"Efficient sequence alignment against millions of prokaryotic genomes with LexicMap"
Shen, Wei; Lees, John; Iqbal, Zamin
Nature Biotechnology (2025)
"Rate variation and recurrent sequence errors in pandemic-scale phylogenetics"
De Maio, Nicola; Willemsen, Myrthe; Guo, Zihao; Saha, Abhratanu; Hunt, Martin; Ly-Trong, Nhan; Minh, Bui Quang; Iqbal, Zamin; Goldman, Nick
Accepted Nature Methods (2025); preprint Biorxiv (2024) —
link"Amira: detection of AMR genes directly from long reads using gene-space de Bruijn graphs"
Anderson, Daniel; Lima, Leandro; Le, Trieu; Judd, Louise; Wick, Ryan; Iqbal, Zamin
"Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling"
Frolova, Daria; Iqbal, Zamin
"Applying rearrangement distances to enable plasmid epidemiology with pling"
Frolova, Daria; Lima, L; Roberts, Leah; Bohnenkamper, Leonard; Wittler, Roland; Stoye, Jens; Iqbal, Zamin
Microbial Genomics (2024)
"CELEBRIMBOR: Core and accessory genes from metagenomes"
Hellewell, Joel; Horsfield, Samuel T; von Wachsmann, Johanna; Gurbich, Tatiana A; Finn, Robert D; Iqbal, Zamin; Roberts, Leah W; Lees, John A
Bioinformatics (btae542), (2024)
"Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis"
Hall, Michael B; Rabodoarivelo, Marie Sylvianne; Koch, Anastasia; Dippenaar, Anzaan; George, Sophie; Grobbelaar, Melanie; Warren, Robin; Walker, Timothy M; Cox, Helen; Gagneux, Sebastien; Crook, Derrick; Peto, Tim; Rakotosamimanana, Niaina; Grandjean Lapierre, Simon; Iqbal, Zamin
Lancet Microbe (2023)
"Drug resistance prediction for Mycobacterium tuberculosis with reference graphs"
Hall, Michael B; Lima, Leandro; Coin, Lachlan JM; Iqbal, Zamin
Microbial Genomics (2023)
"Gramtools enables multiscale variation analysis with genome graphs"
Letcher, Brice; Hunt, Martin; Iqbal, Zamin
Genome Biology (2021)
"Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs"
Colquhoun, Rachel M; Hall, Michael B; Lima, Leandro; Roberts, Leah W; Malone, Kerri M; Hunt, Martin; Letcher, Brice; Hawkey, Jane; George, Sophie; Pankhurst, Louise; Iqbal, Zamin
Genome Biology (2021)
"REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets"
Marchet, Camille; Iqbal, Zamin; Gautheret, Daniel; Salson, Mikaël; Chikhi, Rayan
Bioinformatics (2020)
"Ultrafast search of all deposited bacterial and viral genomic data"
Bradley, Phelim; den Bakker, Henk C; Rocha, Eduardo; McVean, Gil; Iqbal, Zamin
Nature Biotechnology (2019)
"Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe"
Hunt, Martin; Bradley, Phelim; Lapierre, Simon Grandjean; Heys, Simon; Thomsit, Mark; Hall, Michael B; Malone, Kerri M; Wintringer, Penelope; Walker, Timothy M; Cirillo, Daniela M; ..[several authors]… Iqbal, Zamin
Wellcome Open Research (2019)
"COBS: a compact bit-sliced signature index"
Bingmann, Timo; Bradley, Phelim; Gauger, Florian; Iqbal, Zamin
String Processing and Information Retrieval: 26th International Symposium, SPIRE 2019, Segovia, Spain
"A natural encoding of genetic variation in a Burrows-Wheeler transform to enable mapping and genome inference"
Maciuca, Sorina; del Ojo Elias, Carlos; McVean, Gil; Iqbal, Zamin
Algorithms in Bioinformatics: 16th International Workshop, WABI 2016, Aarhus, Denmark
"Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis"
Bradley, Phelim; Gordon, N Claire; Walker, Timothy M; Dunn, Laura; Heys, Simon; Huang, Bill; Earle, Sarah; Pankhurst, Louise J; Anson, Luke; De Cesare, Mariateresa; ..[many authors]… Iqbal, Zamin
Nature Communications (2015)
"High-throughput microbial population genomics using the Cortex variation assembler"
Iqbal, Z; Turner, I; McVean, G
Bioinformatics (2012)
"De novo assembly and genotyping of variants using colored de Bruijn graphs"
Iqbal, Zamin*; Caccamo, Mario*; Turner, Isaac; Flicek, Paul; McVean, Gil
Nature Genetics (2012)
"Pre and Post antibiotic epoch: insights into the historical spread of antimicrobial resistance"
Cazares, Adrian; Figueroa, Wendy; Cazares, Daniel; Lima, Leandro; Turnbull, Jake D; McGregor, Hannah; Dicks, Jo; Alexander, Sarah; Iqbal, Zamin*; Thomson, Nicholas*
"Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi"
Ingle, Danielle; Hawkey, Jane; Hunt, Martin; Iqbal, Zamin; …[many authors]… Holt, Kathryn; Global Typhoid Genomics Consortium
Accepted Genome Medicine (2025); preprint Biorxiv (2024) —
link"Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum"
Letcher, Brice; Maciuca, Sorina; Iqbal, Zamin
PLoS Biology (2024)
"MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis"
Roberts, Leah W; Malone, Kerri M; Hunt, Martin; Joseph, Lavania; Wintringer, Penelope; Knaggs, Jeff; Crook, Derrick; Farhat, Maha R; Iqbal, Zamin; Omar, Shaheed V
Lancet Microbe (2024)
"Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years"
Roberts, Leah W; Enoch, David A; Khokhar, Fahad; Blackwell, Grace A; Wilson, Hayley; Warne, Ben; Gouliouris, Theodore; Iqbal, Zamin*; Török, M Estée*
Microbial Genomics (2023)
"The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis"
Walker, Timothy M; Miotto, Paolo; Köser, Claudio U; Fowler, Philip W; Knaggs, Jeff; Iqbal, Zamin; Hunt, Martin; Chindelevitch, Leonid; Farhat, Maha R; Cirillo, Daniela Maria
Lancet Microbe (2022)
"A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics"
CRyPTIC Consortium
PLoS Biology (2022)
"Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms"
CRyPTIC Consortium
PLoS Biology (2022)
"Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study"
Roberts, Leah W; Khokhar, Fahad A; Hoa, Nguyen Thi; Van Giang, Tran; Bui, Cuong; Ninh, Tran Hai; Binh, Nguyen Gia; Long, Hoang Bao; Huong, Dang Thi; Bryan, James E; Herrick, Archie; Feltwell, Theresa; Nadjm, Behzad; van Doorn, Rogier; Parkhill, Julian; Trung, Nguyen Vu; Kinh, Nguyen Van; Iqbal, Zamin*; Török, Estée*
Lancet Microbe (2022)
"Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei"
Hawkey, Jane; Paranagama, Kalani; Baker, Kate S; Bengtsson, Rebecca J; Weill, François-Xavier; Thomson, Nicholas R; Baker, Stephen; Cerdeira, Louise; Iqbal, Zamin; Hunt, Martin; Ingle, Danielle J; Dallman, Timothy; Jenkins, Claire; Williamson, Deborah A; Holt, Kathryn
Nature Communications (2021)
"Assessing evolutionary risks of resistance for new antimicrobial therapies"
Brockhurst, Michael A; Harrison, Freya; Veening, Jan-Willem; Harrison, Ellie; Blackwell, Grace; Iqbal, Zamin; Maclean, Craig
Nature Ecology & Evolution (2019)
"Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing"
The CRyPTIC Consortium and the 100,000 Genomes Project
New England Journal of Medicine (2018)
"Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples"
Votintseva, Antonina A; Bradley, Phelim; Pankhurst, Louise; del Ojo Elias, Carlos; Loose, Matthew; Nilgiriwala, Kayzad; Chatterjee, Anirvan; Smith, E Grace; Sanderson, Nicolas; Walker, Timothy M; Morgan, Marcus R; Wyllie, David H; Walker, Sarah A; Peto, Tim EA; Crook, Derrick W; Iqbal, Zamin
Journal of Clinical Microbiology (2017)
"Binding of Plasmodium falciparum merozoite surface proteins DBLMSP and DBLMSP2 to human immunoglobulin M is conserved among broadly diverged sequence variants"
Crosnier, Cécile; Iqbal, Zamin; Knuepfer, Ellen; Maciuca, Sorina; Perrin, Abigail J; Kamuyu, Gathoni; Goulding, David; Bustamante, Leyla Y; Miles, Alistair; Moore, Shona C; Dougan, Gordon; Holder, Anthony; Kwiatkowski, Dominic P; Rayner, Julian C; Pleass, Richard J; Wright, Gavin J
Journal of Biological Chemistry (2016)
"Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum"
Miles, Alistair; Iqbal, Zamin; Vauterin, Paul; Pearson, Richard; Campino, Susana; Theron, Michel; Gould, Kelda; Mead, Daniel; Drury, Eleanor; O'Brien, John
Genome Research (2016)