Julian Parkhill

Last updated

Julian Parkhill
FRS FMedSci
Dr Julian Parkhill FMedSci FRS.jpg
Parkhill in 2015
Born (1964-09-23) 23 September 1964 (age 60) [1]
Leigh-on-Sea [1]
Education Westcliff High School for Boys
Alma mater
Known forARTEMIS [2] [3] [4]
Scientific career
Fields
Institutions
Thesis Regulation of transcription of the mercury resistance operon of Tn501  (1991)
Website www.vet.cam.ac.uk/staff/professor-julian-parkhill-frs-fmedsci

Julian Parkhill (born 1964) [1] is Professor of Bacterial Evolution in the Department of Veterinary Medicine [8] at the University of Cambridge. He previously served as head of pathogen genomics at the Wellcome Sanger Institute. [9] [10] [11] [12] [5] [13] [14]

Contents

Education

Parkhill was educated at Westcliff High School for Boys, [1] the University of Birmingham and the University of Bristol where he was awarded a PhD in 1991 [15] for research into the regulation of transcription of the mercury resistance operon. [6] [7] [16]

Career and research

Parkhill uses high throughput sequencing and phenotyping to study pathogen diversity and variation, how they affect virulence and transmission, and what they tell us about the evolution of pathogenicity and host–pathogen interaction. [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [ excessive citations ] Research in the Parkill Laboratory has been funded the Wellcome Trust, the Biotechnology and Biological Sciences Research Council (BBSRC) [30] and the Medical Research Council (MRC). [31]

Awards and honours

Parkhill was elected a Fellow of the Academy of Medical Sciences (FMedSci) in 2009, [32] and a Fellow of the American Academy of Microbiology (FAAM) in 2012.

Dr. Julian Parkhill is currently Head of Pathogen Genomics at the Wellcome Trust Sanger Institute. Over the last decade or so, his group has analysed the genomes of many bacteria of fundamental importance for human health, including the causative agents of tuberculosis, plague, typhoid fever, whooping cough, leprosy, botulism, diphtheria and meningitis, as well as nosocomial pathogens such as Clostridioides difficile and MRSA, and food-borne pathogens such as Campylobacter jejuni , Salmonella Typhimurium and Yersinia enterocolitica . Their current research focuses on the application of high-throughput sequencing techniques to microbiology. They are currently sequencing very large collections of bacterial isolates with broad geographic and temporal spreads, linking genomic variation to epidemiology, acquisition of drug resistance, and recent evolution. In addition, they are working with local and national clinical microbiology groups to build the foundations for the transfer of microbial sequencing to clinical and public health investigations. They are also applying sequencing technologies to phenotypic investigations, particularly saturation transposon mutagenesis, transcriptomics and high-throughput phenotyping. They collaborate widely, particularly with groups in developing countries where infectious diseases are endemic. [33]

Parkhill was elected a Fellow of the Royal Society (FRS) in 2014, [34] his certificate of election reads:

Julian Parkhill has played a major role in determining the reference genome sequences of many key bacterial pathogens, including Mycobacterium tuberculosis , Yersinia pestis and Salmonella typhi. As well as providing complete catalogues of the arsenal of genes carried by each bacterium, Parkhill's work has led to important insights into how bacterial genomes evolve and the effect of variation within supposedly homogeneous bacterial populations. In parallel, tools to understand and visualise genomic data have been developed, and freely disseminated worldwide. Over a decade, Parkhill has been at the forefront of bacterial genomics, most recently using new high throughput sequencing technologies to explore evolution and transmission in bacterial pathogens, and enable the clinical use of these approaches. [34]

Related Research Articles

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<i>Neisseria</i> Genus of bacteria

Neisseria is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens, N. meningitidis and N. gonorrhoeae.

<span class="mw-page-title-main">Metagenomics</span> Study of genes found in the environment

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<span class="mw-page-title-main">Actinomycetales</span> Order of Actinomycota

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<span class="mw-page-title-main">Wellcome Sanger Institute</span> British genomics research institute

The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.

<span class="mw-page-title-main">Microbiota</span> Community of microorganisms

Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.

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<span class="mw-page-title-main">Mark Achtman</span> Canadian bacteriologist

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Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.

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References

  1. 1 2 3 4 Anon (2015). "Parkhill, Prof Julian" . Who's Who (online Oxford University Press  ed.). A & C Black. doi:10.1093/ww/9780199540884.013.U281946.(Subscription or UK public library membership required.)
  2. ↑ Rutherford, K.; Parkhill, J.; Crook, J.; Horsnell, T.; Rice, P.; Rajandream, M.-A.; Barrell, B. (2000). "Artemis: Sequence visualization and annotation". Bioinformatics. 16 (10): 944–5. doi: 10.1093/bioinformatics/16.10.944 . PMID   11120685.
  3. ↑ Carver, T; Berriman, M; Tivey, A; Patel, C; Böhme, U; Barrell, B. G.; Parkhill, J; Rajandream, M. A. (2008). "Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database". Bioinformatics. 24 (23): 2672–6. doi:10.1093/bioinformatics/btn529. PMC   2606163 . PMID   18845581.
  4. ↑ Carver, T.; Harris, S. R.; Berriman, M.; Parkhill, J.; McQuillan, J. A. (2011). "Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data". Bioinformatics. 28 (4): 464–469. doi:10.1093/bioinformatics/btr703. PMC   3278759 . PMID   22199388.
  5. 1 2 Julian Parkhill publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  6. 1 2 Parkhill, J; Brown, N. L. (1990). "Site-specific insertion and deletion mutants in the mer promoter-operator region of Tn501; the nineteen base-pair spacer is essential for normal induction of the promoter by MerR". Nucleic Acids Research. 18 (17): 5157–62. doi:10.1093/nar/18.17.5157. PMC   332137 . PMID   2169606.
  7. 1 2 Brown, N. L.; Camakaris, J; Lee, B. T.; Williams, T; Morby, A. P.; Parkhill, J; Rouch, D. A. (1991). "Bacterial resistances to mercury and copper". Journal of Cellular Biochemistry. 46 (2): 106–14. doi:10.1002/jcb.240460204. PMID   1717500. S2CID   40277026.
  8. ↑ "Professor Julian Parkhill". www.vet.cam.ac.uk. 4 June 2021. Retrieved 10 June 2023.
  9. ↑ "Professor Julian Parkhill, FRS, FMedSci, Senior Group Leader". Archived from the original on 15 March 2016.
  10. ↑ Parkhill, J. (2013). "What has high-throughput sequencing ever done for us?". Nature Reviews Microbiology. 11 (10): 664–5. doi:10.1038/nrmicro3112. PMID   23979431. S2CID   28613490.
  11. ↑ Julian Parkhill publications indexed by Microsoft Academic
  12. ↑ Julian Parkhill at DBLP Bibliography Server OOjs UI icon edit-ltr-progressive.svg
  13. ↑ 57212237926 Julian Parkhill's publications indexed by the Scopus bibliographic database. (subscription required)
  14. ↑ Professor Julian Parkhill visits the Wellcome Collection in London to unravel the Science behind the genome on YouTube
  15. ↑ Parkhill, Julian (1991). Regulation of transcription of the mercury resistance operon of Tn501 (PhD thesis). University of Bristol. OCLC   931563576. ProQuest   301408708.(subscription required)
  16. ↑ Holden, M. T. G.; Feil, E.; Lindsay, J.; Peacock, S.; Day, N.; Enright, M.; Foster, T.; Moore, C.; Hurst, L.; Atkin, R.; Barron, A.; Bason, N.; Bentley, S. D.; Chillingworth, C.; Chillingworth, T.; Churcher, C.; Clark, L.; Corton, C.; Cronin, A.; Doggett, J.; Dowd, L.; Feltwell, T.; Hance, Z.; Harris, B.; Hauser, H.; Holroyd, S.; Jagels, K.; James, K. D.; Lennard, N.; Line, A. (2004). "Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance". Proceedings of the National Academy of Sciences. 101 (26): 9786–9791. Bibcode:2004PNAS..101.9786H. doi: 10.1073/pnas.0402521101 . PMC   470752 . PMID   15213324. Open Access logo PLoS transparent.svg
  17. ↑ Parkhill, J; Birney, E; Kersey, P (2010). "Genomic information infrastructure after the deluge". Genome Biology. 11 (7): 402. doi: 10.1186/gb-2010-11-7-402 . PMC   2926780 . PMID   20670392.
  18. ↑ Cole, S. T.; Brosch, R.; Parkhill, J.; Garnier, T.; Churcher, C.; Harris, D.; Gordon, S. V.; Eiglmeier, K.; Gas, S.; Barry, C. E.; Tekaia, F.; Badcock, K.; Basham, D.; Brown, D.; Chillingworth, T.; Connor, R.; Davies, R.; Devlin, K.; Feltwell, T.; Gentles, S.; Hamlin, N.; Holroyd, S.; Hornsby, T.; Jagels, K.; Krogh, A.; McLean, J.; Moule, S.; Murphy, L.; Oliver, K.; et al. (1998). "Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence". Nature. 393 (6685): 537–44. Bibcode:1998Natur.393..537C. doi: 10.1038/31159 . PMID   9634230.
  19. ↑ Bentley, S. D.; Chater, K. F.; Cerdeño-Tárraga, A. -M.; Challis, G. L.; Thomson, N. R.; James, K. D.; Harris, D. E.; Quail, M. A.; Kieser, H.; Harper, D.; Bateman, A.; Brown, S.; Chandra, G.; Chen, C. W.; Collins, M.; Cronin, A.; Fraser, A.; Goble, A.; Hidalgo, J.; Hornsby, T.; Howarth, S.; Huang, C. -H.; Kieser, T.; Larke, L.; Murphy, L.; Oliver, K.; O'Neil, S.; Rabbinowitsch, E.; Rajandream, M. -A.; et al. (2002). "Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)". Nature. 417 (6885): 141–7. Bibcode:2002Natur.417..141B. doi: 10.1038/417141a . PMID   12000953. S2CID   4430218.
  20. ↑ Qin, J.; Li, R.; Raes, J.; Arumugam, M.; Burgdorf, K. S.; Manichanh, C.; Nielsen, T.; Pons, N.; Levenez, F.; Yamada, T.; Mende, D. R.; Li, J.; Xu, J.; Li, S.; Li, D.; Cao, J.; Wang, B.; Liang, H.; Zheng, H.; Xie, Y.; Tap, J.; Lepage, P.; Bertalan, M.; Batto, J. M.; Hansen, T.; Le Paslier, D.; Linneberg, A.; Nielsen, H. B. R.; Pelletier, E.; Renault, P. (2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC   3779803 . PMID   20203603.
  21. ↑ Parkhill, J.; Wren, B. W.; Mungall, K.; Ketley, J. M.; Churcher, C.; Basham, D.; Chillingworth, T.; Davies, R. M.; Feltwell, T.; Holroyd, S.; Jagels, K.; Karlyshev, A. V.; Moule, S.; Pallen, M. J.; Penn, C. W.; Quail, M. A.; Rajandream, M. A.; Rutherford, K. M.; Van Vliet, A. H. M.; Whitehead, S.; Barrell, B. G. (2000). "The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences". Nature. 403 (6770): 665–8. Bibcode:2000Natur.403..665P. doi: 10.1038/35001088 . PMID   10688204.
  22. ↑ Cole, S. T.; Eiglmeier, K.; Parkhill, J.; James, K. D.; Thomson, N. R.; Wheeler, P. R.; Honoré, N.; Garnier, T.; Churcher, C.; Harris, D.; Mungall, K.; Basham, D.; Brown, D.; Chillingworth, T.; Connor, R.; Davies, R. M.; Devlin, K.; Duthoy, S.; Feltwell, T.; Fraser, A.; Hamlin, N.; Holroyd, S.; Hornsby, T.; Jagels, K.; Lacroix, C.; MacLean, J.; Moule, S.; Murphy, L.; Oliver, K.; Quail, M. A. (2001). "Massive gene decay in the leprosy bacillus". Nature. 409 (6823): 1007–1011. Bibcode:2001Natur.409.1007C. doi:10.1038/35059006. PMID   11234002. S2CID   4307207.
  23. ↑ Parkhill, J.; Wren, B. W.; Thomson, N. R.; Titball, R. W.; Holden, M. T. G.; Prentice, M. B.; Sebaihia, M.; James, K. D.; Churcher, C.; Mungall, K. L.; Baker, S.; Basham, D.; Bentley, S. D.; Brooks, K.; Cerdeño-Tárraga, A. M.; Chillingworth, T.; Cronin, A.; Davies, R. M.; Davis, P.; Dougan, G.; Feltwell, T.; Hamlin, N.; Holroyd, S.; Jagels, K.; Karlyshev, A. V.; Leather, S.; Moule, S.; Oyston, P. C. F.; Quail, M.; et al. (2001). "Genome sequence of Yersinia pestis, the causative agent of plague". Nature. 413 (6855): 523–7. Bibcode:2001Natur.413..523P. doi: 10.1038/35097083 . PMID   11586360.
  24. ↑ Parkhill, J.; Dougan, G.; James, K. D.; Thomson, N. R.; Pickard, D.; Wain, J.; Churcher, C.; Mungall, K. L.; Bentley, S. D.; Holden, M. T. G.; Sebaihia, M.; Baker, S.; Basham, D.; Brooks, K.; Chillingworth, T.; Connerton, P.; Cronin, A.; Davis, P.; Davies, R. M.; Dowd, L.; White, N.; Farrar, J.; Feltwell, T.; Hamlin, N.; Haque, A.; Hien, T. T.; Holroyd, S.; Jagels, K.; Krogh, A.; et al. (2001). "Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18". Nature. 413 (6858): 848–52. Bibcode:2001Natur.413..848P. doi: 10.1038/35101607 . PMID   11677608.
  25. ↑ Parkhill, J.; Achtman, M.; James, K. D.; Bentley, S. D.; Churcher, C.; Klee, S. R.; Morelli, G.; Basham, D.; Brown, D.; Chillingworth, T.; Davies, R. M.; Davis, P.; Devlin, K.; Feltwell, T.; Hamlin, N.; Holroyd, S.; Jagels, K.; Leather, S.; Moule, S.; Mungall, K.; Quail, M. A.; Rajandream, M. -A.; Rutherford, K. M.; Simmonds, M.; Skelton, J.; Whitehead, S.; Spratt, B. G.; Barrell, B. G. (2000). "Complete DNA sequence of a serogroup a strain of Neisseria meningitidis Z2491". Nature . 404 (6777): 502–6. Bibcode:2000Natur.404..502P. doi:10.1038/35006655. PMID   10761919. S2CID   4430718.
  26. ↑ Parkhill, J.; Wren, B. W. (2011). "Bacterial epidemiology and biology - lessons from genome sequencing". Genome Biology. 12 (10): 230. doi: 10.1186/gb-2011-12-10-230 . PMC   3333767 . PMID   22027015.
  27. ↑ Garnier, T.; Eiglmeier, K.; Camus, J. -C.; Medina, N.; Mansoor, H.; Pryor, M.; Duthoy, S.; Grondin, S.; Lacroix, C.; Monsempe, C.; Simon, S.; Harris, B.; Atkin, R.; Doggett, J.; Mayes, R.; Keating, L.; Wheeler, P. R.; Parkhill, J.; Barrell, B. G.; Cole, S. T.; Gordon, S. V.; Hewinson, R. G. (2003). "The complete genome sequence of Mycobacterium bovis". Proceedings of the National Academy of Sciences. 100 (13): 7877–82. Bibcode:2003PNAS..100.7877G. doi: 10.1073/pnas.1130426100 . PMC   164681 . PMID   12788972.
  28. ↑ Parkhill, J.; Sebaihia, M.; Preston, A.; Murphy, L. D.; Thomson, N.; Harris, D. E.; Holden, M. T. G.; Churcher, C. M.; Bentley, S. D.; Mungall, K. L.; Cerdeño-Tárraga, A. M.; Temple, L.; James, K.; Harris, B.; Quail, M. A.; Achtman, M.; Atkin, R.; Baker, S.; Basham, D.; Bason, N.; Cherevach, I.; Chillingworth, T.; Collins, M.; Cronin, A.; Davis, P.; Doggett, J.; Feltwell, T.; Goble, A.; Hamlin, N.; et al. (2003). "Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica". Nature Genetics . 35 (1): 32–40. doi: 10.1038/ng1227 . PMID   12910271.
  29. ↑ Field, D.; Garrity, G.; Gray, T.; Morrison, N.; Selengut, J.; Sterk, P.; Tatusova, T.; Thomson, N.; Allen, M. J.; Angiuoli, S. V.; Ashburner, M.; Axelrod, N.; Baldauf, S.; Ballard, S.; Boore, J.; Cochrane, G.; Cole, J.; Dawyndt, P.; De Vos, P.; Depamphilis, C.; Edwards, R.; Faruque, N.; Feldman, R.; Gilbert, J.; Gilna, P.; Glöckner, F. O.; Goldstein, P.; Guralnick, R.; Haft, D.; et al. (2008). "The minimum information about a genome sequence (MIGS) specification". Nature Biotechnology. 26 (5): 541–7. doi:10.1038/nbt1360. PMC   2409278 . PMID   18464787.
  30. ↑ Anon (2014). "Grants awarded to Julian Parkhill by the BBSRC". BBSRC. Archived from the original on 4 March 2016.
  31. ↑ Anon (2014). "UK Government grants awarded to Julian Parhill". Swindon: Research Councils UK. Archived from the original on 21 April 2015.
  32. ↑ "Fellow | Academy of Medical Sciences". Acmedsci.ac.uk. Archived from the original on 18 November 2016. Retrieved 18 November 2016.
  33. ↑ "Julian Parkhill". Academy.asm.org. Archived from the original on 16 February 2016. Retrieved 18 November 2016.
  34. 1 2 Anon (2014). "Professor Julian Parkhill FMedSci FRS". London: Royal Society. Archived from the original on 17 November 2015. One or more of the preceding sentences incorporates text from the royalsociety.org website where:
    "All text published under the heading 'Biography' on Fellow profile pages is available under Creative Commons Attribution 4.0 International License." -- "Royal Society Terms, conditions and policies". Archived from the original on 25 September 2015. Retrieved 9 March 2016.{{cite web}}: CS1 maint: bot: original URL status unknown (link)
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