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Mark J. Pallen is Professor of Microbial Genomics at the University of Warwick. In recent years, he has been at the forefront of efforts to apply next-generation sequencing to problems in microbiology and ancient DNA research. In 2011, he led an innovative crowdsourcing 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 ^[1]. 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 ^[2]. He has also shown that whole-genome sequencing can be used to track the spread of resistant bacteria ^[3] and to study the emergence of antimicrobial resistance ^[4].

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. 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. 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.

^ Rohde; et al. (2011). "Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4". N Engl J Med. 365: 718–24. doi:10.1056/NEJMoa1107643. PMID 21793736. {{cite journal}}: Explicit use of et al. in: |author= (help)
^ Loman; et al. (2012). "Performance comparison of benchtop high-throughput sequencing platforms". Nature Biotechnology. 30: 434–9. doi:10.1038/nbt.2198. PMID 22522955. {{cite journal}}: Explicit use of et al. in: |author= (help)
^ Halachev; et al. (2014). "Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England". Genome Medicine. 6: 70. doi:10.1186/s13073-014-0070-x. PMID 25414729. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: unflagged free DOI (link)
^ 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: 1499–503. doi:10.1093/jac/dkr168. PMID 21565804. {{cite journal}}: Explicit use of et al. in: |author= (help)

[1] Rohde; et al. (2011). "Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4". N Engl J Med. 365: 718–24. doi:10.1056/NEJMoa1107643. PMID 21793736. {{cite journal}}: Explicit use of et al. in: |author= (help)

[2] Loman; et al. (2012). "Performance comparison of benchtop high-throughput sequencing platforms". Nature Biotechnology. 30: 434–9. doi:10.1038/nbt.2198. PMID 22522955. {{cite journal}}: Explicit use of et al. in: |author= (help)

[3] Halachev; et al. (2014). "Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England". Genome Medicine. 6: 70. doi:10.1186/s13073-014-0070-x. PMID 25414729. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: unflagged free DOI (link)

[4] 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: 1499–503. doi:10.1093/jac/dkr168. PMID 21565804. {{cite journal}}: Explicit use of et al. in: |author= (help)

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+'''Mark J. Pallen''' is Professor of Microbial Genomics at the [[University of Warwick]]. In recent years, he has been at the forefront of efforts to apply [[next-generation sequencing]] to problems in  [[microbiology]] and [[ancient DNA]] research. In 2011, he led an innovative [[crowdsourcing]] analysis of the genome of the outbreak strain from the [[2011_Germany_E._coli_O104:H4_outbreak|2011 German ''E. coli'' O104:H4 outbreak]], which had been genome-sequenced on the [[Ion Torrent]] platform by the [[Beijing_Genomics_Institute|BGI]] <ref>{{cite journal
-#REDIRECT [[Atkinson–Shiffrin memory model]]
+ | author = Rohde et al.
+ | year = 2011
+ | title = Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.
+ | journal = [[N Engl J Med.]]
+ | volume = 365
+ | pages = 718-24
+ | url =  http://www.nejm.org/doi/full/10.1056/NEJMoa1107643
+ | doi = 10.1056/NEJMoa1107643
+ | pmid = 21793736
+}}</ref>. Around the same time, he also led a project in which an isolate from the [[2011_Germany_E._coli_O104:H4_outbreak|2011 German ''E. coli'' O104:H4 outbreak]] was genome-sequenced on three new benchtop sequencing platforms, benchmarking these new platforms <ref>{{cite journal
+ | author = Loman et al.
+ | year = 2012
+ | title = Performance comparison of benchtop high-throughput sequencing platforms.
+ | journal = [[Nature Biotechnology]]
+ | volume = 30
+ | pages = 434-9
+ | url =  http://www.nature.com/nbt/journal/v30/n5/full/nbt.2198.html
+ | doi = 10.1038/nbt.2198
+ | pmid = 22522955
+}}</ref>. He has also shown that [[whole-genome sequencing]] can be used to track the spread of [[antimicrobial resistance|resistant]] bacteria
+<ref>{{cite journal
+ | author = Halachev et al.
+ | year = 2014
+ | title = Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England.
+ | journal = [[BioMed_Central|Genome Medicine]]
+ | volume = 6
+ | pages = 70
+ | url =  http://www.genomemedicine.com/content/6/11/70
+ | doi = 10.1186/s13073-014-0070-x
+ | pmid = 25414729
+}}</ref>  and to study the emergence of [[antimicrobial resistance]]
+<ref>{{cite journal
+ | author = Hornsey et al.
+ | year = 2011
+ | title = Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy.
+ | journal = J Antimicrob Chemother.
+ | volume = 66
+ | pages = 1499-503
+ | url = http://jac.oxfordjournals.org/content/66/7/1499.long
+ | doi = 10.1093/jac/dkr168
+ | pmid = 21565804
+}}</ref>.
+Through analyses of [[feces|fecal]] samples from the [[2011_Germany_E._coli_O104:H4_outbreak|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.  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. With Vince Gaffney and Robin Allaby, he has applied shotgun metagenomics to [[sediment|sedimentary]] ancient DNA samples, showing the presence of [[wheat]] in the [[British Isles]] 2000 years earlier than expected.