Mark Pallen

Mark J. Pallen is a Research Leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. In recent years, he has been at the forefront of efforts to apply next-generation sequencing to problems in microbiology and ancient DNA research.

Mark Pallen
Born
Mark John Pallen

1960 (age 59–60)
Carshalton, England
NationalityBritish
Alma materFitzwilliam College, Cambridge, London Hospital Medical College
Scientific career
FieldsMicrobiology
InstitutionsUniversity of Warwick
Doctoral advisorGordon Dougan
Websitequadram.ac.uk/people/mark-pallen/

Education

Pallen was educated in his home town of Wallington in England, attending Wallington High School. He completed an undergraduate degree in medical sciences at Fitzwilliam College, Cambridge and gained his medical qualification from the London Hospital Medical College. During the mid-1990s, he worked for a PhD under the supervision of Gordon Dougan at Imperial College. During this time, he captained the winning team from Imperial College in the TV quiz show University Challenge,[1] while also writing a series of articles for the British Medical Journal, introducing the medical profession to the Internet.[2]

Bacterial Genomics and Metagenomics

In 2011, Pallen led a crowdsourced 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.[3] 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.[4] He has also shown that whole-genome sequencing can be used to track the spread of resistant bacteria [5] and to study the emergence of antimicrobial resistance .[6]

Through analyses of fecal samples from the 2011 German E. coli O104:H4 outbreak and sputum samples from The Gambia, Pallen showed that metagenomics can be used as a culture-independent approach to the diagnosis of bacterial infection.[7][8] He has pioneered the use of metagenomics to open up new avenues in ancient DNA research, recovering 200-year-old Mycobacterium tuberculosis genomes from human remains and a medieval Brucella genome sequence.[9][10] With Vince Gaffney and Robin Allaby, he has applied shotgun metagenomics to sedimentary ancient DNA samples, showing the presence of wheat in the British Isles 2000 years earlier than expected.[11]

Public Understanding of Science

Pallen is the author of a popular science book, The Rough Guide to Evolution.[12] In the wake of the 2005 Kitzmiller v. Dover Area School District trial, he wrote a review with Nick Matzke, outlining the evidence that the bacterial flagellum is an evolved rather than designed entity. [13] He commissioned and peer-reviewed Baba Brinkman's Rap Guide to Evolution and was responsible for recruiting Alice Roberts to the role of Professor of Public Engagement in Science at the University of Birmingham. In June 2011, Pallen appeared in an episode of Melvin Bragg's In our Time radio programme.[14] In 2014, he shared a platform with Michael Mosley on Medicine and War at the Cheltenham Science Festival.

In 2018, Pallen wrote a book on the 1978 smallpox outbreak in the United Kingdom, The Last Days of Smallpox: Tragedy in Birmingham, [15] which includes a mixture of popular science and a historical narrative of the outbreak and subsequent courtcase.

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References
  1. University Challenge winners – May 1996
  2. Mark Pallen (1995). "Guide to the Internet: Introducing the Internet". British Medical Journal. 311 (7017): 1422–4. doi:10.1136/bmj.311.7017.1422. PMC 2544383. PMID 8520280.
  3. Rohde; et al. (2011). "Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4" (PDF). N Engl J Med. 365 (8): 718–24. doi:10.1056/NEJMoa1107643. PMID 21793736.
  4. Loman; et al. (2012). "Performance comparison of benchtop high-throughput sequencing platforms". Nature Biotechnology. 30 (5): 434–9. doi:10.1038/nbt.2198. PMID 22522955.
  5. Halachev; et al. (2014). "Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England". Genome Medicine. 6 (11): 70. doi:10.1186/s13073-014-0070-x. PMC 4237759. PMID 25414729.
  6. Hornsey; et al. (2011). "Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy". J Antimicrob Chemother. 66 (7): 1499–503. doi:10.1093/jac/dkr168. PMID 21565804.
  7. Loman; et al. (2013). "A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4". JAMA. 309 (14): 1502–10. doi:10.1001/jama.2013.3231. PMID 23571589.
  8. Doughty; et al. (2014). "Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer". PeerJ. 2: e585. doi:10.7717/peerj.585. PMC 4179564. PMID 25279265.
  9. Kay; et al. (2015). "Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe". Nature Communications. 6: 6717. doi:10.1038/ncomms7717. PMC 4396363. PMID 25848958.
  10. Kay; et al. (2015). "Recovery of a medieval Brucella melitensis genome using shotgun metagenomics". MBio. 5 (4): e01337-14. doi:10.1128/mBio.01337-14. PMC 4161259. PMID 25028426.
  11. Smith; et al. (2015). "Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago". Science. 347 (6225): 998–1001. doi:10.1126/science.1261278. hdl:10454/9405. PMID 25722413.
  12. Mark Pallen (2009). The Rough Guide to Evolution. ISBN 978-1858289465.
  13. Mark J. Pallen and Nicholas J. Matzke (2006). "From The Origin of Species to the origin of bacterial flagella" (PDF). Nature Reviews Microbiology. 4 (10): 784–790. doi:10.1038/nrmicro1493. PMID 16953248.
  14. In Our Time: The Origins of Infectious Disease
  15. Mark Pallen (2018). The Last Days of Smallpox: Tragedy in Birmingham. ISBN 978-1980455226.
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