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List of works by Jody Phelan

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages

scientific article published on 23 September 2019

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

scientific article published on 01 February 2021

An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome

scholarly article by Paula J Gomez-Gonzalez et al published 26 March 2019 in Scientific Reports

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

scientific article published on 19 May 2021

COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data

scientific article published on 15 April 2022

Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan

scientific article published on 09 July 2021

Clusters of Drug-Resistant Mycobacterium tuberculosis Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014-2017

scientific article published on 01 March 2021

Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world

scientific article published on 30 April 2020

Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing

scientific article published on 01 December 2020

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

scientific article published in Scientific Reports

Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus

scientific article published on 26 June 2021

Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

article

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

scientific article

Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

scientific article

Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole

scientific article published on 31 October 2017

Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis.

scientific article published on 2 May 2018

Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure.

scientific article

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

scientific article published on 24 June 2019

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally

scientific article published on 9 January 2018

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.

scientific article

Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines

scientific article published on 26 June 2019

Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study

scientific article

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

scientific article published on 26 February 2018

Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis

scientific article published on 08 February 2017

PrimedRPA: primer design for recombinase polymerase amplification assays

scholarly article by Matthew Higgins published in August 2018

Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia

scientific article

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

scientific article

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers

scientific article published on 21 December 2020

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

scientific article

The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

scientific article published on 4 June 2015

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

scientific article

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

scientific article published on 13 October 2016

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

scientific article published in Scientific Reports

Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan

scientific article published on 18 October 2019

Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil

scientific article published in PLoS ONE

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