Jason Limberis, PhD

Title(s)Assistant Researcher, Medicine
SchoolSchool of Medicine
Address2540 23rd Street, #3300
San Francisco CA 94110
ORCID ORCID Icon0000-0002-7893-8416 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Stellenbosch University, South AfricaBSc Molecular Biology with Biotechnology
    Stellenbosch University, South AfricaBSc HonsMolecular Biology
    University of Cape Town, South AfricaPhDMedicine
    The Centre for Genomic Regulation, SpainInternshipBioinformatics

    Collapse Overview 
    Collapse Overview
    My research focusses on the causative agent of tuberculosis, Mycobacterium tuberculosis: I apply a combination of wet work and bioinformatics to investigate genomic and transcriptional associates of drug resistance, clinical outcomes, and patient infectiousness. See www.SemiQuant.com for more information.
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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. PLoS Pathog. 2024 May; 20(5):e1012205. Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD. PMID: 38701094; PMCID: PMC11095722.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR. BMC Bioinformatics. 2023 Dec 12; 24(1):468. Limberis JD, Metcalfe JZ. PMID: 38082220; PMCID: PMC10714587.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing. PLoS One. 2023; 18(11):e0289442. Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ. PMID: 38015898; PMCID: PMC10684010.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    4. Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study. Lancet Microbe. 2023 12; 4(12):e972-e982. Derendinger B, Dippenaar A, de Vos M, Huo S, Alberts R, Tadokera R, Limberis J, Sirgel F, Dolby T, Spies C, Reuter A, Folkerts M, Allender C, Lemmer D, Van Rie A, Gagneux S, Rigouts L, Te Riele J, Dheda K, Engelthaler DM, Warren R, Metcalfe J, Cox H, Theron G. PMID: 37931638; PMCID: PMC10842724.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    5. A simple, single-tube overlapping amplicon-targeted Illumina sequencing assay. PLoS One. 2023; 18(9):e0288687. Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ. PMID: 37708184; PMCID: PMC10501585.
      View in: PubMed   Mentions:    Fields:    
    6. primerJinn - a tool for rationally designing multiplex PCR primer sets and in silico PCR. Res Sq. 2023 Jun 26. Limberis JD, Metcalfe JZ. PMID: 37461503; PMCID: PMC10350116.
      View in: PubMed   Mentions:
    7. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. Res Sq. 2023 Jun 15. Zheng W, Chang IC, Limberis J, Budzik J, Zha BS, Howard Z, Chen L, Ernst J. PMID: 37398178; PMCID: PMC10312915.
      View in: PubMed   Mentions:
    8. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. bioRxiv. 2023 May 28. Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD. PMID: 36711606; PMCID: PMC9882350.
      View in: PubMed   Mentions: 1  
    9. Circularization of rv0678 for Genotypic Bedaquiline Resistance Testing of Mycobacterium tuberculosis. Microbiol Spectr. 2023 Mar 06; e0412722. Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ. PMID: 36877083; PMCID: PMC10100719.
      View in: PubMed   Mentions: 1     Fields:    
    10. Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis. J Clin Microbiol. 2022 01 19; 60(1):e0190721. Whitfield MG, Engelthaler DM, Allender C, Folkerts M, Heupink TH, Limberis J, Warren RM, Van Rie A, Metcalfe JZ. PMID: 34757831; PMCID: PMC8769725.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    11. Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis. Lancet Microbe. 2021 11; 2(11):e604-e616. Ismail N, Rivière E, Limberis J, Huo S, Metcalfe JZ, Warren RM, Van Rie A. PMID: 34796339; PMCID: PMC8597953.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    12. Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine. 2021 May; 67:103374. Naidoo CC, Nyawo GR, Sulaiman I, Wu BG, Turner CT, Bu K, Palmer Z, Li Y, Reeve BWP, Moodley S, Jackson JG, Limberis J, Diacon AH, van Helden PD, Clemente JC, Warren RM, Noursadeghi M, Segal LN, Theron G. PMID: 33975252; PMCID: PMC8122180.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    13. Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis. Nat Med. 2020 09; 26(9):1435-1443. Theron G, Limberis J, Venter R, Smith L, Pietersen E, Esmail A, Calligaro G, Te Riele J, de Kock M, van Helden P, Gumbo T, Clark TG, Fennelly K, Warren R, Dheda K. PMID: 32601338; PMCID: PMC8353872.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    14. A Human Lung Challenge Model to Evaluate the Safety and Immunogenicity of PPD and Live Bacillus Calmette-Guérin. Am J Respir Crit Care Med. 2020 05 15; 201(10):1277-1291. Davids M, Pooran A, Hermann C, Mottay L, Thompson F, Cardenas J, Gu J, Koeuth T, Meldau R, Limberis J, Gina P, Srivastava S, Calder B, Esmail A, Tomasicchio M, Blackburn J, Gumbo T, Dheda K. PMID: 31860339.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    15. Differential RD-1-specific IFN-γ host responses to diverse Mycobacterium tuberculosis strains in HIV-uninfected persons may be explained by genotypic variation in the ESX-1 region. Int J Infect Dis. 2020 Jul; 96:240-243. Tomasicchio M, Limberis J, van der Merwe R, Jacobson R, Meldau R, Theron G, Nicol M, Warren R, Dheda K. PMID: 32339714.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    16. A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC Med. 2020 02 04; 18(1):24. Klopper M, Heupink TH, Hill-Cawthorne G, Streicher EM, Dippenaar A, de Vos M, Abdallah AM, Limberis J, Merker M, Burns S, Niemann S, Dheda K, Posey J, Pain A, Warren RM. PMID: 32014024; PMCID: PMC6998097.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansPHPublic Health
    17. A regimen containing bedaquiline and delamanid compared to bedaquiline in patients with drug-resistant tuberculosis. Eur Respir J. 2020 01; 55(1). Olayanju O, Esmail A, Limberis J, Dheda K. PMID: 31619478.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    18. Same-Day Tools, Including Xpert Ultra and IRISA-TB, for Rapid Diagnosis of Pleural Tuberculosis: a Prospective Observational Study. J Clin Microbiol. 2019 09; 57(9). Meldau R, Randall P, Pooran A, Limberis J, Makambwa E, Dhansay M, Esmail A, Dheda K. PMID: 31270183; PMCID: PMC6711909.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    19. Linezolid interruption in patients with fluoroquinolone-resistant tuberculosis receiving a bedaquiline-based treatment regimen. Int J Infect Dis. 2019 Aug; 85:74-79. Olayanju O, Esmail A, Limberis J, Gina P, Dheda K. PMID: 31100421.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    20. Long-term bedaquiline-related treatment outcomes in patients with extensively drug-resistant tuberculosis from South Africa. Eur Respir J. 2018 05; 51(5). Olayanju O, Limberis J, Esmail A, Oelofse S, Gina P, Pietersen E, Fadul M, Warren R, Dheda K. PMID: 29700106.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    21. Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study. Lancet Respir Med. 2017 04; 5(4):269-281. Dheda K, Limberis JD, Pietersen E, Phelan J, Esmail A, Lesosky M, Fennelly KP, Te Riele J, Mastrapa B, Streicher EM, Dolby T, Abdallah AM, Ben-Rached F, Simpson J, Smith L, Gumbo T, van Helden P, Sirgel FA, McNerney R, Theron G, Pain A, Clark TG, Warren RM. PMID: 28109869.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    22. Selected questions and controversies about bedaquiline: a view from the field. Int J Tuberc Lung Dis. 2016 12 01; 20(12):24-32. Dheda K, Esmail A, Limberis J, Maartens G. PMID: 28240569.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    23. Xpert MTB/RIF Results in Patients With Previous Tuberculosis: Can We Distinguish True From False Positive Results? Clin Infect Dis. 2016 Apr 15; 62(8):995-1001. Theron G, Venter R, Calligaro G, Smith L, Limberis J, Meldau R, Chanda D, Esmail A, Peter J, Dheda K. PMID: 26908793; PMCID: PMC4803105.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells