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Author Details

Nabil-Fareed Alikhan
Quadram Institute Bioscience
2011
27
14
PMIDPaper TitleJournal TitlePublished Year
37171866Corrigendum: Naming the unnamed: over 65,000 <i>Candidatus</i> names for unnamed <i>Archaea</i> and <i>Bacteria</i> in the Genome Taxonomy Database.Int J Syst Evol Microbiol2023
37523225Genomic diversity and epidemiological significance of non-typhoidal <i>Salmonella</i> found in retail food collected in Norfolk, UK.Microb Genom2023
35169842Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.Gigascience2022
35653335Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health.PLoS Genet2022
36409097Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals.Microbiol Spectr2022
36125864Naming the unnamed: over 65,000 <i>Candidatus</i> names for unnamed <i>Archaea</i> and <i>Bacteria</i> in the Genome Taxonomy Database.Int J Syst Evol Microbiol2022
36093336Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.PeerJ2022
35876490Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.Microb Genom2022
33253086Genomic diversity of <i>Escherichia coli</i> isolates from backyard chickens and guinea fowl in the Gambia.Microb Genom2021
33868800Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.PeerJ2021
33563320CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.Genome Med2021
33505796Genomic diversity of <i>Escherichia coli</i> from healthy children in rural Gambia.PeerJ2021
34812716Invasive atypical non-typhoidal <i>Salmonella</i> serovars in The Gambia.Microb Genom2021
34846280SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021.Microb Genom2021
32924917Genomic diversity of <i>Escherichia coli</i> isolates from non-human primates in the Gambia.Microb Genom2020
31809257The EnteroBase user's guide, with case studies on <i>Salmonella</i> transmissions, <i>Yersinia pestis</i> phylogeny, and <i>Escherichia</i> core genomic diversity.Genome Res2020
32094538Emergence of human-adapted Salmonella enterica is linked to the Neolithization process.Nat Ecol Evol2020
29621240A genomic overview of the population structure of Salmonella.PLoS Genet2018
30049790GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens.Genome Res2018
30033331Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.Curr Biol2018
30138580Principles of Systems Biology, No. 31.Cell Syst2018
29574242Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.Int J Food Microbiol2018
29026660Comparison of classical multi-locus sequence typing software for next-generation sequencing data.Microb Genom2017
27114281Mechanisms Involved in Acquisition of blaNDM Genes by IncA/C2 and IncFIIY Plasmids.Antimicrob Agents Chemother2016
25667270Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.Infect Immun2015
21183677Genome sequence of the emerging pathogen Aeromonas caviae.J Bacteriol2011
21824423BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.BMC Genomics2011
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Collaborators

Zhemin Zhou
Pasteurien College, Suzhou Medical College of Soochow University
Co-authored papers 6
Mark Achtman
Warwick Medical School, University of Warwick
Co-authored papers 6
Nina Luhmann
Warwick Medical School, University of Warwick
Co-authored papers 2
Ileana M Cristea
Princeton University
Co-authored papers 1
Alan Christoffels
Co-authored papers 1
Bonnie Berger
Massachusetts Institute of Technology
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Peter J Oefner
Institute of Functional Genomics, University of Regensburg
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Michael Altenbuchinger
University Medical Center Gottingen
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Rainer Spang
University of Regensburg
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University of Padova
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Jian Peng
University of Illinois
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Simona Cristea
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Broad Institute
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Torsten Seemann
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Cyril Galitzine
From the ++College of Science, Northeastern University
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Dorit S Hochbaum
University of California berkeley
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Hyunghoon Cho
Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Stanford University, Yale University
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Stefan Solbrig
Institute of Theoretical Physics, University of Regensburg
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Anjanette Johnston
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 1
Rebecca Sarto Basso
University of California at Berkeley
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Ilene Karsch-Mizrachi
Co-authored papers 1
Ruth E Timme
Center for Food Safety and Applied Nutrition, College Park
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Olga Vitek
Khoury College of Computer Sciences, Northeastern University
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Migun Shakya
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Christopher Quince
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