Z. Iqbal

发表

Mapping copy number variation by population scale genome sequencing

Kenny Q. Ye, G. T. Marth, Hugo Y. K. Lam, 2010, Nature.

De novo assembly and genotyping of variants using colored de Bruijn graphs

G. McVean, Z. Iqbal, P. Flicek, 2011, Nature Genetics.

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

G. McVean, A. Halpern, E. H. Margulies, 2016, bioRxiv.

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

Zamin Iqbal, Jared T. Simpson, Richard Durbin, 2016, bioRxiv.

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

Ryan D. Hernandez, P. Donnelly, A. Auton, 2012, Science.

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

G. McVean, Z. Iqbal, I. Mathieson, 2014, Nature Genetics.

Severe infections emerge from the microbiome by adaptive evolution

Daniel J. Wilson, Z. Iqbal, Chieh-Hsi Wu, 2017, bioRxiv.

Engineering a Compact Bit-Sliced Signature Index for Approximate Search on Genomic Data

P. Sanders, Z. Iqbal, Florian Gauger, 2018 .

The genomic and phenotypic diversity of Schizosaccharomyces pombe

Brendan D. O'Fallon, Danny A. Bitton, Tammy M. K. Cheng, 2015, Nature Genetics.

The global distribution and spread of the mobilized colistin resistance gene mcr-1

Z. Iqbal, F. Balloux, X. Didelot, 2018, Nature Communications.

Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation

Z. Iqbal, T. Walker, T. Peto, 2022, medRxiv.

Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

Phelim Bradley, Gil McVean, Zamin Iqbal, 2016, Nature Communications.

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

Zamin Iqbal, Richard M. Leggett, Jonathan D. G. Jones, 2013, PloS one.

Improved genome inference in the MHC using a population reference graph

Gil McVean, Zamin Iqbal, Alexander Dilthey, 2014, Nature Genetics.

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

Phelim Bradley, Gil McVean, Zamin Iqbal, 2015, Nature Communications.

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples

Phelim Bradley, Zamin Iqbal, Matthew Loose, 2016 .

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

Nucleotide-resolution bacterial pan-genomics with reference graphs

Z. Iqbal, L. Pankhurst, Martin Hunt, 2020, bioRxiv.

Detection of simple and complex de novo mutations with multiple reference sequences

Juliana M. Sá, K. Garimella, G. McVean, 2020, Genome research.

Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping

Phelim Bradley, Zamin Iqbal, Derrick W. Crook, 2017, Journal of Clinical Microbiology.

Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe

Z. Iqbal, J. Gardy, S. Niemann, 2019, Wellcome open research.

SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex

Z. Iqbal, S. Niemann, T. Walker, 2019, Emerging infectious diseases.

DNA Sequencing Predicts 1st-Line Tuberculosis Drug Susceptibility Profiles

Daniel J. Wilson, Matthew W. Snyder, J. Shendure, 2018, The New England Journal of Medicine.

Drug-Resistant Tuberculosis in Pet Ring-Tailed Lemur, Madagascar

Z. Iqbal, M. Rabodoarivelo, N. Rakotosamimanana, 2021, Emerging infectious diseases.

Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms

Daniel J. Wilson, Z. Iqbal, D. Clifton, 2022, PLoS biology.

Reference‐free SNP discovery for the Eurasian beaver from restriction site–associated DNA paired‐end data

Z. Iqbal, T. Cezard, K. Gharbi, 2013, Molecular ecology.

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.

N. V. Trung, Z. Iqbal, T. Feltwell, 2022, The Lancet. Microbe.

A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference

G. McVean, Z. Iqbal, C. del Ojo Elias, 2016, bioRxiv.

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Z. Iqbal, S. Niemann, P. Rancoita, 2022, PLoS biology.

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

David A. Clifton, Gil McVean, Zamin Iqbal, 2015, Nature Microbiology.

The global distribution and spread of the mobilized colistin resistance gene mcr-1

Z. Iqbal, F. Balloux, X. Didelot, 2017, bioRxiv.

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Z. Iqbal, L. Pankhurst, Martin Hunt, 2021, Genome Biology.

A genomic epidemiology study of multidrug-resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii in two intensive care units in Hanoi, Vietnam

N. V. Trung, Z. Iqbal, T. Feltwell, 2020, medRxiv.

An integrated map of genetic variation from 1,092 human genomes

Kenny Q. Ye, Mauricio O. Carneiro, Francisco M. De La Vega, 2012, Nature.

Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data

Zamin Iqbal, John D. O'Brien, Jason Wendler, 2016, PLoS Comput. Biol..

An integrative statistical model for inferring strain admixture within clinical Plasmodium falciparum isolates

Z. Iqbal, John D. O'Brien, L. Amenga-Etego, 2015, 1505.08171.

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

Gil McVean, Zamin Iqbal, Alistair Miles, 2016, Genome research.

Genome variation and meiotic recombination in Plasmodium falciparum: insights from deep sequencing of genetic crosses

Gil McVean, Zamin Iqbal, Alistair Miles, 2015, bioRxiv.

A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

Zamin Iqbal, Daniel Falush, Xavier Didelot, 2013, Genetics.

Detection of simple and complex de novo mutations without, with, or with multiple reference sequences

Zamin Iqbal, Gilean McVean, Kiran V. Garimella, 2019, bioRxiv.

A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing

Z. Iqbal, S. Niemann, T. Peto, 2017, bioRxiv.

Binding of Plasmodium falciparum Merozoite Surface Proteins DBLMSP and DBLMSP2 to Human Immunoglobulin M Is Conserved among Broadly Diverged Sequence Variants

J. Rayner, D. Kwiatkowski, Z. Iqbal, 2016, The Journal of Biological Chemistry.

Gramtools enables multiscale variation analysis with genome graphs

Z. Iqbal, Martin Hunt, B. Letcher, 2021, Genome biology.

Enabling multiscale variation analysis with genome graphs

Z. Iqbal, Martin Hunt, B. Letcher, 2021, bioRxiv.

Integrating long-range connectivity information into de Bruijn graphs

Gil McVean, Zamin Iqbal, Kiran V. Garimella, 2017, bioRxiv.

Repeated evolution of bedaquiline resistance in Mycobacterium tuberculosis is driven by truncation of mmpR5

Z. Iqbal, D. Crook, Martin Hunt, 2022, bioRxiv.

Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants

Z. Iqbal, M. Torres-Puente, I. Comas, 2023, Microbiology spectrum.

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

Blaise T. F. Alako, Z. Iqbal, N. Thomson, 2021, bioRxiv.

Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples

Phelim Bradley, Zamin Iqbal, Matthew Loose, 2016, Journal of Clinical Microbiology.

COBS: a Compact Bit-Sliced Signature Index pdf

Phelim Bradley, Zamin Iqbal, Timo Bingmann, 2019, SPIRE.

Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches

Zamin Iqbal, Sophie George, Anna E. Sheppard, 2017, Microbial genomics.

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

M. Schatz, Z. Iqbal, Martin Hunt, 2022, Genome Biology.

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

M. Schatz, Z. Iqbal, Martin Hunt, 2021, Genome Biology.

Genomic sequence characteristics and the empiric accuracy of short-read sequencing

Maximillian G. Marin, Z. Iqbal, A. Rosenthal, 2021, bioRxiv.

Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach

Z. Iqbal, S. Niemann, Martin Hunt, 2021, bioRxiv.

High-throughput microbial population genomics using the Cortex variation assembler

Gil McVean, Zamin Iqbal, Isaac Turner, 2012, Bioinform..

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

T. Dallman, Z. Iqbal, K. Holt, 2020, Nature Communications.

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

Z. Iqbal, L. Freschi, Avika Dixit, 2021, Genome Medicine.

DNA Sequencing Predicts 1st-Line Tuberculosis Drug Susceptibility Profiles

Phelim Bradley, Zamin Iqbal, Baoli Zhu, 2018, The New England journal of medicine.

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

Phelim Bradley, Zamin Iqbal, Daniel J. Wilson, 2015, The Lancet. Infectious diseases.

Ultra-fast search of all deposited bacterial and viral genomic data

Phelim Bradley, Henk C den Bakker, Eduardo P C Rocha, 2019, Nature Biotechnology.

Ultrafast search of all deposited bacterial and viral genomic data

G. McVean, E. Rocha, Z. Iqbal, 2019, Nature Biotechnology.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Peter Donnelly, Zamin Iqbal, Richard G. Everitt, 2012, Proceedings of the National Academy of Sciences.

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

Alexander T. Dilthey, Gil McVean, Zamin Iqbal, 2016, PLoS Comput. Biol..

Severe infections emerge from commensal bacteria by adaptive evolution

Zamin Iqbal, John Paul, Tanya Golubchik, 2017, eLife.

High-accuracy HLA type inference from whole-genome sequencing data

Gil McVean, Zamin Iqbal, Alexander Dilthey, 2015, bioRxiv.

DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing

Z. Iqbal, T. Peto, D. Crook, 2018, Journal of medical microbiology.

REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

Daniel Gautheret, Zamin Iqbal, Rayan Chikhi, 2020, bioRxiv.

Gene conversion drives allelic dimorphism in two paralogous surface antigens of the malaria parasite P. falciparum

Z. Iqbal, B. Letcher, Sorina Maciuca, 2023, bioRxiv.

Assessing evolutionary risks of resistance for new antimicrobial therapies

Zamin Iqbal, Craig Maclean, Freya Harrison, 2019, Nature Ecology & Evolution.

Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis

Phelim Bradley, Gil McVean, Zamin Iqbal, 2015, bioRxiv.

Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data

David A. Clifton, Yang Yang, Zamin Iqbal, 2017, Bioinform..

Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis

Z. Iqbal, M. Wiedmann, M. Allard, 2014, Emerging infectious diseases.

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Daniel J. Wilson, Youwen Qin, M. Inouye, 2022, The Lancet. Microbe.

High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region

Z. Iqbal, D. Clifton, V. Srinivasan, 2022, Genome Medicine.

Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences

Phelim Bradley, Zamin Iqbal, A. Sarah Walker, 2018, Journal of Clinical Microbiology.

Assessing evolutionary risks of resistance for new antimicrobial therapies

Z. Iqbal, J. Veening, F. Harrison, 2019, Nature Ecology & Evolution.

GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes

Daniel J. Wilson, Z. Iqbal, D. Clifton, 2019, bioRxiv.

Drug resistance prediction for Mycobacterium tuberculosis with reference graphs

Michael B. Hall, Z. Iqbal, L. Coin, 2023, bioRxiv.

A data compendium of Mycobacterium tuberculosis antibiotic resistance

Daniel J. Wilson, G. Rodger, Z. Iqbal, 2021, bioRxiv.

Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis

G. Rodger, Z. Iqbal, S. Gharbia, 2023, The Lancet. Microbe.

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Carla A. Cummins, Peter W. Harrison, R. Leinonen, 2023, bioRxiv.

Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome

Maximillian G. Marin, Z. Iqbal, A. Rosenthal, 2022, Bioinform..

Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction

G. Rodger, Z. Iqbal, T. Walker, 2022, bioRxiv.

The 2021 WHO Catalogue of Mycobacterium Tuberculosis Complex Mutations Associated with Drug Resistance: A New Global Standard for Molecular Diagnostics

Z. Iqbal, L. Chindelevitch, T. Walker, 2021, SSRN Electronic Journal.

Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis

Z. Iqbal, T. Walker, T. Peto, 2022, The Lancet. Microbe.

Mapping copy number variation by population scale genome sequencing

Joshua M. Korn, Kenny Q. Ye, G. T. Marth, 2010, Nature.

Evolution and spread of bacterial transposons

Zamin Iqbal, Nick Thomson, Grace Blackwell, 2019, Access Microbiology.

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

G. Kucherov, Z. Iqbal, R. Chikhi, 2023, bioRxiv.

Severe infections emerge from commensal bacteria by adaptive evolution

Z. Iqbal, Chieh-Hsi Wu, T. Peto, 2017, eLife.

Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years

Z. Iqbal, B. Warne, D. Enoch, 2023, Microbial genomics.

Real-time search of all bacterial and viral genomic data

Phelim Bradley, Gil McVean, Zamin Iqbal, 2017, bioRxiv.

Drug resistance prediction for Mycobacterium tuberculosis with reference graphs

Michael B. Hall, Z. Iqbal, L. Coin, 2023, Microbial genomics.

Drug resistance prediction for Mycobacterium 1 tuberculosis with reference graphs

Z. Iqbal, M. B. Hall, L. Lima, 2023 .

Comprehensive genome-wide evaluation of lapatinib-induced liver injury yields a single genetic signal centered on known risk allele HLA-DRB1*07:01

A. J. Slater, G. McVean, K. King, 2015, The Pharmacogenomics Journal.

The genomic and phenotypic diversity of Schizosaccharomyces pombe

Brendan D. O'Fallon, Thomas M. Keane, Danny A. Bitton, 2015, Nature Genetics.

Title: A genomic epidemiology study of multidrug-resistant Escherichia coli , Klebsiella pneumoniae 1 and Acinetobacter baumannii in two intensive care units in Hanoi, Vietnam

N. V. Trung, Z. Iqbal, T. Feltwell, 2021 .

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

Z. Iqbal, S. Kouchaki, P. Rancoita, 2024, Nature communications.

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

P. Donnelly, A. Auton, G. McVean, 2012, Science.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease Major category: BIOLOGICAL SCIENCES Minor category: Evolution

Z. Iqbal, R. Everitt, X. Didelot, 2011 .