, including the underpinning principles of molecular biology that allow the acquisition, analysis and storage of information about genomes, transcriptomes and proteomes. The principles, practices and challenges of curating and making accessible biological information in databases will also be discussed. Topics in the introduction will be expanded in subsequent lectures.
  • Genome organisation and evolution:
    This topic will cover the contents, organising principles and analysis of both simple and complex genomes. The challenges of genome annotation and functional genomics will be explored, along with the opportunities offered by comparative genomics. Human population genomics and its applications in the study of human identification and demographics will also be a focus.
  • Gene expression and regulation:
    Building on basic concepts of gene expression this topic seeks to integrate transcriptomic and proteomic analyses to explore the basis and operation of regulatory networks in simple and complex biological systems.
  • Scientific publications and archives:
    This topic will explore how the development of the scientific literature has influenced the practice of science, particularly in the light of the explosion in the amount of information and the evolution of its form, content and access. Computational approaches to managing and searching the literature will be a focus.
  • Bioinformatic databases and information retrieval:
    Effectively accessing molecular data held in online databases is an essential skill for the bioinformatician. This topic will review the plethora of databases available and the many access routes, as well as efficient search strategies.
  • Alignments and phylogenetic trees:
    Alignment of sequence pairs and multiple sequences is an underpinning analysis approach in bioinformatics and this topic explores the process in theory and in practice. A major application of aligned sequences, the construction of phylogenetic trees, will be a key focus.
  • Structural bioinformatics and drug discovery:
    Computational visualisation of protein structural data is central to understanding how linear amino acids sequences specify 3D molecular shapes. How this challenge informs our attempts towards rational drug design will be explored in this topic.
  • Introduction to systems biology:
    As a modern trend in biology the integrative theme of systems biology links together many levels of bioinformatics. In this topic an introduction to the concepts, capabilities and limitations of characterising biological systems in mathematical terms will be presented.
  • Metabolic pathways:
    The unifying understanding of biological metabolism is very successful in facilitating analysis of novel genomes, transcriptomes and proteomes, but has limitations. A focus will be how modelling of metabolism provides insight into metabolic networks and their properties.
  • Bioinformatics in practice: Now and the Future:
    Lectures in this topic will review the current state of the art, in terms of how technology (both hardware and software) is transforming the field of biology. We will seek to highlight new trends and emerging technologies to equip students with an appreciation of future developments in the field.

Learning

  • 30 one-hour lectures
  • 15 hours of practicals
  • 10 one-hour tutorials

Assessment

  • Exam, 2 hours (55%)
  • 3 practical reports (15% + 15% + 15%)