Mark J. Pallen is a research leader at the

Quadram Institute The Quadram Institute is a centre for food and health research, combining Quadram Institute Bioscience (formerly the Institute of Food Research), the Norfolk and Norwich University Hospitals' endoscopy centre and aspects of the University of E ...

and Professor of Microbial Genomics at the

University of East Anglia The University of East Anglia (UEA) is a Public university, public research university in Norwich, England. Established in 1963 on a campus university, campus west of the city centre, the university has four faculties and twenty-six schools of ...

. In recent years, he has been at the forefront of efforts to apply

next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...

to problems in

microbiology Microbiology () is the branches of science, scientific study of microorganisms, those being of unicellular organism, unicellular (single-celled), multicellular organism, multicellular (consisting of complex cells), or non-cellular life, acellula ...

and

ancient DNA Ancient DNA (aDNA) is DNA isolated from ancient sources (typically Biological specimen, specimens, but also environmental DNA). Due to degradation processes (including Crosslinking of DNA, cross-linking, deamination and DNA fragmentation, fragme ...

research.

Education

Pallen was educated at

Wallington High School Wallington Jr./Sr. High School is a six-year comprehensive public high school that serves students in seventh through twelfth grades from Wallington, in Bergen County, in the U.S. state of New Jersey, operating as the lone secondary school of ...

. He completed an undergraduate degree in medical sciences at

Fitzwilliam College, Cambridge Fitzwilliam College is a constituent college of the University of Cambridge, England. The college has origins from 1869, with the foundation of the Non-Collegiate Students Board, a venture intended to offer academically excellent students of all ...

and gained his medical qualification from the

London Hospital Medical College The London Hospital Medical College was a medical school, medical and later dental school based at the London Hospital (later Royal London Hospital) in Whitechapel, London. Founded in 1785, it was the first purpose-built medical college in Englan ...

. During the early 1990s, he gained an MD while working at

St Bartholomew's Hospital Medical College Barts and The London School of Medicine and Dentistry, commonly known as Barts or BL, is a medical and dental school in London, England. The school is part of Queen Mary University of London, a constituent college of the federal University of L ...

. In the mid-1990s, he worked for a PhD under the supervision of Gordon Dougan at

Imperial College Imperial College London, also known as Imperial, is a public research university in London, England. Its history began with Prince Albert, husband of Queen Victoria, who envisioned a cultural district in South Kensington that included museums ...

. During this time, he captained the winning team from

in the TV quiz show

University Challenge ''University Challenge'' is a British television quiz programme which first aired in 1962. ''University Challenge'' aired for 913 episodes on ITV from 21 September 1962 to 31 December 1987, presented by quizmaster Bamber Gascoigne. The BBC ...

, while also writing a series of articles for the ''

British Medical Journal ''The BMJ'' is a fortnightly peer-reviewed medical journal, published by BMJ Publishing Group Ltd, which in turn is wholly-owned by the British Medical Association (BMA). ''The BMJ'' has editorial freedom from the BMA. It is one of the world ...

'', introducing the medical profession to the Internet.

Microbial genomics, metagenomics and bioinformatics

In 2011, Pallen led a

crowdsourced Crowdsourcing involves a large group of dispersed participants contributing or producing goods or services—including ideas, votes, micro-tasks, and finances—for payment or as volunteers. Contemporary crowdsourcing often involves digit ...

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 Ion semiconductor sequencing is a method of DNA sequencing based on the detection of hydrogen ions that are released during the polymerization of DNA. This is a method of "sequencing by synthesis", during which a complementary strand is built base ...

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. He has also shown that

whole-genome sequencing Whole genome sequencing (WGS), also known as full genome sequencing or just genome sequencing, is the process of determining the entirety of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's ...

can be used to track the spread of resistant bacteria and to study the emergence of

antimicrobial resistance Antimicrobial resistance (AMR or AR) occurs when microbes evolve mechanisms that protect them from antimicrobials, which are drugs used to treat infections. This resistance affects all classes of microbes, including bacteria (antibiotic resista ...

. Through analyses of

fecal Feces (also known as faeces or fæces; : faex) are the solid or semi-solid remains of food that was not digested in the small intestine, and has been broken down by bacteria in the large intestine. Feces contain a relatively small amount of ...

samples from the 2011 German ''E. coli'' O104:H4 outbreak and

sputum Sputum is mucus that is coughed up from the lower airways (the trachea and bronchi). In medicine, sputum samples are usually used for a naked-eye examination, microbiological investigation of respiratory infections, and Cytopathology, cytological ...

samples from

The Gambia The Gambia, officially the Republic of The Gambia, is a country in West Africa. Geographically, The Gambia is the List of African countries by area, smallest country in continental Africa; it is surrounded by Senegal on all sides except for ...

, Pallen showed that

metagenomics Metagenomics is the study of all genetics, genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the mic ...

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 ''Mycobacterium tuberculosis'' (M. tb), also known as Koch's bacillus, is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis. First discovered in 1882 by Robert Koch, ''M. tuberculosis'' ha ...

'' genomes from human remains and a

medieval In the history of Europe, the Middle Ages or medieval period lasted approximately from the 5th to the late 15th centuries, similarly to the post-classical period of World history (field), global history. It began with the fall of the West ...

Brucella ''Brucella'' is a genus of Gram-negative bacterium, bacteria, named after David Bruce (microbiologist), David Bruce (1855–1931). They are small (0.5 to 0.7 by 0.6 to 1.5 μm), non-Bacterial capsule, encapsulated, non-motile, facultatively ...

'' genome sequence. With Vince Gaffney and Robin Allaby, he has applied shotgun metagenomics to

sediment Sediment is a solid material that is transported to a new location where it is deposited. It occurs naturally and, through the processes of weathering and erosion, is broken down and subsequently sediment transport, transported by the action of ...

ary ancient DNA samples, showing the presence of wheat in the

British Isles The British Isles are an archipelago in the Atlantic Ocean, North Atlantic Ocean off the north-western coast of continental Europe, consisting of the islands of Great Britain, Ireland, the Isle of Man, the Inner Hebrides, Inner and Outer Hebr ...

2000 years earlier than expected. Pallen has also used metagenomics to investigate the

chicken The chicken (''Gallus gallus domesticus'') is a domesticated subspecies of the red junglefowl (''Gallus gallus''), originally native to Southeast Asia. It was first domesticated around 8,000 years ago and is now one of the most common and w ...

gut microbiome Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the g ...

, the

of patients on the

intensive care unit An intensive care unit (ICU), also known as an intensive therapy unit or intensive treatment unit (ITU) or critical care unit (CCU), is a special department of a hospital or health care facility that provides intensive care medicine. An inten ...

and the microbes that inhabit ticks. From 2014 to 2020, Pallen was Principal Investigator on the £8 million MRC-funded

cloud-computing Cloud computing is "a paradigm for enabling network access to a scalable and elastic pool of shareable physical or virtual resources with self-service provisioning and administration on-demand," according to ISO. Essential characteristics ...

project the ''Cloud Infrastructure for Microbial Bioinformatics'' (CLIMB) and now serves as director of the successor project ''CLIMB-BIG-DATA''. In 2020, the CLIMB project received the ''HPCWire Readers’ Best High Performance Computing Collaboration Award'' for supporting analysis and publication of coronavirus genome sequences during the

COVID-19 pandemic The COVID-19 pandemic (also known as the coronavirus pandemic and COVID pandemic), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), began with an disease outbreak, outbreak of COVID-19 in Wuhan, China, in December ...

Microbial nomenclature

Pallen's studies on the chicken gut microbiome led him to propose over 800 new names for bacterial taxa found in this setting. Pallen then developed a system for automating the creation of

taxonomic 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme of classes (a taxonomy) and the allocation ...

names for bacteria, which resulted in the publication of over a million new names available for use by the microbiology research community to name new bacterial genera. Subsequently, in an opinion piece in the journal ''New Microbes and New Infections'' and an invited talk for ''Bergey's International Society for Microbial Systematics'', Pallen outlined his ideas for making bacterial nomenclature more accessible. In 2022, Pallen published over 65,000 names for previously unnamed bacterial and archaeal taxa in the

Genome Taxonomy Database The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving parap ...

, using

Python Python may refer to: Snakes * Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia ** ''Python'' (genus), a genus of Pythonidae found in Africa and Asia * Python (mythology), a mythical serpent Computing * Python (prog ...

scripts to create user-friendly

arbitrary Arbitrariness is the quality of being "determined by chance, whim, or impulse, and not by necessity, reason, or principle". It is also used to refer to a choice made without any specific criterion or restraint. Arbitrary decisions are not necess ...

names that comply with the

phonotactics Phonotactics (from Ancient Greek 'voice, sound' and 'having to do with arranging') is a branch of phonology that deals with restrictions in a language on the permissible combinations of phonemes. Phonotactics defines permissible syllable struc ...

and grammar of Latin. Pallen has also been active in viral nomenclature, starting with the creation of over 400 species epithets for the bacterial positive-sense single-stranded viruses in the family Leviviridae. In March 2021, Pallen suggested in an ''Opinion'' article in ''

New Scientist ''New Scientist'' is a popular science magazine covering all aspects of science and technology. Based in London, it publishes weekly English-language editions in the United Kingdom, the United States and Australia. An editorially separate organ ...

'' that an alternative should be found to the use of geographical names for

variants of SARS-CoV-2 Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are viruses that, while similar to the original, have genetic changes that are of enough significance to lead virologists to label them separately. SARS-CoV-2 is the v ...

, raiding the

classical world Classical antiquity, also known as the classical era, classical period, classical age, or simply antiquity, is the period of cultural European history between the 8th century BC and the 5th century AD comprising the interwoven civilization ...

for options. In early 2021, Pallen participated in a

WHO The World Health Organization (WHO) is a specialized agency of the United Nations which coordinates responses to international public health issues and emergencies. It is headquartered in Geneva, Switzerland, and has 6 regional offices and 15 ...

working group, priming adoption of a scheme for naming

after letters in the

Greek alphabet The Greek alphabet has been used to write the Greek language since the late 9th or early 8th century BC. It was derived from the earlier Phoenician alphabet, and is the earliest known alphabetic script to systematically write vowels as wel ...

. In recognition of Pallen's efforts in automating creation of names for microbes, in 2022 the name '' Palleniella'' was created for a new bacterial genus previously within the genus

Prevotella ''Prevotella'' is a genus of Gram-negative bacteria. ''Prevotella'' species are widely distributed across varied ecological habitats, with 57 characterized species spanning both human and other mammalian hosts. In mammals, this genus is notabl ...

Public understanding of science

Pallen is the author of a popular science book, ''The Rough Guide to Evolution''. In the wake of the 2005 Kitzmiller v. Dover Area School District trial, he wrote a review with

Nick Matzke Nicholas J. Matzke is the former Public Information Project Director at the National Center for Science Education (NCSE) and served an instrumental role in NCSE's preparation for the 2005 '' Kitzmiller v. Dover Area School District'' trial. One of ...

, outlining the evidence that the bacterial flagellum is an evolved rather than designed entity. He commissioned and peer-reviewed

Baba Brinkman Dirk Murray Brinkman (born October 22, 1978) is a Canadian rapper and playwright best known for recordings and performances that combine hip hop music with literature, theatre, and science. Early life and education Born in the remote community ...

's ''Rap Guide to Evolution'' and was responsible for recruiting

Alice Roberts Alice May Roberts (born 19 May 1973) is an English academic, TV presenter and author. Since 2012 she has been professor of Public Engagement in Science at the University of Birmingham. She was president of the charity Humanists UK from Januar ...

to the role of Professor of Public Engagement in Science at the

University of Birmingham The University of Birmingham (informally Birmingham University) is a Public university, public research university in Birmingham, England. It received its royal charter in 1900 as a successor to Queen's College, Birmingham (founded in 1825 as ...

. In June 2011, Pallen appeared in an

episode An episode is a narrative unit within a larger dramatic work or documentary production, such as a serial (radio and television), series intended for radio, television or Streaming media, streaming consumption. Etymology The noun ''episode'' is ...

Melvin Bragg Melvyn Bragg, Baron Bragg (born 6 October 1939) is an English broadcaster, author and parliamentarian. He is the editor and presenter of '' The South Bank Show'' (1978–2010, 2012–2023), and the presenter of the BBC Radio 4 documentary serie ...

's ''In our Time'' radio programme. In 2018, Pallen self-published a book on the 1978 smallpox outbreak in the United Kingdom, '' The Last Days of Smallpox: Tragedy in Birmingham'', which includes a mixture of popular science and a historical narrative of the outbreak and subsequent court case. Pallen has served alongside

on the advisory board of the Milner Centre for Evolution at the

University of Bath The University of Bath is a public research university in Bath, England. Bath received its royal charter in 1966 as Bath University of Technology, along with a number of other institutions following the Robbins Report. Like the University ...

References

{{DEFAULTSORT:Pallen, Mark 1960 births Living people People educated at Wallington County Grammar School Alumni of Fitzwilliam College, Cambridge Alumni of the London Hospital Medical College Alumni of Imperial College London Academics of the University of Birmingham Academics of the University of Warwick Academics of the University of East Anglia British microbiologists English microbiologists British bacteriologists English bacteriologists Pathogen genomics 20th-century British medical doctors