List of works - Nicholas J. Loman

A complete bacterial genome assembled de novo using only nanopore sequencing data

scientific article

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

scientific article published on 13 December 2013

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

scientific article

A disruptive sequencer meets disruptive publishing

scientific article

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

scientific article

APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016

scientific article published on 02 November 2023

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

scientific article published in July 2001

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

article published in 2018

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

scientific article published on August 23, 2011

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

scientific article published on 25 March 2021

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

scientific article

Binning metagenomic contigs by coverage and composition

scientific article

Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target

scientific article

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

publication published on 01 July 2021

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

scientific article

Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli

scientific article published on 24 July 2014

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

scientific article

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

scientific article

Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK.

scientific article published on 4 April 2013

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

scientific article

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

scientific article

Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium

scientific article published on 20 August 2015

Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound

scientific article

Ebola Virus Persistence in Breast Milk After No Reported Illness: A Likely Source of Virus Transmission From Mother to Child

scientific article

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

scientific article

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

scientific article

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article

Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing

scientific article published on 17 October 2013

Erratum: A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer

scientific article published on 13 February 2015

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article (publication date: 24 May 2017)

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

scientific article published on 08 January 2021

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition

scientific article published on 3 November 2015

Extreme genetic fragility of the HIV-1 capsid.

scientific article

First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador

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

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

scientific article published on 20 July 2023

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

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

scientific article published on 17 March 2010

Identification of KasA as the cellular target of an anti-tubercular scaffold

scientific article

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

scientific article

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

scientific article published on 04 September 2020

Microbial TIR domains: not necessarily agents of subversion?

scientific article published on 28 August 2009

Mobile real-time surveillance of Zika virus in Brazil

scientific article published on 29 September 2016

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

scientific article

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

scientific article (publication date: 9 January 2017)

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

scientific article

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

scientific article

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

scientific article

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

scientific article

Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.

scientific article

Performance comparison of benchtop high-throughput sequencing platforms

scientific article

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network

scientific article published on 25 August 2016

Poretools: a toolkit for analyzing nanopore sequence data

scientific article

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. ⬇️

Scientific report published 18 December 2020

Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs

scientific article published on 2 September 2014

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

scientific article

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

scientific article

Real-time, portable genome sequencing for Ebola surveillance

scientific article

Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days

scientific article

Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter?

scientific article

STOP-Colitis pilot trial protocol: a prospective, open-label, randomised pilot study to assess two possible routes of faecal microbiota transplant delivery in patients with ulcerative colitis

scientific article published on 11 November 2019

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

scientific article

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

scientific article

So you want to be a computational biologist?

scientific article published in November 2013

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing

scientific article published on 02 December 2016

Successful test launch for nanopore sequencing

scientific article

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

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

scientific article published on 20 December 2011

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

scientific article

The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred

scientific article

The effect of DNA extraction methodology on gut microbiota research applications.

scientific article

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

scientific article

Tricorn-like proteases in bacteria

scientific article

Twenty years of bacterial genome sequencing

scientific article published on 9 November 2015

Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015

scientific article

Videos, photographs, and patient consent. Medical educationalists can free themselves from constraints of "real world" images

scientific article published on November 1998

Virus genomes reveal factors that spread and sustained the Ebola epidemic

scientific article (publication date: 12 April 2017)

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

scientific article published in April 2008

xBASE2: a comprehensive resource for comparative bacterial genomics.

scientific article published on 5 November 2007

List of works by Nicholas J. Loman

A complete bacterial genome assembled de novo using only nanopore sequencing data

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

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

A disruptive sequencer meets disruptive publishing

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016

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

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

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

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

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

Binning metagenomic contigs by coverage and composition

Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

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

Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

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

Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK.

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

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

Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium

Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound

Ebola Virus Persistence in Breast Milk After No Reported Illness: A Likely Source of Virus Transmission From Mother to Child

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

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing

Erratum: A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition

Extreme genetic fragility of the HIV-1 capsid.

First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador

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

Genome sequence of the emerging pathogen Helicobacter canadensis

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

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

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

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

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

Identification of KasA as the cellular target of an anti-tubercular scaffold

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

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Microbial TIR domains: not necessarily agents of subversion?

Mobile real-time surveillance of Zika virus in Brazil

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

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

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

Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.

Performance comparison of benchtop high-throughput sequencing platforms

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network

Poretools: a toolkit for analyzing nanopore sequence data

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. ⬇️

Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Real-time, portable genome sequencing for Ebola surveillance

Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days

Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter?

STOP-Colitis pilot trial protocol: a prospective, open-label, randomised pilot study to assess two possible routes of faecal microbiota transplant delivery in patients with ulcerative colitis

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

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

So you want to be a computational biologist?

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing

Successful test launch for nanopore sequencing

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

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

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

The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred

The effect of DNA extraction methodology on gut microbiota research applications.

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

Tricorn-like proteases in bacteria

Twenty years of bacterial genome sequencing