BI3ART1: Advanced Research Techniques

Module code: BI3ART1

Module provider: School of Biological Sciences

Credits: 20

Level: 6

When you’ll be taught: Semester 1

Module convenor: Dr Connor Sharp , email: c.sharp@reading.ac.uk

Module co-convenor: Professor Kimberly Watson, email: k.a.watson@reading.ac.uk

Pre-requisite module(s):

Co-requisite module(s):

Pre-requisite or Co-requisite module(s):

Module(s) excluded:

Placement information: NA

Academic year: 2025/6

Available to visiting students: No

Talis reading list: Yes

Last updated: 3 April 2025

Overview

Module aims and purpose

Advances in technology have transformed the life sciences. New tools allow us to examine the details of protein folding, structure, and function with increasing precision. Although the first bacterial genome was sequenced only in 1995, research now involves analysing thousands of genomes. Modern life science research combines multiple techniques and data types to study biology on various scales, from changes in entire populations to the atomic structure of individual proteins. 

In this module, you will learn the state-of-the-art techniques and tools used in modern life science research and how they can be combined to answer real research questions. This module will provide you with an understanding of modern techniques in genomics, transcriptomics, proteomics, and metabolomics. You will learn the strengths and limitations of these techniques, how to interpret the diverse data types produced in modern biology, and how to combine various techniques to address real research questions. 

Module learning outcomes

By the end of the module, it is expected that students will be able to: 

1. Describe the different types of data encountered in modern biological research and the tools needed for its analysis 
2. Use web-based tools to retrieve, manipulate, analyse and interpret biological data. 
3. Explain how researchers integrate different techniques and data to answer questions in biology and evaluate the strengths and weaknesses of current, state-of-the-art approaches. 

Module content

Lecture material includes the following topics:

• The types and scales of data encountered in biology research and the need for tools to analyse data
• The interplay between computational and experimental biology.

Genomics

• Sequencing genomes: Sequencing methods (Sanger, NGS, Nanopore) and assembling short reads
• Sequencing as a tool: ChIP-Seq, Tn-Seq/TraDIS,
• Functional annotation of genomes: Finding genes, motifs and domains, functional prediction, identifying AMR genes and virulence factors, and structure prediction
• Biological data resources: Online databases and tools for analysing genomes
• Sequence alignment and phylogenetics: Homology, sequence evolution, phylogenetics, sequencing populations, Genome-wide association studies, bacterial pangenomes and comparative genomics
• Metagenomics: Profiling microbial community composition with 16S/18S, metagenomic assembled genomes, sequencing the human microbiome

Transcriptomics

• Gene regulation: DNA motifs, transcription factor binding sites and regulons
• Principles of measuring transcription: RNAseq, normalization, differential analysis
• Advances in transcriptomics: singles cell, meta- and spatial transcriptomics

Proteomics and metabolomics

• Quantifying changes in protein abundance
• Modelling metabolic pathways and systems

Protein Structure and Function

• Protein expression and engineering
• Protein structure and folds
• Protein design
• Protein structure tools – X-ray crystallography and Cryo-Electron Microscopy 
• Artificial intelligence in studying proteins

Practical classes include:

• Running common bioinformatics software
• Assembly and analysis of bacterial genomes
• Using genomic and proteomic databases to analyse protein structure and function
• Analysing complex biological data and interpreting results

Structure

Teaching and learning methods

The learning outcomes will be achieved through a mixture of lectures, computer-based practicals, self-directed learning and directed independent study. Appropriate supplementary information and reading lists will be provided on Blackboard. 

Study hours

At least 40 hours of scheduled teaching and learning activities will be delivered in person, with the remaining hours for scheduled and self-scheduled teaching and learning activities delivered either in person or online. You will receive further details about how these hours will be delivered before the start of the module.

Please note the independent study hours above are notional numbers of hours; each student will approach studying in different ways. We would advise you to reflect on your learning and the number of hours you are allocating to these tasks.

Semester 1 The hours in this column may include hours during the Christmas holiday period.

Semester 2 The hours in this column may include hours during the Easter holiday period.

Summer The hours in this column will take place during the summer holidays and may be at the start and/or end of the module.

Assessment

Requirements for a pass

Students need to achieve an overall module mark of 40% to pass this module.

Summative assessment

Penalties for late submission of summative assessment

The Support Centres will apply the following penalties for work submitted late:

Assessments with numerical marks

• where the piece of work is submitted after the original deadline (or any formally agreed extension to the deadline): 10% of the total marks available for that piece of work will be deducted from the mark for each working day (or part thereof) following the deadline up to a total of three working days;
• the mark awarded due to the imposition of the penalty shall not fall below the threshold pass mark, namely 40% in the case of modules at Levels 4-6 (i.e. undergraduate modules for Parts 1-3) and 50% in the case of Level 7 modules offered as part of an Integrated Masters or taught postgraduate degree programme;
• where the piece of work is awarded a mark below the threshold pass mark prior to any penalty being imposed, and is submitted up to three working days after the original deadline (or any formally agreed extension to the deadline), no penalty shall be imposed;
• where the piece of work is submitted more than three working days after the original deadline (or any formally agreed extension to the deadline): a mark of zero will be recorded.

Assessments marked Pass/Fail

• where the piece of work is submitted within three working days of the deadline (or any formally agreed extension of the deadline): no penalty will be applied;
• where the piece of work is submitted more than three working days after the original deadline (or any formally agreed extension of the deadline): a grade of Fail will be awarded.

The University policy statement on penalties for late submission can be found at: /cqsd/-/media/project/functions/cqsd/documents/qap/penaltiesforlatesubmission.pdf

You are strongly advised to ensure that coursework is submitted by the relevant deadline. You should note that it is advisable to submit work in an unfinished state rather than to fail to submit any work.

Formative assessment

Formative assessment is any task or activity which creates feedback (or feedforward) for you about your learning, but which does not contribute towards your overall module mark.

Formative assessments will include interactive quiz questions and/or discussions to be held at regular intervals during the lectures and practicals, which will help to reinforce and recap on the key points raised. The quizzes and discussions will help to improve student attainment, as well as being used to monitor the group progress and understanding of the module material. 

Reassessment

Additional costs