My Publications | Happykhan.com - Nabil-Fareed Alikhan

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Alikhan et al. (2022) PLOS Genetics 18:6 e1010174

Castillo-Bravo et al. (2022) Microbiology Spectrum 10:6 e02229-22

Eales et al. (2022) Wellcome Open Research 7102

Griffiths et al. (2022) GigaScience 11giac003

Merhi et al. (2022) Microbial Genomics 8:7

Pallen et al. (2022) International Journal of Systematic and Evolutionary Microbiology 72:9

Snell et al. (2022) Clinical Microbiology and Infection 28:1 93-100

Twohig et al. (2022) The Lancet Infectious Diseases 22:1 35-42

Xiaoli et al. (2022) PeerJ 10e13821

Achtman et al. (2021) Wellcome Open Research 5223

Alikhan et al. (2021) PREPRINT

Baker et al. (2021) Genome Medicine 13:1 21

de Silva et al. (2021) iScience 24:11 103353

Foster-Nyarko et al. (2021) PeerJ 9e10572

Gilroy et al. (2021) PeerJ 9e10941

Graham et al. (2021) The Lancet Public Health 6:5 e335-e345

Kanteh et al. (2021) Microbial Genomics 7:11

Meng et al. (2021) Cell Reports 35:13 109292

Page et al. (2021) Microbial Genomics 7:6

Riley et al. (2021) PREPRINT

Riley et al. (2021) PREPRINT

Sarwar et al. (2021) Microbial Genomics 7:11

Volz et al. (2021) Cell 184:1 64-75.e11

Barylski et al. (2020) Journal of General Virology 101:4 362-363

Bawn et al. (2020) PLOS Genetics 16:6 e1008850

Foster-Nyarko et al. (2020) Access Microbiology 2:7A

Foster-Nyarko et al. (2020) Access Microbiology 2:7A

Key et al. (2020) Nature Ecology \& Evolution 4:3 324-333

Page et al. (2020) PREPRINT

Rasheed et al. (2020) Microorganisms 8:9 1336

Zhou et al. (2020) Genome Research 30:1 138-152

Alikhan et al. (2019) PREPRINT

Chen et al. (2019) Cell Reports 29:2 511-521.e2

Foster-Nyarko et al. (2019) PREPRINT

Alikhan et al. (2018) PLoS genetics 14:4 e1007261

Cho et al. (2018) Cell Systems 7:2 133-135

Pearce et al. (2018) International Journal of Food Microbiology 2741-11

Zhou et al. (2018) Genome Research 28:9 1395-1404

Zhou et al. (2018) Current Biology 28:15 2420-2428.e10

Zhou et al. (2018) 10812225-240

Page et al. (2017) Microbial Genomics 3:8 e000124

Wailan et al. (2016) Antimicrobial Agents and Chemotherapy 60:7 4082-4088

Beatson et al. (2015) Infection and Immunity 83:5 1749-1764

Alikhan et al. (2011) BMC genomics 12402

Beatson et al. (2011) Journal of Bacteriology 193:5 1286-1287

Publications (45)

Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health

Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals

Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

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

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

Defining the analytical and clinical sensitivity of the ARTIC method for the detection of SARS-CoV-2

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Genomic diversity of Escherichia coli from healthy children in rural Gambia

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

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Invasive atypical non-typhoidal Salmonella serovars in The Gambia

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant

REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown

SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

ICTV Virus Taxonomy Profile: Herelleviridae

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

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

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

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli

Genome-wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems

Within-Host Diversity and Vertical Transmission of Group B Streptococcus Among Mother-infant Dyads in The Gambia

A genomic overview of the population structure of Salmonella

Principles of Systems Biology, No. 31

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

Comparison of classical multi-locus sequence typing software for next-generation sequencing data

Mechanisms Involved in acquisition of bla_NDM Genes by IncA/C2 and IncFIIY Plasmids

Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

Genome Sequence of the Emerging Pathogen Aeromonas caviae