Mark Pallen

Mark Pallen a Research Leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. In recent years, he have been at the forefront of efforts to apply high-throughput sequencing to problems in microbiology and ancient DNA research. He started academic life as a medical microbiologist, with training in medicine (BA from Cambridge MBBS, MD from London) and laboratory research (PhD in Gordon Dougan’s lab at Imperial College, during which I captained the winning team in University Challenge).

He have a track record of over fifteen years of research council funding for a research programme that spans bioinformatics and bench-based research. His research interests have included bacterial protein secretion and gene regulation, particularly in E. coli; the evolution of domains, proteins and bacterial flagella; and microbial pathogenomics.

In 2011, He wrote-up a crowd-sourced analysis of the genome of the outbreak strain from the 2011 German E. coli O104:H4 outbreak, which had been genome-sequenced on the Ion Torrent platform by the BGI. Around the same time, he also led a project in which an isolate from the 2011 German E. coli O104:H4 outbreak was genome-sequenced on three new benchtop sequencing platforms, benchmarking these new platforms.

In recent years, Mark have turned my attention to the genomic epidemiology of bacterial pathogens of humans and animals (e.g. multi-drug resistant Acinetobacter baumannii, MDR-TB in Africa, Staphylococcus aureus in monkeys and Brachyspira in pigs) and to pioneering new applications of metagenomics, including the characterisation of complex microbial communities (particularly gut microbiomes), the detection of pathogens in historical samples (includes recovery of medieval Brucella and leprosy genomes) and sedimentary ancient DNA studies (shedding light on the Neolithic transition).

Through analyses of faecal samples from the 2011 German E. coli O104:H4 outbreak and sputum samples from the Gambia, he have shown that metagenomics can be used as a culture-independent approach to the diagnosis of bacterial infection. With collaborators in Palestine, he have been using metagenomics approaches to detect pathogens in ticks. Since joining the Quadram Institute, Mark have developed an interest in the development of smart probiotics using synthetic biology approaches and consolidated my interests in the gut microbiomes of food animals and of critically ill patients.