Nabil-Fareed Alikhan
Nabil-Fareed Alikhan
Quadram Institute Biosciences
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BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
NF Alikhan, NK Petty, NLB Zakour, SA Beatson
BMC genomics 12 (1), 402, 2011
A genomic overview of the population structure of Salmonella
NF Alikhan, Z Zhou, MJ Sergeant, M Achtman
PLoS genetics 14 (4), e1007261, 2018
GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, ...
Genome research 28 (9), 1395-1404, 2018
Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak
ME Pearce, NF Alikhan, TJ Dallman, Z Zhou, K Grant, MCJ Maiden
International journal of food microbiology 274, 1-11, 2018
Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C Lineage for millennia
Z Zhou, I Lundstrøm, A Tran-Dien, S Duchêne, NF Alikhan, MJ Sergeant, ...
Current Biology 28 (15), 2420-2428. e10, 2018
The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
Z Zhou, NF Alikhan, K Mohamed, Y Fan, M Achtman, D Brown, ...
Genome research 30 (1), 138-152, 2020
Genome sequence of the emerging pathogen Aeromonas caviae
SA Beatson, MG de Luna, NL Bachmann, NF Alikhan, KR Hanks, ...
Journal of bacteriology 193 (5), 1286-1287, 2011
Mechanisms involved in acquisition of blaNDM genes by IncA/C2 and IncFIIY plasmids
AM Wailan, HE Sidjabat, WK Yam, NF Alikhan, NK Petty, AL Sartor, ...
Antimicrobial agents and chemotherapy 60 (7), 4082-4088, 2016
Comparison of classical multi-locus sequence typing software for next-generation sequencing data
AJ Page, NF Alikhan, HA Carleton, T Seemann, JA Keane, LS Katz
Microbial genomics 3 (8), 2017
Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition
SA Beatson, NLB Zakour, M Totsika, BM Forde, RE Watts, AN Mabbett, ...
Infection and immunity 83 (5), 1749-1764, 2015
Accurate reconstruction of microbial strains from metagenomic sequencing using representative reference genomes
Z Zhou, N Luhmann, NF Alikhan, C Quince, M Achtman
International Conference on Research in Computational Molecular Biology, 225-240, 2018
Genome-wide identification and characterization of a superfamily of bacterial extracellular Contractile Injection Systems
L Chen, N Song, B Liu, N Zhang, NF Alikhan, Z Zhou, Y Zhou, S Zhou, ...
Cell reports 29 (2), 511-521. e2, 2019
Emergence of human-adapted Salmonella enterica is linked to the Neolithization process
FM Key, C Posth, LR Esquivel-Gomez, R Hübler, MA Spyrou, ...
Nature ecology & evolution 4 (3), 324-333, 2020
ICTV Virus Taxonomy Profile: Herelleviridae
J Barylski, AM Kropinski, NF Alikhan, EM Adriaenssens
Journal of General Virology 101 (4), 362-363, 2020
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
M Bawn, NF Alikhan, G Thilliez, M Kirkwood, NE Wheeler, L Petrovska, ...
Plos Genetics 16 (6), e1008850, 2020
CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing
DJ Baker, GL Kay, A Aydin, T Le-Viet, S Rudder, AP Tedim, A Kolyva, ...
bioRxiv, 2020
Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru
AJ Page, NF Alikhan, M Strinden, T Le Viet, T Skvortsov
bioRxiv, 2020
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
E Foster-Nyarko, NF Alikhan, A Ravi, NM Thomson, S Jarju, ...
bioRxiv, 2020
Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
E Foster-Nyarko, NF Alikhan, A Ravi, G Thilliez, N Thomson, JD Cramer, ...
bioRxiv, 2020
Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan
F Rasheed, M Saeed, NF Alikhan, D Baker, M Khurshid, EV Ainsworth, ...
medRxiv, 2020
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