Jody Phelan

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

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How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (2)

• PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.
  2022 L1 85/100
• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.
  2021 78/100

2 assessed by us (2 reproduced) · 204 not yet assessed — every PubMed paper on record, linked below.

• Diagnostic Discordance During MDR-TB Treatment: Retrospective Identification of Mycobacterium avium Complex-Associated Nontuberculous Mycobacterium by Whole-Genome Sequencing ↗

  Microorganisms · 2026 · PMID 42514100
  not yet assessed
• Genomic surveillance reveals co-occurrence of Plasmodium falciparum drug resistance variants across diverse transmission settings in Ethiopia ↗

  Nature Microbiology · 2026
  not yet assessed
• Rapid detection of antibiotic resistance in Burkholderia pseudomallei using MALDI-TOF mass spectrometry ↗

  Scientific Reports · 2025 · PMID 40594774
  not yet assessed
• Genome wide population genetics and molecular surveillance of insecticide resistance in Anopheles stephensi mosquitoes from Awash Sebat Kilo in Ethiopia ↗

  Scientific Reports · 2025 · PMID 40355632
  not yet assessed
• Comparative genomic insights into multidrug resistance in classical and hypervirulent K. pneumoniae clinical isolates ↗

  Scientific Reports · 2025 · PMID 41353259
  not yet assessed
• Dissemination of arr-2 and arr-3 is associated with class 1 integrons in Klebsiella pneumoniae clinical isolates from Portugal ↗

  Medical Microbiology and Immunology · 2025 · PMID 39775075
  not yet assessed
• Genome-wide analysis of genetic diversity in Anopheles darlingi from Rondônia State, Brazil ↗

  Communications Biology · 2025 · PMID 41345227
  not yet assessed
• Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil ↗

  Scientific Reports · 2025 · PMID 39753672
  not yet assessed
• Preferential transmission of minority and drug-resistant clones in polyclonal infections in Mali ↗

  Malaria Journal · 2025 · PMID 40188328
  not yet assessed
• Whole-genome sequencing analysis of Burkholderia pseudomallei comparing drug-resistant and pan-susceptible isolates reveals novel biomarkers for drug resistance ↗

  Infection Genetics and Evolution · 2025 · PMID 40480595
  not yet assessed
• The <i>ahpC</i> c−54t compensatory mutation is not always a valid surrogate for isoniazid resistance in <i>Mycobacterium tuberculosis</i> ↗

  Antimicrobial Agents and Chemotherapy · 2025 · PMID 40261011
  not yet assessed
• Genome-wide analysis and longitudinal study of Klebsiella pneumoniae in Portugal: Tracing the evolution and spread of carbapenem resistance ↗

  International Journal of Antimicrobial Agents · 2025 · PMID 40750043
  not yet assessed
• Genomic decoding of drug-resistant tuberculosis transmission in Thailand over three decades ↗

  Scientific Reports · 2025 · PMID 40796628
  not yet assessed
• Genomic insights into pyrazinamide and fluoroquinolone resistance in multidrug-resistant tuberculosis in Khyber Pakhtunkhwa, Pakistan ↗

  International Journal of Medical Microbiology · 2025 · PMID 40997731
  not yet assessed
• Enhancing whole genome DNA amplification of Plasmodium falciparum for advanced molecular surveillance in malaria control ↗

  Malaria Journal · 2025 · PMID 41419877
  not yet assessed
• All parts of the WHO <i>Mycobacterium tuberculosis</i> mutation catalog need to be applied when evaluating its performance ↗

  Microbiology Spectrum · 2025 · PMID 40172190
  not yet assessed
• Towards an open analysis ecosystem for <i>Plasmodium</i> genomic epidemiology ↗

  medRxiv · 2025 · PMID 40236429
  not yet assessed
• A novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• Genome-wide analyses of Mycobacterium tuberculosis complex isolates reveal insights into circulating lineages and drug resistance mutations in The Gambia ↗

  Research Square · 2025 · PMID 40060042
  not yet assessed
• Author Correction: An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates ↗

  Scientific Reports · 2025 · PMID 40185861
  not yet assessed
• Genomic analysis of Mycobacterium tuberculosis in Thailand reveals circulating lineage diversity, transmission, and drug resistance mutations ↗

  Research Square · 2025
  not yet assessed
• Complete and draft genome sequences of clinical <i>Mycobacterium tuberculosis</i> isolates from the Philippines ↗

  Microbiology Resource Announcements · 2025 · PMID 40492771
  not yet assessed
• Convergent Evolution of Artemisinin and Chloroquine Resistance in Ethiopian Plasmodium falciparum Parasites ↗

  2025
  not yet assessed
• PPE50 variants as novel phylogeographic signatures of host-pathogen co-evolution in tuberculosis ↗

  Communications Biology · 2025 · PMID 40634678
  not yet assessed
• Emerging Rifampicin Resistance in M. tuberculosis: First Report on Characterization of a Novel rpoB(Ser431Phe) Mutation and Phylogenetic Lineages in Khyber Pakhtunkhwa, Pakistan ↗

  Research Square · 2025
  not yet assessed
• Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children ↗

  Pathogens · 2025 · PMID 41156578
  not yet assessed
• A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections ↗

  UNC Libraries · 2025
  not yet assessed
• Corrigendum to ‘A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections’ ↗

  UNC Libraries · 2025
  not yet assessed
• A multi-stage machine learning framework for stepwise prediction of tuberculosis treatment outcomes: Integrating gradient boosted decision trees and feature-level analysis for clinical decision support ↗

  Research Square · 2025
  not yet assessed
• Expanding Tuberculosis Drug Resistance Prediction beyond binary: Deep Learning for Minimum Inhibitory Concentration prediction ↗

  Research Square · 2025
  not yet assessed
• TOAST: a novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies ↗

  BMC Genomics · 2025 · PMID 41257730
  not yet assessed
• Decoding Positive Selection in Mycobacterium tuberculosis with Phylogeny-Guided Graph Attention Models ↗

  arXiv (Cornell University) · 2025
  not yet assessed
• Newly Identified <i>Mycobacterium africanum</i> Lineage 10, Central Africa ↗

  Emerging infectious diseases · 2024 · PMID 38407162
  not yet assessed
• Leveraging large-scale Mycobacterium tuberculosis whole genome sequence data to characterise drug-resistant mutations using machine learning and statistical approaches ↗

  Scientific Reports · 2024 · PMID 39511309
  not yet assessed
• Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications ↗

  Scientific Reports · 2024 · PMID 38431684
  not yet assessed
• Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines ↗

  Scientific Reports · 2024 · PMID 39179783
  not yet assessed
• Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance ↗

  Scientific Reports · 2024 · PMID 38811658
  not yet assessed
• Genomic analysis of global Plasmodium vivax populations reveals insights into the evolution of drug resistance ↗

  Nature Communications · 2024 · PMID 39738010
  not yet assessed
• Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau ↗

  Parasites & Vectors · 2024 · PMID 39294791
  not yet assessed
• Long short-term memory-based deep learning model for the discovery of antimicrobial peptides targeting <i>Mycobacterium tuberculosis</i> ↗

  Bioinformatics Advances · 2024 · PMID 41230490
  not yet assessed
• Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance ↗

  Parasites & Vectors · 2024 · PMID 38178249
  not yet assessed
• New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri ↗

  Scientific Reports · 2024 · PMID 38360879
  not yet assessed
• Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network ↗

  Nucleic Acids Research · 2024 · PMID 38769067
  not yet assessed
• Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility ↗

  Nature Communications · 2024 · PMID 39738025
  not yet assessed
• Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes ↗

  Frontiers in Microbiology · 2024 · PMID 38312499
  not yet assessed
• Comparative genomics of Leishmania donovani progeny from genetic crosses in two sand fly species and impact on the diversity of diagnostic and vaccine candidates ↗

  PLoS neglected tropical diseases · 2024 · PMID 38295092
  not yet assessed
• An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates ↗

  Scientific Reports · 2024 · PMID 39433543
  not yet assessed
• TGV: suite of tools to visualize transmission graphs ↗

  NAR Genomics and Bioinformatics · 2024 · PMID 39660255
  not yet assessed
• Careful classification of potential bedaquiline resistance mutations is critical when analysing their clinical impact ↗

  The International Journal of Tuberculosis and Lung Disease · 2024 · PMID 38822482
  not yet assessed
• Acute and long-term outcomes of SARS-CoV-2 infection in school-aged children in England: Study protocol for the joint analysis of the COVID-19 schools infection survey (SIS) and the COVID-19 mapping and mitigation in schools (CoMMinS) study ↗

  PLoS ONE · 2024 · PMID 38776311
  not yet assessed
• hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Profiling insecticide resistance phenotypes and genotypes in Aedes aegypti populations across four regions in Puerto Rico ↗

  Research Square · 2024
  not yet assessed
• Genome-wide population genetics and molecular surveillance of insecticide resistance in Anopheles stephensi mosquitoes from Ethiopia ↗

  Research Square · 2024
  not yet assessed
• Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications ↗

  Research Square · 2024
  not yet assessed
• Profiling Insecticide Resistance Phenotypes and Genotypes in Aedes Aegypti Populations Across Four Regions in Puerto Rico ↗

  SSRN Electronic Journal · 2024
  not yet assessed
• Genome-wide association study of global Plasmodium vivax populations provides insights into the evolution of drug resistance ↗

  Research Square · 2024
  not yet assessed
• ResMAP—a saturation mutagenesis platform enabling parallel profiling of target-specific resistance-conferring mutations in <i>Plasmodium</i> ↗

  mBio · 2024 · PMID 39191404
  not yet assessed
• Whole genome analysis of Plasmodium malariae identifies reduced susceptibility to pyrimethamine, validated using ortholog replacement in P. knowlesi ↗

  Research Square · 2024
  not yet assessed
• Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease ↗

  Nature Communications · 2023 · PMID 36725857
  not yet assessed
• Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host ↗

  Frontiers in Microbiology · 2023 · PMID 37876785
  not yet assessed
• Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis ↗

  Scientific Reports · 2023 · PMID 36635309
  not yet assessed
• Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control ↗

  Genome Medicine · 2023 · PMID 37950308
  not yet assessed
• Genome dynamics of high-risk resistant and hypervirulent Klebsiella pneumoniae clones in Dhaka, Bangladesh ↗

  Frontiers in Microbiology · 2023 · PMID 37303793
  not yet assessed
• Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay ↗

  Scientific Reports · 2023 · PMID 37019918
  not yet assessed
• Detection of insecticide resistance markers in Anopheles funestus from the Democratic Republic of the Congo using a targeted amplicon sequencing panel ↗

  Scientific Reports · 2023 · PMID 37833354
  not yet assessed
• Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis ↗

  Scientific Reports · 2023 · PMID 37816829
  not yet assessed
• The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China ↗

  Microbiology Spectrum · 2023 · PMID 36912683
  not yet assessed
• Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites ↗

  Scientific Reports · 2023 · PMID 36792622
  not yet assessed
• Emergence of KPC-3- and OXA-181-producing ST13 and ST17 <i>Klebsiella pneumoniae</i> in Portugal: genomic insights on national and international dissemination ↗

  Journal of Antimicrobial Chemotherapy · 2023 · PMID 36999363
  not yet assessed
• Population dynamics and drug resistance mutations in Plasmodium falciparum on the Bijagós Archipelago, Guinea-Bissau ↗

  Scientific Reports · 2023 · PMID 37072433
  not yet assessed
• Genome-wide genetic variation and molecular surveillance of drug resistance in Plasmodium falciparum isolates from asymptomatic individuals in Ouélessébougou, Mali ↗

  Scientific Reports · 2023 · PMID 37308503
  not yet assessed
• Post-COVID-19 condition and persisting symptoms in English schoolchildren: repeated surveys to March 2022 ↗

  BMC Infectious Diseases · 2023 · PMID 37020190
  not yet assessed
• TB-ML—a framework for comparing machine learning approaches to predict drug resistance of<i>Mycobacterium tuberculosis</i> ↗

  Bioinformatics Advances · 2023 · PMID 37033466
  not yet assessed
• Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing ↗

  Scientific Reports · 2023 · PMID 37452073
  not yet assessed
• fastlin: an ultra-fast program for <i>Mycobacterium tuberculosis</i> complex lineage typing ↗

  Bioinformatics · 2023 · PMID 37871178
  not yet assessed
• Case report: A successfully treated case of community-acquired urinary tract infection due to Klebsiella aerogenes in Bangladesh ↗

  Frontiers in Medicine · 2023 · PMID 37435536
  not yet assessed
• Genomic and functional portrait of multidrug-resistant, hydrogen sulfide (H2S)-producing variants of Escherichia coli ↗

  Frontiers in Microbiology · 2023 · PMID 37577429
  not yet assessed
• High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing ↗

  Scientific Reports · 2023 · PMID 37495620
  not yet assessed
• Feature weighted models to address lineage dependency in drug-resistance prediction from <i>Mycobacterium tuberculosis</i> genome sequences ↗

  Bioinformatics · 2023 · PMID 37428143
  not yet assessed
• Bayesian compositional regression with microbiome features via variational inference ↗

  BMC Bioinformatics · 2023 · PMID 37217852
  not yet assessed
• Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data ↗

  Parasites & Vectors · 2023 · PMID 37543604
  not yet assessed
• Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay targeting vgsc, rdl, gste2 and ace1 loci ↗

  Research Square · 2023
  not yet assessed
• Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil ↗

  Research Square · 2023
  not yet assessed
• Second-line drug resistance markers as proxy indicators of time to sputum culture conversion among second-line drug resistant tuberculosis patients tested in Uganda: A cross-sectional study ↗

  F1000Research · 2023
  not yet assessed
• Bayesian compositional regression with microbiome features via variational inference ↗

  Research Square · 2023
  not yet assessed
• fastlin: an ultra-fast program for <i>Mycobacterium tuberculosis</i> complex lineage typing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study ↗

  Wellcome Open Research · 2023 · PMID 38638914
  not yet assessed
• Correction: TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis ↗

  PLoS ONE · 2023 · PMID 37847720
  not yet assessed
• School-level COVID-19 preventive measures and infection rates in England’s primary and secondary schools in the Autumn 2021: an ecological analysis ↗

  ISEE Conference Abstracts · 2023
  not yet assessed
• Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study

  Institutional Repositories DataBase (IRDB) · 2023
  not yet assessed
• TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis ↗

  PLoS ONE · 2022 · PMID 36584023
  not yet assessed
• Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance ↗

  Scientific Reports · 2022 · PMID 35963896
  not yet assessed
• Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes ↗

  Scientific Reports · 2022 · PMID 36587059
  not yet assessed
• A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis ↗

  BMC Genomics · 2022 · PMID 35016609
  not yet assessed
• High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors ↗

  Scientific Reports · 2022 · PMID 35974073
  not yet assessed
• Portable sequencing of <i>Mycobacterium tuberculosis</i> for clinical and epidemiological applications ↗

  Briefings in Bioinformatics · 2022 · PMID 35894606
  not yet assessed
• Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan ↗

  Scientific Reports · 2022 · PMID 35545649
  not yet assessed
• PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies

  Communications Biology · 2022 · PMID 35338232
  L1 85/100
• A phylogenomic approach for the analysis of colistin resistance-associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance ↗

  International Journal of Antimicrobial Agents · 2022 · PMID 35378228
  not yet assessed
• A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde ↗

  PLoS neglected tropical diseases · 2022 · PMID 36512510
  not yet assessed
• Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia ↗

  Microbial Genomics · 2022 · PMID 35302932
  not yet assessed
• Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones ↗

  Frontiers in Microbiology · 2022 · PMID 36406419
  not yet assessed
• Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year’s review ↗

  BMC Infectious Diseases · 2022 · PMID 35410160
  not yet assessed
• Intra-annual variation in feed and milk composition in smallholder dairy farms in Kenya ↗

  NJAS Impact in Agricultural and Life Sciences · 2022
  not yet assessed
• Geographical classification of malaria parasites through applying machine learning to whole genome sequence data ↗

  Scientific Reports · 2022 · PMID 36476815
  not yet assessed
• Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020–2021 ↗

  The Lancet Regional Health - Europe · 2022 · PMID 36035630
  not yet assessed
• Genetic mutations underlying isoniazid-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan ↗

  Tuberculosis · 2022 · PMID 36463715
  not yet assessed
• Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016 ↗

  Tuberculosis · 2022 · PMID 35636102
  not yet assessed
• COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data ↗

  BMC Bioinformatics · 2022 · PMID 35428185
  not yet assessed
• Bayesian Compositional Regression with Microbiome Features via Variational Inference ↗

  Research Square · 2022
  not yet assessed
• Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes ↗

  Research Square · 2022
  not yet assessed
• Towards environmental detection, quantification, and molecular characterization of <i>Anopheles stephensi</i> and <i>Aedes aegypti</i> from larval breeding sites ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

  Genome Medicine · 2021 · PMID 34461978
  78/100
• Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa ↗

  Nature Communications · 2021 · PMID 34039976
  not yet assessed
• Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid ↗

  Scientific Reports · 2021 · PMID 34593898
  not yet assessed
• An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities ↗

  Scientific Reports · 2021 · PMID 34012005
  not yet assessed
• Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan ↗

  Scientific Reports · 2021 · PMID 34244539
  not yet assessed
• An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets ↗

  Genome Medicine · 2021 · PMID 33413610
  not yet assessed
• Using deep learning to identify recent positive selection in malaria parasite sequence data ↗

  Malaria Journal · 2021 · PMID 34126997
  not yet assessed
• A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling ↗

  Cell Reports · 2021 · PMID 33535039
  not yet assessed
• Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes ↗

  Microbial Genomics · 2021 · PMID 34889724
  not yet assessed
• Clusters of Drug-Resistant <i>Mycobacterium tuberculosis</i> Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014–2017 ↗

  Emerging infectious diseases · 2021 · PMID 33622486
  not yet assessed
• Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals ↗

  Scientific Reports · 2021 · PMID 33753763
  not yet assessed
• Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus ↗

  Parasites & Vectors · 2021 · PMID 34174947
  not yet assessed
• Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages ↗

  Frontiers in Molecular Biosciences · 2021 · PMID 34422898
  not yet assessed
• Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates ↗

  Tuberculosis · 2021 · PMID 34673379
  not yet assessed
• An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. ↗

  Apollo (University of Cambridge) · 2021
  not yet assessed
• Corrigendum to ‘A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections’ ↗

  EBioMedicine · 2021 · PMID 33639399
  not yet assessed
• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Author Correction: Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan ↗

  Scientific Reports · 2021 · PMID 34282262
  not yet assessed
• Evolutionary trajectories and transmission dynamics of multidrug-resistant <i>Mycobacterium tuberculosis</i> in Tibet, China ↗

  medRxiv · 2021
  not yet assessed
• Additional file 1 of GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning ↗

  London School of Hygiene & Tropical Medicine · 2021
  not yet assessed
• Evolutionary Trajectories and Transmission Dynamics of Multidrug-Resistant &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; in Tibet, China ↗

  SSRN Electronic Journal · 2021
  not yet assessed
• Additional file 4 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus ↗

  Figshare · 2021
  not yet assessed
• Additional file 5 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus ↗

  Figshare · 2021
  not yet assessed
• Additional file 1 of GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning ↗

  Figshare · 2021
  not yet assessed
• Additional file 7 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus ↗

  Figshare · 2021
  not yet assessed
• Additional file 3 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus ↗

  Figshare · 2021
  not yet assessed
• Additional file 6 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus ↗

  Figshare · 2021
  not yet assessed
• Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies ↗

  Genome Medicine · 2020 · PMID 33317631
  not yet assessed
• Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study ↗

  Microbial Genomics · 2020 · PMID 32048983
  not yet assessed
• A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections ↗

  EBioMedicine · 2020 · PMID 32403083
  not yet assessed
• Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania ↗

  BMC Genomics · 2020 · PMID 32085703
  not yet assessed
• A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria ↗

  PLoS Genetics · 2020 · PMID 32053607
  not yet assessed
• Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants ↗

  BMJ Nutrition Prevention & Health · 2020 · PMID 33521535
  not yet assessed
• Combining structure and genomics to understand antimicrobial resistance ↗

  Computational and Structural Biotechnology Journal · 2020 · PMID 33294134
  not yet assessed
• Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain ↗

  Microorganisms · 2020 · PMID 33322205
  not yet assessed
• Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital ↗

  Microbial Genomics · 2020 · PMID 32234124
  not yet assessed
• Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers ↗

  PLoS Computational Biology · 2020 · PMID 33347430
  not yet assessed
• Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto <b>-</b> Beijing genotype ↗

  Emerging Microbes & Infections · 2020 · PMID 33205698
  not yet assessed
• Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal ↗

  Scientific Reports · 2020 · PMID 32054988
  not yet assessed
• Emergence of multidrug-resistant <i>Mycobacterium tuberculosis</i> of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing ↗

  Emerging Microbes & Infections · 2020 · PMID 32538300
  not yet assessed
• A potential antigenic mimicry between viral and human proteins linking Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) with autoimmunity: The case of HPV immunization ↗

  Autoimmunity Reviews · 2020 · PMID 32062027
  not yet assessed
• Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• A Novel Multiplex qPCR Assay for Detection of <i>Plasmodium falciparum</i> with <i>Histidine-rich Protein 2 and 3 (pfhrp2 and pfhrp3)</i> Deletions in Polyclonal Infections ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• An integrated <i>in silico</i> immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Genomic diversity and antimicrobial resistance among non-typhoidal <i>Salmonella</i> associated with human disease in The Gambia ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto<b>-</b>Beijing genotype ↗

  Figshare · 2020
  not yet assessed
• Ribosome profiling in <i>Mycobacterium tuberculosis</i> reveals robust leaderless translation ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs ↗

  Genome Medicine · 2019 · PMID 31234910
  not yet assessed
• Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data ↗

  Frontiers in Genetics · 2019 · PMID 31616478
  not yet assessed
• A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages ↗

  Scientific Reports · 2019 · PMID 31548561
  not yet assessed
• Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance ↗

  BMC Genomics · 2019 · PMID 30922221
  not yet assessed
• Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines ↗

  Scientific Reports · 2019 · PMID 31243306
  not yet assessed
• Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan ↗

  Scientific Reports · 2019 · PMID 31628383
  not yet assessed
• An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome ↗

  Scientific Reports · 2019 · PMID 30914757
  not yet assessed
• Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335,046 UK Biobank participants ↗

  medRxiv · 2019
  not yet assessed
• Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs ↗

  London School of Hygiene & Tropical Medicine · 2019
  not yet assessed
• Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs ↗

  Figshare · 2019
  not yet assessed
• Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis ↗

  Nature Genetics · 2018 · PMID 29358649
  not yet assessed
• Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data ↗

  BMC Genomics · 2018 · PMID 30107785
  not yet assessed
• PrimedRPA: primer design for recombinase polymerase amplification assays ↗

  Bioinformatics · 2018 · PMID 30101342
  not yet assessed
• Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis ↗

  Scientific Reports · 2018 · PMID 30337649
  not yet assessed
• Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis ↗

  Infection Genetics and Evolution · 2018 · PMID 29729386
  not yet assessed
• 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 ↗

  PLoS ONE · 2018 · PMID 30110370
  not yet assessed
• Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates ↗

  Scientific Reports · 2018 · PMID 30072734
  not yet assessed
• Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally ↗

  Scientific Reports · 2018 · PMID 29317751
  not yet assessed
• Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure ↗

  PLoS neglected tropical diseases · 2018 · PMID 29902183
  not yet assessed
• Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity ↗

  Genome Medicine · 2018 · PMID 29482619
  not yet assessed
• Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis ↗

  Nature Genetics · 2018 · PMID 29674744
  not yet assessed
• A bioinformatic analysis of Mycobacterium tuberculosis and host genomic data ↗

  LSHTM Research Online (London School of Hygiene and Tropical Medicine) · 2018
  not yet assessed
• Does genetic risk of obesity modify associations between the neighbourhood environment and body-mass index? A cross-sectional analysis of the UK Biobank dataset ↗

  The Lancet · 2018
  not yet assessed
• A 15-YEAR SPATIOTEMPORAL ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS LINEAGES 1 AND 2 IN CHIANG RAI, THAILAND ↗

  Russian Journal of Infection and Immunity · 2018
  not yet assessed
• Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data ↗

  London School of Hygiene & Tropical Medicine · 2018
  not yet assessed
• Additional file 1: of Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity ↗

  Figshare · 2018
  not yet assessed
• Evaluation of the performance of MinION sequencing to identify multi- and extensively drug resistant tuberculosis

  2018
  not yet assessed
• Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data ↗

  Figshare · 2018
  not yet assessed
• Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study ↗

  The Lancet Respiratory Medicine · 2017 · PMID 28109869
  not yet assessed
• Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis ↗

  Scientific Reports · 2017 · PMID 28176867
  not yet assessed
• Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax ↗

  PLoS neglected tropical diseases · 2017 · PMID 28759591
  not yet assessed
• Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole ↗

  Scientific Reports · 2017 · PMID 29089615
  not yet assessed
• Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan ↗

  Tuberculosis · 2017 · PMID 29050768
  not yet assessed
• Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia ↗

  BMC Infectious Diseases · 2017 · PMID 28697808
  not yet assessed
• Population-based analysis of ocular <i>Chlamydia trachomatis</i> in trachoma-endemic West African communities identifies genomic markers of disease severity ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance ↗

  BMC Medicine · 2016 · PMID 27005572
  not yet assessed
• Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages ↗

  BMC Genomics · 2016 · PMID 26923687
  not yet assessed
• The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs ↗

  Genome Medicine · 2016 · PMID 28003022
  not yet assessed
• Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor ↗

  Infection Genetics and Evolution · 2016 · PMID 27746295
  not yet assessed
• Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance ↗

  King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · 2016
  not yet assessed
• Additional file 1: Table S1. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance ↗

  INDIGO (University of Illinois at Chicago) · 2016
  not yet assessed
• Additional file 2: Figure S1. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance ↗

  Figshare · 2016
  not yet assessed
• Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages ↗

  King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · 2016
  not yet assessed
• The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae ↗

  International Journal of Mycobacteriology · 2015 · PMID 27649868
  not yet assessed
• Whole genome sequences for M.tuberculosis isolates from the TDR strain bank

  London School of Hygiene & Tropical Medicine · 2015
  not yet assessed
• Quantifying badger exposure and the risk of bovine tuberculosis for cattle herds in county Kilkenny, Ireland ↗

  Preventive Veterinary Medicine · 2006 · PMID 16488029
  not yet assessed