Jason Limberis, PhD | UCSF Center for TB

Assistant Researcher

M_MED-ZSFG-PULM

+1 628 206-8101

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.

Publications

URAdime - a tool for analyzing primer sequences in sequencing data to identify dimers and super-amplicons.

Limberis JD, Metcalfe JZ

spotPCR: A Rapid and Efficient Approach for Indexing Individual Template Molecules using Unique Molecular Identifiers.

Limberis JD, Nagel RJ, Chakravorty S, Block D, Dewell S, Nalyvayko A, Metcalfe JZ

stilPCR increases the effective sequencing length of Illumina targeted next-generation sequencing.

Research Square

Limberis JD, Nagel RJ, Chakravorty S, Block D, Dewell S, Nalyvayko A, Howard Z, Theron G, Venter R, Metcalfe JZ

Turbolysis: A low-cost, small footprint alternative to commercial bead beaters for cell lysis.

Limberis JD, Metcalfe JZ

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.

Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD

primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR.

Limberis JD, Metcalfe JZ

selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing.

Research Square

Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ

Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study.

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

A simple, single-tube overlapping amplicon-targeted Illumina sequencing assay.

Research Square

Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ

primerJinn - a tool for rationally designing multiplex PCR primer sets and in silico PCR.

Limberis JD, Metcalfe JZ

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.

Zheng W, Chang IC, Limberis J, Budzik J, Zha BS, Howard Z, Chen L, Ernst J

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during persistent infection.

Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Ernst JD

Circularization of rv0678 for Genotypic Bedaquiline Resistance Testing of Mycobacterium tuberculosis.

Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ

Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis.

rfs

Whitfield MG, Engelthaler DM, Allender C, Folkerts M, Heupink TH, Limberis J, Warren RM, Van Rie A, Metcalfe JZ

Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis.

Ismail N, Rivière E, Limberis J, Huo S, Metcalfe JZ, Warren RM, Van Rie A

Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis.

D_Cell and Tissue Biology

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

Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis.

P_Pharmaceutical Chemistry

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

A Human Lung Challenge Model to Evaluate the Safety and Immunogenicity of PPD and Live Bacillus Calmette-Guérin.

member

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

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.

Tomasicchio M, Limberis J, van der Merwe R, Jacobson R, Meldau R, Theron G, Nicol M, Warren R, Dheda K

A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic.

Public health

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

A regimen containing bedaquiline and delamanid compared to bedaquiline in patients with drug-resistant tuberculosis.

student

Olayanju O, Esmail A, Limberis J, Dheda K

Same-Day Tools, Including Xpert Ultra and IRISA-TB, for Rapid Diagnosis of Pleural Tuberculosis: a Prospective Observational Study.

rfs

Meldau R, Randall P, Pooran A, Limberis J, Makambwa E, Dhansay M, Esmail A, Dheda K

Linezolid interruption in patients with fluoroquinolone-resistant tuberculosis receiving a bedaquiline-based treatment regimen.

Olayanju O, Esmail A, Limberis J, Gina P, Dheda K

Long-term bedaquiline-related treatment outcomes in patients with extensively drug-resistant tuberculosis from South Africa.

student

Olayanju O, Limberis J, Esmail A, Oelofse S, Gina P, Pietersen E, Fadul M, Warren R, Dheda K

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

M_Epidemiology & Biostatistics

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

Selected questions and controversies about bedaquiline: a view from the field.

JCI insight

Dheda K, Esmail A, Limberis J, Maartens G

Xpert MTB/RIF Results in Patients With Previous Tuberculosis: Can We Distinguish True From False Positive Results?

The American journal of tropical medicine and hygiene

Theron G, Venter R, Calligaro G, Smith L, Limberis J, Meldau R, Chanda D, Esmail A, Peter J, Dheda K