Maha Farhat
Reproducibility track record
1
assessed papers
78/100
mean reproducibility
1
reproduced (C1–C2)
0
flagged
0
total citations
flag rate:
0%
(0/1)
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.
Authorship role
first author: 0
last author: 1
Topics
—
Funders
—
Frequent co-authors
Martin Owens 1Matthias I. Gröschel 1Avika Dixit 1Roger Vargas 1Jody Phelan 1Luca Freschi 1Zamin Iqbal 1Maximilian G. Marin 1
Institutions
Harvard University 1Center for Systems Biology 1London School of Hygiene & Tropical Medicine 1European Bioinformatics Institute 1Boston Children's Hospital 1Massachusetts General Hospital 1
Geography (author institutions)
US 1GB 1
Co-author network
Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.
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 (1)
Complete publication record (190)
Request a reproduction →1 assessed by us (1 reproduced) · 189 not yet assessed — every PubMed paper on record, linked below.
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Tuberculosis Disease Severity Assessment Using Clinical Variables and Radiology Enabled by Artificial Intelligence ↗The Journal of Infectious Diseases · 2026 · PMID 41989328not yet assessed
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Convolutional neural networks quantify antibiotic resistance in Mycobacterium tuberculosis with diagnostic grade accuracy and predict treatment response ↗Nature Communications · 2026 · PMID 42031767not yet assessed
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Within-host pathogen population diversity predicts treatment response in Tuberculosis ↗medRxiv · 2026 · PMID 42369478not yet assessed
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Improving Generalizability in Whole-Cell Antibiotic Discovery Through Active Learning ↗bioRxiv (Cold Spring Harbor Laboratory) · 2026 · PMID 42427732not yet assessed
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Pitfalls of bacterial pan-genome analysis approaches: a case study of <i>Mycobacterium tuberculosis</i> and two less clonal bacterial species ↗Bioinformatics · 2025 · PMID 40341387not yet assessed
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Frequently arising ESX-1-associated phase variants influence <i>Mycobacterium tuberculosis</i> fitness in the presence of host and antibiotic pressures ↗mBio · 2025 · PMID 39873486not yet assessed
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Multivariable regression models improve accuracy and sensitive grading of antibiotic resistance mutations in Mycobacterium tuberculosis ↗Nature Communications · 2025 · PMID 40032816not yet assessed
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Complete genome sequence of a virulent barcoded <i>Mycobacterium tuberculosis</i> str. Erdman commonly used for non-human primate infection studies ↗Microbiology Resource Announcements · 2025 · PMID 39964179not yet assessed
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Patient Determinants and Effects on Adherence of Adverse Drug Reactions to Tuberculosis Treatment: A Prospective Cohort Analysis ↗Clinical Infectious Diseases · 2025 · PMID 39973802not yet assessed
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Contamination rates in serially sampled sputum specimens obtained during tuberculosis treatment to capture culture conversion ↗Microbiology Spectrum · 2025 · PMID 40879468not yet assessed
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Future-proofing tuberculosis therapy: framework for concurrent drug and resistance testing development ↗The Lancet Infectious Diseases · 2025 · PMID 42223242not yet assessed
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The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference ↗eLife · 2025not yet assessed
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not yet assessed
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Fleming: An AI Agent for Antibiotic Design for Mycobacterium tuberculosis ↗bioRxiv (Cold Spring Harbor Laboratory) · 2025not yet assessed
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The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference ↗eLife · 2025not yet assessed
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Contamination rates in serially sampled sputum specimens obtained during tuberculosis treatment to capture culture conversion ↗medRxiv · 2025 · PMID 40196277not yet assessed
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The structural context of mutations in proteins predicts their effect on antibiotic resistance ↗eLife · 2025not yet assessed
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Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models ↗bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 39896621not yet assessed
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Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry ↗Pneumologie · 2025not yet assessed
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Genome‐Wide Association Study Identifies a Locus at 17p13 to Be Associated With Intestinal Malrotation ↗World Journal of Surgery · 2025 · PMID 40200404not yet assessed
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not yet assessed
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The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference ↗eLife · 2025not yet assessed
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not yet assessed
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Awareness of management of pulmonary multidrug-resistant tuberculosis (MDR-TB) among private practitioners in suburban areas of Pune city, India: Input for developing an educational tool ↗PLOS Global Public Health · 2025 · PMID 40961043not yet assessed
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The structural context of mutations in proteins predicts their effect on antibiotic resistance ↗bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 41040149not yet assessed
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Tuberculosis Disease Prevalence Among People Who Smoke Illicit Drugs: A Respondent- Driven Sampling Study in the Western Cape, South Africa ↗The Journal of Infectious Diseases · 2025 · PMID 41060285not yet assessed
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Insights into the Role of Rifampicin Exposure and Clinical Baseline Covariates on the Response to Pulmonary Tuberculosis Treatment ↗Clinical Infectious Diseases · 2025 · PMID 41133922not yet assessed
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An Integrated Data-Driven Model for Clinical Phenotyping of Tuberculosis Disease Severity ↗medRxiv · 2025 · PMID 41358303not yet assessed
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The structural context of mutations in proteins predicts their effect on antibiotic resistance ↗eLife · 2025not yet assessed
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Drug-resistant tuberculosis: a persistent global health concern ↗Nature Reviews Microbiology · 2024 · PMID 38519618not yet assessed
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Implications of Race Adjustment in Lung-Function Equations ↗New England Journal of Medicine · 2024 · PMID 38767252not yet assessed
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Evaluating generalizability of artificial intelligence models for molecular datasets ↗Nature Machine Intelligence · 2024not yet assessed
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Exploring gene content with pangene graphs ↗Bioinformatics · 2024 · PMID 39041615not yet assessed
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Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains ↗The Lancet Microbe · 2024 · PMID 38734030not yet assessed
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Transcriptomic responses to antibiotic exposure in <i>Mycobacterium tuberculosis</i> ↗Antimicrobial Agents and Chemotherapy · 2024 · PMID 38587412not yet assessed
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A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for<i>Mycobacterium tuberculosis</i>complex ↗European Respiratory Journal · 2024 · PMID 38991722not yet assessed
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Precision phenotyping for curating research cohorts of patients with unexplained post-acute sequelae of COVID-19 ↗Med · 2024 · PMID 39520983not yet assessed
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Differential rates of Mycobacterium tuberculosis transmission associate with host–pathogen sympatry ↗Nature Microbiology · 2024 · PMID 39090390not yet assessed
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MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis ↗The Lancet Microbe · 2024 · PMID 38851206not yet assessed
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Beyond diagnostic connectivity: Leveraging digital health technology for the real-time collection and provision of high-quality actionable data on infectious diseases in Uganda ↗PLOS Digital Health · 2024 · PMID 39178177not yet assessed
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Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning ↗BMJ Global Health · 2024 · PMID 38548342not yet assessed
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Drug Resistance and Epidemiological Success of Modern <i>Mycobacterium tuberculosis</i> Lineages in Western India ↗The Journal of Infectious Diseases · 2024 · PMID 38819323not yet assessed
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For Tuberculosis, Not “To Screen or Not to Screen?” but “Who?” and “How?” ↗Clinical Infectious Diseases · 2024 · PMID 38636953not yet assessed
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A Genome-Wide Association Study Reveals a Novel Susceptibility Locus for Pancreas Divisum at 3q29 ↗Journal of Surgical Research · 2024 · PMID 39393116not yet assessed
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Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets ↗Microbiology Spectrum · 2024 · PMID 38874407not yet assessed
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Biosensors application for SARS-CoV-2 detection ↗Medical Research Archives · 2024not yet assessed
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Analysis of the limited <i>M. tuberculosis</i> accessory genome reveals potential pitfalls of pan-genome analysis approaches ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 38585972not yet assessed
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Evaluating generalizability of artificial intelligence models for molecular datasets ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 38464295not yet assessed
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The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference ↗eLife · 2024not yet assessed
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Systematic review and meta-analysis of protocols and yield of direct from sputum sequencing of <i>Mycobacterium tuberculosis</i> ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 39677639not yet assessed
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Regression for accurate and sensitive grading of mutations diagnostic of antibiotic resistance in <i>Mycobacterium tuberculosis</i> ↗medRxiv · 2024not yet assessed
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The <i>Mycobacterium tuberculosis</i> complex pangenome is small and shaped by sub-lineage-specific regions of difference ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024not yet assessed
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Precision Phenotyping for Curating Research Cohorts of Patients with Post-Acute Sequelae of COVID-19 (PASC) as a Diagnosis of Exclusion ↗medRxiv · 2024 · PMID 38699316not yet assessed
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Erratum for Poonawala et al., “Transcriptomic responses to antibiotic exposure in <i>Mycobacterium tuberculosis</i> ” ↗Antimicrobial Agents and Chemotherapy · 2024 · PMID 39297642not yet assessed
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Exploring gene content with pangene graphs ↗PubMed · 2024 · PMID 38463499not yet assessed
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not yet assessed
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not yet assessed
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not yet assessed
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Tuberculosis Disease Prevalence Among People Who Smoke Illicit Drugs: A Respondent-Driven Sampling Study in the Western Cape, South Africa ↗SSRN Electronic Journal · 2024not yet assessed
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Tuberculosis disease severity assessment using clinical variables and radiology enabled by artificial intelligence ↗medRxiv · 2024 · PMID 39228708not yet assessed
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Multimodal learning with graphs ↗Nature Machine Intelligence · 2023 · PMID 38076673not yet assessed
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COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation ↗Critical Care · 2023 · PMID 36691080not yet assessed
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Phase variation as a major mechanism of adaptation in <i>Mycobacterium tuberculosis</i> complex ↗Proceedings of the National Academy of Sciences · 2023 · PMID 37399390not yet assessed
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Rethinking global digital health and AI-for-health innovation challenges ↗PLOS Global Public Health · 2023 · PMID 37115743not yet assessed
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Genotype–Phenotype Characterization of Serial <i>Mycobacterium tuberculosis</i> Isolates in Bedaquiline-Resistant Tuberculosis ↗Clinical Infectious Diseases · 2023 · PMID 37874928not yet assessed
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Smoked drug use in patients with TB is associated with higher bacterial burden ↗The International Journal of Tuberculosis and Lung Disease · 2023 · PMID 37231597not yet assessed
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Mutation rates and adaptive variation among the clinically dominant clusters of <i>Mycobacterium abscessus</i> ↗Proceedings of the National Academy of Sciences · 2023 · PMID 37216535not yet assessed
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Analysis of Genome-Wide Mutational Dependence in Naturally Evolving <i>Mycobacterium tuberculosis</i> Populations ↗Molecular Biology and Evolution · 2023 · PMID 37352142not yet assessed
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Assessment and validation of enrichment and target capture approaches to improve <i>Mycobacterium tuberculosis</i> WGS from direct patient samples ↗Journal of Clinical Microbiology · 2023 · PMID 37728909not yet assessed
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Addressing patients’ unmet needs related to multidrug-resistant tuberculosis (MDR-TB) care: A qualitative research study from Pune city, India ↗PLoS ONE · 2023 · PMID 38153918not yet assessed
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HEALTH SYSTEM RELATED BARRIERS TO MULTIDRUG-RESISTANT TUBERCULOSIS (MDR-TB) CARE IN AN INDIAN SETTING: FROM PATIENTS’ PERSPECTIVE ↗International Journal of Infectious Diseases · 2023not yet assessed
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Genomic approaches to tuberculosis management and control ↗European Respiratory Society eBooks · 2023not yet assessed
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Assessment and validation of enrichment and target capture approaches to improve <i>Mycobacterium tuberculosis</i> WGS from direct patient samples ↗bioRxiv (Cold Spring Harbor Laboratory) · 2023not yet assessed
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High-throughput phenogenotyping <i>of Mycobacteria tuberculosis</i> clinical strains reveals bacterial determinants of treatment outcomes ↗bioRxiv (Cold Spring Harbor Laboratory) · 2023 · PMID 37090677not yet assessed
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not yet assessed
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Single nucleotide variation catalogue from clinical isolates mapped on tertiary and quaternary structures of ESX-1 related proteins reveals critical regions as putative Mtb therapeutic targets ↗bioRxiv (Cold Spring Harbor Laboratory) · 2023not yet assessed
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Is Ignorance Bliss? The Role of Post Hoc Explanation Faithfulness and Alignment in Model Trust in Laypeople and Domain Experts ↗arXiv (Cornell University) · 2023not yet assessed
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The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis ↗The Lancet Microbe · 2022 · PMID 35373160not yet assessed
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A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis ↗Nature Communications · 2022 · PMID 35780211not yet assessed
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Benchmarking the empirical accuracy of short-read sequencing across the<i>M. tuberculosis</i>genome ↗Bioinformatics · 2022 · PMID 35020793not yet assessed
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Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment ↗European Respiratory Journal · 2022 · PMID 35422426not yet assessed
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High Throughput Sequencing for Clinical Tuberculosis: An Overview ↗Pathogens · 2022 · PMID 36422596not yet assessed
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Optimizing DNA Extraction from Pediatric Stool for Diagnosis of Tuberculosis and Use in Next-Generation Sequencing Applications ↗Microbiology Spectrum · 2022 · PMID 36475757not yet assessed
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Whole Genome Sequencing Assessing Impact of Diabetes Mellitus on Tuberculosis Mutations and Type of Recurrence in India ↗Clinical Infectious Diseases · 2022 · PMID 34984435not yet assessed
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Management of childhood MDR-TB in Europe and Central Asia: report of a Regional WHO meeting ↗The International Journal of Tuberculosis and Lung Disease · 2022 · PMID 35505487not yet assessed
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COVID-19 and global childhood tuberculosis notifications ↗The Lancet Global Health · 2022 · PMID 36400072not yet assessed
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Repeated evolution of bedaquiline resistance in <i>Mycobacterium tuberculosis</i> is driven by truncation of <i>mmpR5</i> ↗bioRxiv (Cold Spring Harbor Laboratory) · 2022not yet assessed
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Phase variation as a major mechanism of adaptation in <i>Mycobacterium tuberculosis</i> complex ↗bioRxiv (Cold Spring Harbor Laboratory) · 2022not yet assessed
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Host-pathogen sympatry and differential transmissibility of <i>Mycobacterium tuberculosis complex</i> ↗medRxiv · 2022not yet assessed
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not yet assessed
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Mutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus ↗Research Square · 2022not yet assessed
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Self-Supervised Pretraining Enables High-Performance Chest X-Ray Interpretation Across Clinical Distributions ↗medRxiv · 2022not yet assessed
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Mutation rates and adaptive variation among the clinically dominant clusters of <i>Mycobacterium abscessus</i> ↗bioRxiv (Cold Spring Harbor Laboratory) · 2022not yet assessed
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Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations ↗medRxiv · 2022 · PMID 36032980not yet assessed
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Multimodal learning with graphs ↗arXiv (Cornell University) · 2022not yet assessed
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The discovery of genome-wide mutational dependence in naturally evolving populations ↗bioRxiv (Cold Spring Harbor Laboratory) · 2022not yet assessed
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Population structure, biogeography and transmissibility of Mycobacterium tuberculosis ↗Nature Communications · 2021 · PMID 34671035not yet assessed
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Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistanceDIGITAL.CSIC (Spanish National Research Council (CSIC)) · 2021not yet assessed
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GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learningGenome Medicine · 2021 · PMID 3446197878/100
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Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex ↗Antimicrobial Agents and Chemotherapy · 2021 · PMID 34460306not yet assessed
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In-host population dynamics of Mycobacterium tuberculosis complex during active disease ↗eLife · 2021 · PMID 33522489not yet assessed
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Measuring health-care delays among privately insured patients with tuberculosis in the USA: an observational cohort study ↗The Lancet Infectious Diseases · 2021 · PMID 33770534not yet assessed
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Globally diverse Mycobacterium tuberculosis resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences ↗The Lancet Microbe · 2021 · PMID 33912853not yet assessed
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Multisystem outcomes and predictors of mortality in critically ill patients with COVID-19: Demographics and disease acuity matter more than comorbidities or treatment modalities ↗The Journal of Trauma: Injury, Infection, and Critical Care · 2021 · PMID 33891572not yet assessed
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Tuberculosis Pathways to Care and Transmission of Multidrug Resistance in India ↗American Journal of Respiratory and Critical Care Medicine · 2021 · PMID 34706203not yet assessed
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Association Between <i>NEDD4L</i> Variation and the Genetic Risk of Acute Appendicitis ↗JAMA Surgery · 2021 · PMID 34319380not yet assessed
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Fecal microbiota transplantation and Clostridioides difficile infection among privately insured patients in the United States ↗Journal of Gastroenterology · 2021 · PMID 34495400not yet assessed
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1397. Modern Lineages of <i>Mycobacterium tuberculosis</i> Were Recently Introduced in Western India and Demonstrate Increased Transmissibility ↗Open Forum Infectious Diseases · 2021not yet assessed
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Advancing TB research using digitized programmatic data ↗The International Journal of Tuberculosis and Lung Disease · 2021 · PMID 34686230not yet assessed
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GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning ↗bioRxiv (Cold Spring Harbor Laboratory) · 2021not yet assessed
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Genomic sequence characteristics and the empiric accuracy of short-read sequencing ↗bioRxiv (Cold Spring Harbor Laboratory) · 2021not yet assessed
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The role of epistasis in amikacin, kanamycin, bedaquiline, and clofazimine resistance in <i>Mycobacterium tuberculosis</i> complex ↗bioRxiv (Cold Spring Harbor Laboratory) · 2021not yet assessed
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The 2021 WHO Catalogue of <i>Mycobacterium Tuberculosis</i> Complex Mutations Associated with Drug Resistance: A New Global Standard for Molecular Diagnostics ↗SSRN Electronic Journal · 2021not yet assessed
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not yet assessed
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A convolutional neural network highlights mutations relevant to antimicrobial resistance in <i>Mycobacterium tuberculosis</i> ↗bioRxiv (Cold Spring Harbor Laboratory) · 2021not yet assessed
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A legacy of disease ↗The Lancet Infectious Diseases · 2021not yet assessed
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Additional file 1 of GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning ↗London School of Hygiene & Tropical Medicine · 2021not yet assessed
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Additional file 1 of GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning ↗Figshare · 2021not yet assessed
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Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events ↗Science · 2020 · PMID 33303686not yet assessed
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Systematic review of mutations associated with resistance to the new and repurposed<i>Mycobacterium tuberculosis</i>drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid ↗Journal of Antimicrobial Chemotherapy · 2020 · PMID 32361756not yet assessed
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The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia ↗Nature Communications · 2020 · PMID 32341346not yet assessed
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Gastrointestinal Complications in Critically Ill Patients With and Without COVID-19 ↗JAMA · 2020 · PMID 32970139not yet assessed
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GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes ↗Molecular Biology and Evolution · 2020 · PMID 32167543not yet assessed
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Bacterial and fungal microbiome characterization in patients with rosacea and healthy controls ↗British Journal of Dermatology · 2020 · PMID 32533846not yet assessed
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Antibiotic treatment and selection for <i>glpK</i> mutations in patients with active tuberculosis disease ↗Proceedings of the National Academy of Sciences · 2020 · PMID 32075922not yet assessed
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Identification of a new genetic variant associated with cholecystitis: A multicenter genome-wide association study ↗The Journal of Trauma: Injury, Infection, and Critical Care · 2020 · PMID 32118827not yet assessed
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Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events ↗medRxiv · 2020 · PMID 32869040not yet assessed
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Population structure, biogeography and transmissibility of <i>Mycobacterium tuberculosis</i> ↗bioRxiv (Cold Spring Harbor Laboratory) · 2020not yet assessed
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not yet assessed
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Measuring and Understanding Delays in Multidrug-Resistant Tuberculosis Care in India ↗SSRN Electronic Journal · 2020not yet assessed
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not yet assessed
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not yet assessed
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not yet assessed
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Multi-Organ System Outcomes and Predictors of Mortality in Critically Ill Patients with COVID-19 ↗SSRN Electronic Journal · 2020not yet assessed
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Mentorship at a distance ↗Science · 2020 · PMID 33093113not yet assessed
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Surgical Resection Compared to Medical Management in localized Mycobacteria Avium Complex Pulmonary Infections-A Case Control Study ↗Research Square · 2020not yet assessed
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1653. Estimation of country-specific tuberculosis antibiograms using a wide and deep neural net on a large genomic dataset ↗Open Forum Infectious Diseases · 2020not yet assessed
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues ↗Nature Reviews Microbiology · 2019 · PMID 31209399not yet assessed
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Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe ↗Wellcome Open Research · 2019 · PMID 32055708not yet assessed
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GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions ↗Nature Communications · 2019 · PMID 31086182not yet assessed
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Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction ↗EBioMedicine · 2019 · PMID 31047860not yet assessed
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DeepAMR for predicting co-occurrent resistance of <i>Mycobacterium tuberculosis</i> ↗Bioinformatics · 2019 · PMID 30689732not yet assessed
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Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates ↗Journal of Antimicrobial Chemotherapy · 2019 · PMID 30793747not yet assessed
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Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting ↗Scientific Reports · 2019 · PMID 30944370not yet assessed
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In-host population dynamics of <i>M. tuberculosis</i> during treatment failure ↗bioRxiv (Cold Spring Harbor Laboratory) · 2019not yet assessed
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The global phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist <i>Stenotrophomonas maltophilia</i> ↗bioRxiv (Cold Spring Harbor Laboratory) · 2019not yet assessed
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Tuberculosis resistance acquisition in space and time: an analysis of globally diverse <i>M. tuberculosis</i> whole genome sequences ↗bioRxiv (Cold Spring Harbor Laboratory) · 2019not yet assessed
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phenotype_NNvalid.tab ↗Harvard Dataverse · 2019not yet assessed
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Replication Data for: Input Mycobacterium tuberculosis data for Resistance Deep Learning Model ↗Harvard Dataverse · 2019not yet assessed
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genotype_NNvalid.tab ↗Harvard Dataverse · 2019not yet assessed
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pheno_merged.tab ↗Harvard Dataverse · 2019not yet assessed
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Input Mycobacterium tuberculosis data for Resistance Deep Learning Model ↗Harvard Dataverse · 2019not yet assessed
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geno_merged.tab ↗Harvard Dataverse · 2019not yet assessed
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Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings ↗Nature Microbiology · 2018 · PMID 30510172not yet assessed
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Discovery of a unique Mycobacterium tuberculosis protein through proteomic analysis of urine from patients with active tuberculosis ↗Microbes and Infection · 2018 · PMID 29306028not yet assessed
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Deep learning predicts tuberculosis drug resistance status from genome sequencing data ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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Genome wide association with quantitative resistance phenotypes in <i>Mycobacterium tuberculosis</i> reveals novel resistance genes and regulatory regions ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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Genome-wide discovery of epistatic loci affecting antibiotic resistance using evolutionary couplings ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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Rifampicin and rifabutin resistance in 1000 <i>Mycobacterium tuberculosis</i> clinical isolates ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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Genotypic clustering does not imply recent tuberculosis transmission in a high prevalence setting: A genomic epidemiology study in Lima, Peru ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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Genotypic Clustering Does Not Imply Recent Tuberculosis Transmission in a High Prevalence Setting: A Genomic Epidemiology Study in Lima, Peru ↗SSRN Electronic Journal · 2018not yet assessed
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Transmissible <i>Mycobacterium tuberculosis</i> Strains Share Genetic Markers and Immune Phenotypes ↗American Journal of Respiratory and Critical Care Medicine · 2017 · PMID 27997216not yet assessed
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Fluoroquinolone Resistance Mutation Detection Is Equivalent to Culture-Based Drug Sensitivity Testing for Predicting Multidrug-Resistant Tuberculosis Treatment Outcome: A Retrospective Cohort Study ↗Clinical Infectious Diseases · 2017 · PMID 29017248not yet assessed
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Genetic Determinants of Drug Resistance in <i>Mycobacterium tuberculosis</i> and Their Diagnostic Value ↗American Journal of Respiratory and Critical Care Medicine · 2016 · PMID 26910495not yet assessed
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Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis ↗Journal of Clinical Microbiology · 2016 · PMID 26763957not yet assessed
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Connectivity of diagnostic technologies: improving surveillance and accelerating tuberculosis elimination ↗The International Journal of Tuberculosis and Lung Disease · 2016 · PMID 27393530not yet assessed
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Concordance of <i>Mycobacterium tuberculosis</i> fluoroquinolone resistance testing: implications for treatment ↗The International Journal of Tuberculosis and Lung Disease · 2015 · PMID 25686144not yet assessed
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The nature, patterns, clinical outcomes, and financial impact of intraoperative adverse events in emergency surgery ↗The American Journal of Surgery · 2015 · PMID 26601649not yet assessed
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matrix_subset_merged_wphenotype.tab ↗Harvard Dataverse · 2015not yet assessed
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matrix_subset_merged_wphenotype.tab ↗Harvard Dataverse · 2015not yet assessed
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matrix.tab ↗Harvard Dataverse · 2015not yet assessed
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Strain and host phenotype ↗Harvard Dataverse · 2015not yet assessed
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genetic variation ↗Harvard Dataverse · 2015not yet assessed
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matrix_subset.tab ↗Harvard Dataverse · 2015not yet assessed
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Strain_Host_Phenotype.tab ↗Harvard Dataverse · 2015not yet assessed
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A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens ↗Genome Medicine · 2014 · PMID 25484920not yet assessed
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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis ↗Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) · 2013not yet assessed
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Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis ↗Journal of Antimicrobial Chemotherapy · 2013 · PMID 24055765not yet assessed
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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis ↗Nature Genetics · 2013 · PMID 23995135not yet assessed
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Disturbance of respiratory muscle control in a patient with early-stage multiple sclerosis ↗European Respiratory Journal · 2013 · PMID 23728406not yet assessed
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not yet assessed
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A comparison of early versus late initiation of renal replacement therapy in critically ill patients with acute kidney injury: a systematic review and meta-analysis ↗Critical Care · 2011 · PMID 21352532not yet assessed
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not yet assessed
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Chemical disinfection of Legionella in hot water systems biofilm: a pilot-scale 1 study.HAL (Le Centre pour la Communication Scientifique Directe) · 2011not yet assessed
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Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production ↗PLoS Computational Biology · 2009 · PMID 19714220not yet assessed
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Étude de la survie des légionelles et de la dynamique des populations microbiennes des réseaux d'eau chaude : rôle des procédés de décontamination2009not yet assessed
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Thinking in three dimensions: a web-based algorithm to aid the interpretation of tuberculin skin test results. ↗PubMed · 2008 · PMID 18419884not yet assessed
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False-positive tuberculin reactions due to non-tuberculous mycobacterial infections. ↗PubMed · 2007 · PMID 17705966not yet assessed
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False-positive tuberculin skin tests: what is the absolute effect of BCG and non-tuberculous mycobacteria? ↗PubMed · 2006 · PMID 17131776not yet assessed
Full bibliography from OpenAlex; reproducibility verdicts matched by PMID.
Author attribution follows OpenAlex disambiguation, which is imperfect — a researcher's papers can be split across profiles or mixed with a namesake.
Merged across profiles sharing this ORCID where present. See every “Farhat M” paper on PubMed ↗