Iqbal group

The Iqbal lab works on methods for studying the DNA (the genome) of different organisms, and to compare the genomes of different individuals. For example, we might compare the DNA of Plasmodium  parasites that cause drug-resistant malaria with DNA from those that are susceptible to drug treatment. Among other things, this allows us to:

(Click to enlarge) By encoding many genomes together as multicoloured graphs (each colour is a sample/individual), both genetic variants and repeats can be detected. Figure from Iqbal et al (Nature Genetics, 2012)

Research overview

We work on computational methods for detecting and representing genetic variation, particularly from high-throughput sequencing data.  There are many situations where genomic regions of considerable biomedical interest (eg the HLA genes in humans, many surface antigens in P. falciparum, and many antibiotic-resistance-conferring mobile elements in bacteria) are too diverse and have too complex evolutionary histories to be accessible to standard computational approaches. We develop algorithms and data structures for representing and detecting simple and complex genetic variation without using a reference genome. These methods are based on so-called 'de novo assembly', because they make no prior assumptions about the structure of the genome. Typically challenges involve dealing with large data volumes (efficiency of data structures and software implementation), developing appropriate algorithms to analyse complex variants, and incorporating ideas from population genetics into assembly. The initial publication of these methods was Iqbal et al, Nature Genetics (2012), and the software is called Cortex.

Applications to pathogen genomics

We work with collaborators to apply these methods to pathogens, to enable better surveillance of pathogen evolution (within host, within hospital and across the world) and to better understand variation in important drug-resistance and immune-target genes. We focus particularly on: 

Key collaborators are Dominic Kwiatkowski (MalariaGEN consortium), Derrick Crook (the Modernising Medical Microbiology Consortium) and Henk den Bakker (Cornell and New York State Department of Health)