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List of works by Mark J. Pallen

'Going wrong with confidence': misleading sequence analyses of CiaB and ClpX

scientific article published on 01 October 1999

12.1 Internet Resources for Research on Bacterial Pathogenesis

A beta-propeller domain within TolB

scientific article published on 01 January 1999

A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.

scientific article published on 27 August 2010

A cryptic promoter in the LEE1 regulatory region of enterohaemorrhagic Escherichia coli: promoter specificity in AT-rich gene regulatory regions.

scientific article

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

scientific article

A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis

scientific article published in December 2005

A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile

scientific article published in September 1996

A novel EspA-associated surface organelle of enteropathogenic Escherichia coli involved in protein translocation into epithelial cells ⬇️

scientific article published on April 15, 1998

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria

scientific article

A prehistoric Egyptian mummy: Evidence for an ‘embalming recipe’ and the evolution of early formative funerary treatments

scholarly article

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.

scientific article published on 18 July 2017

An abundance of bacterial ADP-ribosyltransferases--implications for the origin of exotoxins and their human homologues

scientific article published in July 2001

An analysis of type-III secretion gene clusters in Chromobacterium violaceum

scientific article

An embarrassment of sortases - a richness of substrates?

scientific article

An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination

scientific article

An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana.

scientific article

Analysis of host response to bacterial infection using error model based gene expression microarray experiments

scientific article

Analysis of host response to bacterial infection using error model based gene expression microarray experiments.

scientific article

Archaeology. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago.

scientific article

Are diagnostic and public health bacteriology ready to become branches of genomic medicine? ⬇️

scientific article published on August 23, 2011

ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes

scientific article

Assembly of hundreds of novel bacterial genomes from the chicken caecum

scientific article published on 12 February 2020

Bacterial FHA domains: neglected players in the phospho-threonine signalling game?

scientific article published on December 2002

Bacterial Flagellins: Does Size Matter?

scientific article published on 16 December 2017

Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

scientific article

Bacterial flagellar diversity and evolution: seek simplicity and distrust it?

scientific article

Bacterial flagellar diversity in the post-genomic era.

scientific article

Bacterial genomes for the masses: relevance to the clinical laboratory

scientific article published on January 2004

Bacterial heat-shock proteins and serodiagnosis

Bacterial pathogenomics

scientific article

Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion

scientific article

Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective

scientific article

Bridging the gap between the technological singularity and mainstream medicine: highlighting a course on technology and the future of medicine

scientific article

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

scientific article

Calculating orthologs in bacteria and Archaea: a divide and conquer approach

scientific article

Cellulose mediates attachment of Salmonella enterica Serovar Typhimurium to tomatoes

scientific article published on 30 May 2011

Characterization of novel LPXTG-containing proteins of Staphylococcus aureus identified from genome sequences

scientific article published in March 2003

Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine

scientific article

Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation.

scientific article

Comparative cell wall core biosynthesis in the mycolated pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriae

scientific article published on May 2004

Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042

scientific article published on 20 January 2010

Complete genome sequence of Pig-tailed macaque rhadinovirus 2 and its evolutionary relationship with rhesus macaque rhadinovirus and human herpesvirus 8/Kaposi's sarcoma-associated herpesvirus.

scientific article published on 21 January 2015

Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605

scientific article

Creation of Golden Gate constructs for gene doctoring

scientific article published on 07 October 2020

Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer

scientific article published on 23 September 2014

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

scientific article

Deletion of TnAbaR23 results in both expected and unexpected antibiogram changes in a multidrug-resistant Acinetobacter baumannii strain

scientific article (publication date: April 2012)

Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

scientific article

Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children

scientific article

Down-regulation of key virulence factors makes the Salmonella enterica serovar Typhimurium rfaH mutant a promising live-attenuated vaccine candidate

scientific article

Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound

scientific article

Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci

scientific article published on 18 August 2016

Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca

scientific article (publication date: 26 May 2016)

Editorial

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

scientific article

Enterohemorrhagic Escherichia coli exploits EspA filaments for attachment to salad leaves

scientific article published on 29 February 2008

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

scientific article

Erratum: Corrigendum: Performance comparison of benchtop high-throughput sequencing platforms

scholarly article published in Nature Biotechnology

Escherichia Coli: From Genome Sequences to Consequences (or "Ceci n'est pas un éléphant...").

scientific article

Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali

scientific article published on 15 January 2020

Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases

scientific article

Extensive microbial and functional diversity within the chicken cecal microbiome

scientific article

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

scientific article published on 06 April 2021

Flagella mediate attachment of enterotoxigenic Escherichia coli to fresh salad leaves

scientific article published in February 2011

Forensic Analysis Reveals Acute Decompensation of Chronic Heart Failure in a 3500-Year-Old Egyptian Dignitary.

scientific article published on 30 June 2016

Formation of prokaryote names from personal names: a review of current practice and a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes

scholarly article published on 16 January 2024

From The Origin of Species to the origin of bacterial flagella

scientific article

Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa

scientific article published in 2020

Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

scientific article

Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa

scientific article

Genome sequence of the emerging pathogen Helicobacter canadensis

scientific article published on 19 June 2009

Genome sequences of three Acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78.

scientific article published on 11 March 2011

Genome sequencing in clinical microbiology

scientific article published on 01 November 2012

Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4.

scientific article

Genomic analysis of secretion systems

scientific article

Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824.

scientific article published in September 2005

Genomic diversity of <i>Escherichia coli</i> from healthy children in rural Gambia

scientific article published on 06 January 2021

Genomic diversity of <i>Escherichia coli</i> isolates from backyard chickens and guinea fowl in the Gambia

scientific article published on 30 November 2020

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

scientific article published on 14 September 2020

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England

scientific article

Genomics and outbreak investigation: from sequence to consequence

scientific article published on 29 April 2013

Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria

scientific article published in PLoS ONE

Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria

scientific article published on 17 November 2017

Glucoamylase-like domains in the alpha- and beta-subunits of phosphorylase kinase

scientific article

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.

scientific article published on 06 August 2012

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

scientific article published on 16 September 2010

High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature

scientific article

High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak

scientific article published on 17 March 2010

Identification of amino acid residues within the N-terminal domain of EspA that play a role in EspA filament biogenesis and function

scientific article published on 4 January 2008

Identification of novel imidazo[1,2-a]pyridine inhibitors targeting M. tuberculosis QcrB

scientific article

Identification of the anti-mycobacterial functional properties of piperidinol derivatives.

scientific article published on 14 February 2017

Immune response to environmental mycobacteria

scientific article published on 01 December 1986

Interaction of Salmonella enterica with basil and other salad leaves

scientific article published on 2 October 2008

Interaction of enteroaggregative Escherichia coli with salad leaves

scientific article

Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?

scientific article published in May 2007

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

scientific article published on 11 September 2019

Metagenomic analysis of tuberculosis in a mummy.

scientific article published in July 2013

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity

scientific article published on 23 March 2022

Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus

scientific article published on 14 January 2019

Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains

scientific article published on 14 January 2014

Microbial TIR domains: not necessarily agents of subversion?

scientific article published on 28 August 2009

Microbial bioinformatics 2020.

scientific article published on 29 July 2016

Microbial genomes

scientific article published in June 1999

Microbial genomics

Mutations affecting the Rossman fold of isoleucyl-tRNA synthetase are correlated with low-level mupirocin resistance in Staphylococcus aureus

scientific article published on February 2002

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database ⬇️

scientific article published in 2022

Netlines

article published in 1998

Netlines

scientific article published in October 1996

New strategies in microbiological diagnosis ⬇️

scientific article published on June 1, 1991

Next-generation sequencing--the promise and perils of charting the great microbial unknown.

scientific article

Non-human primates in the Gambia harbour human-associated pathogenic Escherichia coli strains

scientific article published in 2020

Nucleotide sequence of two genes from Helicobacter pylori encoding for urease subunits

scientific article published on January 1990

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

scientific article

Organization and architecture of AggR-dependent promoters from enteroaggregative Escherichia coli

scientific article published on 18 December 2018

Organization of the LEE1 operon regulatory region of enterohaemorrhagic Escherichia coli O157:H7 and activation by GrlA.

scientific article published on 21 November 2010

PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide

scientific article published on 12 August 2002

Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.

scientific article

Performance comparison of benchtop high-throughput sequencing platforms

scientific article

Phage-encoded genes and Salmonella virulence

scientific article published in June 1998

Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages

scientific article

Point mutations in the DNA- and cNMP-binding domains of the homologue of the cAMP receptor protein (CRP) in Mycobacterium bovis BCG: implications for the inactivation of a global regulator and strain attenuation.

scientific article

Recovery of a medieval Brucella melitensis genome using shotgun metagenomics

scientific article

Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157:H7.

scientific article

Remarkable genomic diversity among <i>Escherichia</i> isolates recovered from healthy chickens

scientific article published on 01 March 2022

Reply to Updating benchtop sequencing performance comparison ⬇️

scientific article published on April 1, 2013

Response to Comment on "Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago"

scientific article published in Science

Restoration of wild-type motility to flagellin-knockout <i>Escherichia coli</i> by varying promoter, copy number and induction strength in plasmid-based expression of flagellin

scientific article published on 01 November 2020

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology

scientific article

RpoN-dependent transcription of rpoH?

scientific article published on 01 January 1999

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

scientific article published in 2021

Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing

scientific article

SepL resembles an aberrant effector in binding to a class 1 type III secretion chaperone and carrying an N-terminal secretion signal

scientific article published on 10 September 2010

Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei

scientific article (publication date: 22 February 2003)

Shifts from glucose to certain secondary carbon-sources result in activation of the extracytoplasmic function sigma factor sigmaE in Salmonella enterica serovar Typhimurium

scientific article

Sigma(s)-Dependent carbon-starvation induction of pbpG (PBP 7) is required for the starvation-stress response in Salmonella enterica serovar Typhimurium

scientific article

Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching

scientific article

Subversion of actin dynamics by EspM effectors of attaching and effacing bacterial pathogens

scientific article published on 5 March 2008

Tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide and N-benzyl-6',7'-dihydrospiro[piperidine-4,4'-thieno[3,2-c]pyran] analogues with bactericidal efficacy against Mycobacterium tuberculosis targeting MmpL3

scientific article

Tetratricopeptide repeats in the type III secretion chaperone, LcrH: their role in substrate binding and secretion

scientific article published on January 2006

Tetratricopeptide-like repeats in type-III-secretion chaperones and regulators

scientific article

The Coiled-coil Domain of EspA Is Essential for the Assembly of the Type III Secretion Translocon on the Surface of Enteropathogenic Escherichia coli

scientific article published in Journal of Biological Chemistry

The ESAT-6/WXG100 superfamily -- and a new Gram-positive secretion system?

scientific article published on May 2002

The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition

scientific article

The Enigmatic Esx Proteins: Looking Beyond Mycobacteria

scientific article published on 25 November 2016

The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli

scientific article

The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?

scientific article published on 3 May 2017

The Human Microbiome and Host–Pathogen Interactions

The Next Million Names for Archaea and Bacteria

scientific article published on 14 November 2020

The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella

scientific article published on 20 December 2011

The coiled-coil domain of EspA is essential for the assembly of the type III secretion translocon on the surface of enteropathogenic Escherichia coli. Vol. 274 (1999) 35969–35974

scientific article published in 2005

The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats

scientific article

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

scientific article

The emerging threat of pre-extensively drug-resistant tuberculosis in West Africa: preparing for large-scale tuberculosis research and drug resistance surveillance

scientific article

The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

scientific article

The gut-adherent microbiota of PSC-IBD is distinct to that of IBD.

scientific article

The homodimeric GBS1074 from Streptococcus agalactiae

scientific article

The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis

scientific article

The status for uncultured taxa of and : SWOT analysis

scientific article published in 2021

The ‘Annie Hypothesis': Did the Death of His Daughter Cause Darwin to ‘Give up Christianity’? ⬇️

scientific article published on January 1, 2012

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

Time to recognise that mitochondria are bacteria?

scientific article published on 01 December 2010

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology

scientific article published on 15 June 2019

Translation of a minigene in the 5' leader sequence of the enterohaemorrhagic Escherichia coli LEE1 transcription unit affects expression of the neighbouring downstream gene

scientific article published on January 2012

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing

scientific article

Tricorn-like proteases in bacteria

scientific article

Twenty years of bacterial genome sequencing

scientific article published on 9 November 2015

Type III secretion: what's in a name?

scientific article published on 14 March 2006

Type VI secretion: a beginner's guide

scientific article

Variation in bacterial flagellins: from sequence to structure

scientific article

Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy

scientific article

Whole-genome sequence of the emerging pathogen Mycobacterium abscessus strain 47J26.

scientific article published on January 2012

Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria.

scientific article published on 19 September 2017

XDR-TB genome sequencing: a glimpse of the microbiology of the future

scientific article published in April 2008

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.

scientific article published on January 2004

xBASE, a collection of online databases for bacterial comparative genomics

scientific article

xBASE2: a comprehensive resource for comparative bacterial genomics.

scientific article published on 5 November 2007

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