Infectious Disease 'Omics

Coronavirus Notice - Infectious Disease 'Omics
Course dates: 4 -7 December 2023

The course will have a hybrid format and students can choose to attend in person in London or online. Offer holders will be required to confirm before the course start date whether they are planning to attend online or in person.

LSHTM understands this is an uncertain time and rules around international travel could change at very short notice. We strongly advise candidates that choose to attend the course in person in London to only book refundable tickets and accommodation, and to ensure you have checked and comply with all UK entry requirements.

Overview - Infectious Disease 'Omics

Infectious diseases, such as HIV-AIDS, malaria, pneumonia and tuberculosis, account for 25% of global mortality and more than half of all deaths in children under the age of five years. The genetic epidemiology of these diseases can be complex, especially as they may involve several genomes, including the host, pathogen(s) and a vector. There is also a need to look beyond the genome to consider other ‘omes, such as the transcriptome, in a more systems biology framework.

High throughput genotyping and sequencing technologies are providing insights into these genomes, metabolomes, transcriptomes and proteomes, thereby revolutionising genetic epidemiological studies and biomedical research. The use of SNP chips in large-scale genome-wide studies of association and genic selection has revolutionized the study of human disease susceptibility. Whole genome studies of pathogens using high throughput sequencing technologies is leading to the ability to track microbial evolution over time and space, as well as identify variants correlated with phenotypes such as anti-microbial resistance. Further, RNAseq methodologies are being used to measure transcript abundance and differential gene expression across isolates.

To take full advantage of new ‘omic technologies requires the ability to analyse large amounts of data using methods from bioinformatics, population genetics and statistics – the focus of this course. Specifically, this course offers hands-on experience of processing sequencing data to construct genomes, identifying genomic variants and applying downstream methods, such as phylogenetics. Further, the course covers transcriptomic and proteomic analysis in human and pathogen settings. High profile examples, including malaria, TB and MRSA, will be used to illustrate the concepts, and there is a strong emphasis on how to implement the methods in practice, with the majority of sessions computer-based.


This course focuses on bioinformatic, population genetic, statistical and genetic epidemiological methods for analysing large genetic datasets.  Participants would be expected have some familiarity with molecular biology, and relevant statistical concepts such as a linear regression.

Course fee

The fee for 2023 is £575.

Course objectives
Course objectives - Infectious Disease 'Omics


By the end of the course participants will be able to:

  • Process raw sequence into a set of informative variants, through mapping to a reference genome or using de novo or reference-free assembly approaches;
  • Conduct transcriptomic and proteomic analysis, in an integrated systems biology approach
  • Perform downstream population genetic and association analysis

Teaching Programme

The programme will include the following concepts:

  • Genomic variation and technologies, data visualisation and quality control
  • Mapping to a reference pathogen genome and variant detection
  • Transcriptomics and RNA-seq
  • Assembly of pathogen genomes
  • Phylogenetic analysis and detection of genic selection
  • Exploring Host-pathogen interactions


There is no formal assessment but a Certificate of Attendance will be provided.

How to apply
How to apply - Infectious Disease 'Omics

Applying for this course

Applications are now closed. You can register your interest and we will let you know when applications reopen.

Please read LSHTM's Admissions policies prior to submitting your application.