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A complete high quality nanopore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf03402035openalex-snapshot

The Multidrug Transporters Belonging to Major Facilitator Superfamily (MFS) in Mycobacterium tuberculosis

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Signal transduction in the mammalian cell during bacterial attachment and entry

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Assessing the performance of the Oxford Nanopore Technologies MinION

inferredcites →https://doi.org/10.1016/j.ijid.2017.01.031openalex-snapshot

The risk of global epidemic replacement with drug-resistant Mycobacterium tuberculosis strains

inferredcites →https://doi.org/10.1016/j.ijmyco.2016.09.067openalex-snapshot

Increased expression of efflux pump genes in extensively drug-resistant isolates of Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1016/j.tube.2010.09.006openalex-snapshot

The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes

inferredcites →https://doi.org/10.1016/j.tube.2015.01.005openalex-snapshot

Differential expression of efflux pump genes of Mycobacterium tuberculosis in response to varied subinhibitory concentrations of antituberculosis agents

inferredcites →https://doi.org/10.1016/j.tube.2017.07.012openalex-snapshot

Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan

inferredcites →https://doi.org/10.1016/j.ygeno.2017.07.004openalex-snapshot

Limitations of the Mycobacterium tuberculosis reference genome H37Rv in the detection of virulence-related loci

inferredcites →https://doi.org/10.1016/s1473-3099(07)70108-1openalex-snapshot

Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development

inferredcites →https://doi.org/10.1016/s1473-3099(13)70030-6openalex-snapshot

Drug-resistant tuberculosis: time for visionary political leadership

inferredcites →https://doi.org/10.1016/s2213-2600(17)30079-6openalex-snapshot

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

inferredcites →https://doi.org/10.1038/nature16996openalex-snapshot

Real-time, portable genome sequencing for Ebola surveillance

inferredcites →https://doi.org/10.1038/nbt.3103openalex-snapshot

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

inferredcites →https://doi.org/10.1038/ncomms8119openalex-snapshot

Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain

inferredcites →https://doi.org/10.1038/ng.1038openalex-snapshot

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

inferredcites →https://doi.org/10.1038/ng.2735openalex-snapshot

Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance

inferredcites →https://doi.org/10.1038/ng.2878openalex-snapshot

Evolution and transmission of drug-resistant tuberculosis in a Russian population

inferredcites →https://doi.org/10.1038/ng.3195openalex-snapshot

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot

A complete bacterial genome assembled de novo using only nanopore sequencing data

inferredcites →https://doi.org/10.1038/nprot.2015.053openalex-snapshot

The Phyre2 web portal for protein modeling, prediction and analysis

inferredcites →https://doi.org/10.1038/nrg3226openalex-snapshot

Transforming clinical microbiology with bacterial genome sequencing

inferredcites →https://doi.org/10.1038/nrmicro.2015.13openalex-snapshot

Within-host evolution of bacterial pathogens

inferredcites →https://doi.org/10.1073/pnas.2433882100openalex-snapshot

Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon

inferredcites →https://doi.org/10.1074/jbc.m109.006940openalex-snapshot

The Pks13/FadD32 Crosstalk for the Biosynthesis of Mycolic Acids in Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1080/23744235.2017.1330553openalex-snapshot

Differential carriage of virulence-associated loci in the New Zealand Rangipo outbreak strain ofMycobacterium tuberculosis

inferredcites →https://doi.org/10.1089/omi.2008.0017openalex-snapshot

Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation

inferredcites →https://doi.org/10.1098/rsob.160105openalex-snapshot

Structural and functional analysis of the solute-binding protein UspC from Mycobacterium tuberculosis that is specific for amino sugars

inferredcites →https://doi.org/10.1101/172601openalex-snapshot

Multi-clonal evolution of MDR/XDR M. tuberculosis in a high prevalence setting in Papua New Guinea over three decades

inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot

Circos: An information aesthetic for comparative genomics

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

inferredcites →https://doi.org/10.1101/gr.128678.111openalex-snapshot

Microevolution of extensively drug-resistant tuberculosis in Russia

inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation

inferredcites →https://doi.org/10.1111/j.1365-2958.2008.06354.xopenalex-snapshot

Biosynthesis of mycobacterial arabinogalactan: identification of a novel α(1→3) arabinofuranosyltransferase

inferredcites →https://doi.org/10.1111/mmi.12981openalex-snapshot

Phylogeny to function: PE / PPE protein evolution and impact on M ycobacterium tuberculosis pathogenicity

inferredcites →https://doi.org/10.1128/aac.00298-08openalex-snapshot

Identification of a Novel Multidrug Efflux Pump of Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1128/aac.05546-11openalex-snapshot

The Antibiotic Resistance Arrow of Time: Efflux Pump Induction Is a General First Step in the Evolution of Mycobacterial Drug Resistance

inferredcites →https://doi.org/10.1128/genomea.00510-17openalex-snapshot

Complete Genome Sequences of Three Representative Mycobacterium tuberculosis Beijing Family Strains Belonging to Distinct Genotype Clusters in Hanoi, Vietnam, during 2007 to 2009

inferredcites →https://doi.org/10.1128/iai.69.6.4185-4191.2001openalex-snapshot

Antigens of Mycobacterium tuberculosis Expressed during Preclinical Tuberculosis: Serological Immunodominance of Proteins with Repetitive Amino Acid Sequences

inferredcites →https://doi.org/10.1128/jb.178.13.3791-3795.1996openalex-snapshot

Active efflux of fluoroquinolones in Mycobacterium smegmatis mediated by LfrA, a multidrug efflux pump

inferredcites →https://doi.org/10.1128/jcm.00200-13openalex-snapshot

Epidemic Spread of Multidrug-Resistant Tuberculosis in Johannesburg, South Africa

inferredcites →https://doi.org/10.1128/jcm.02483-16openalex-snapshot

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

inferredcites →https://doi.org/10.1136/thoraxjnl-2012-201663openalex-snapshot

MDR, XDR, TDR tuberculosis: ominous progression

inferredcites →https://doi.org/10.1155/2011/497203openalex-snapshot

Mycobacterial PE/PPE Proteins at the Host-Pathogen Interface

inferredcites →https://doi.org/10.1159/000329489openalex-snapshot

Transcriptional Regulation of Mycobacterium tuberculosis PE/PPE Genes: A Molecular Switch to Virulence

inferredcites →https://doi.org/10.1186/1471-2164-11-670openalex-snapshot

The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa

inferredcites →https://doi.org/10.1186/1471-2164-8-60openalex-snapshot

A phylogenomic analysis of the Actinomycetales mce operons

inferredcites →https://doi.org/10.1186/1756-0500-1-110openalex-snapshot

Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot

Versatile and open software for comparing large genomes

inferredcites →https://doi.org/10.1186/s12864-016-2467-yopenalex-snapshot

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

inferredcites →https://doi.org/10.1186/s13059-015-0849-0openalex-snapshot

Circlator: automated circularization of genome assemblies using long sequencing reads

inferredcites →https://doi.org/10.1371/journal.pmed.1001880openalex-snapshot

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

inferredcites →https://doi.org/10.1371/journal.pone.0117771openalex-snapshot

Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

inferredcites →https://doi.org/10.1371/journal.pone.0122979openalex-snapshot

Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

inferredcites →https://doi.org/10.1371/journal.pone.0131694openalex-snapshot

Genome Analysis of the First Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance

inferredcites →https://doi.org/10.1371/journal.pone.0149806openalex-snapshot

The Burden of Drug-Resistant Tuberculosis in Papua New Guinea: Results of a Large Population-Based Survey

inferredcites →https://doi.org/10.1371/journal.ppat.1001100openalex-snapshot

High Content Phenotypic Cell-Based Visual Screen Identifies Mycobacterium tuberculosis Acyltrehalose-Containing Glycolipids Involved in Phagosome Remodeling

inferredcites →https://doi.org/10.3390/ijms17091417openalex-snapshot

Bioinformatics Identification of Drug Resistance-Associated Gene Pairs in Mycobacterium tuberculosis

inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

inferredcites →https://doi.org/10.5588/ijtld.15.0389openalex-snapshot

Mechanisms of drug resistance in Mycobacterium tuberculosis: update 2015

inferredcites →https://doi.org/10.7554/elife.05166openalex-snapshot

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/434118openalex-snapshot

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

inferred← citeshttps://doi.org/10.1186/s12864-018-5381-7openalex-snapshot

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

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