Author

M. R. Farhat

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Microbiology· 5 Evolutionary Biology· 3

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:whole-genome sequencing· 8 Approach:statistical model· 6 Research Focus:cell type annotation· 3 Research Focus:chromatin & epigenetic regulation· 3 Approach:experimental assay· 3 Research Focus:drug response / drug discovery· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2

Frequent Co-Authors

L. Freschi· 4 shared R. Calderon· 3 shared R. Vargas· 3 shared C. J. Meehan· 2 shared J. Sacchettini· 2 shared M. Marin· 2 shared M. Murray· 2 shared A. Barbova· 1 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

4 shared papersMicrobiology

L. Freschi

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference

M. Behruznia, M. Marin, D. J. Whiley, M. R. Farhat, J. C. Thomas, M. R. Domingo-Sananes, C. J. Meehan

The paper quantifies the MTBC pangenome, revealing a small, closed genome with lineage-specific regions of difference and implications for virulence and drug resistance.

bioRxiv · Mar 12, 2024Evolutionary Biology

High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes

S. Stanley, C. N. Spaulding, Q. Liu, M. R. Chase, D. T. M. Ha, P. V. K. Thai, N. H. Lan, D. D. A. Thu, N. L. Quang, J. Brown, N. D. Hicks, X. Wang, M. Marin, N. C. Howard, A. J. Vickers, , S. M. Fortune

This study uses high-throughput phenogenotyping to link Mtb genetic variants to clinical outcomes, identifying bacterial traits associated with treatment failure and transmission.

bioRxiv · Apr 9, 2023 · PreprintMicrobiology

Repeated evolution of bedaquiline resistance in Mycobacterium tuberculosis is driven by truncation of mmpR5

L. W. Roberts, K. M. Malone, M. Hunt, L. Joseph, P. Wintringer, J. Knaggs, D. Crook, M. R. Farhat, Z. Iqbal, S. V. Omar

The paper identifies truncation of mmpR5 as a driver of bedaquiline resistance in Mycobacterium tuberculosis through analysis of clinical isolates and MIC measurements.

bioRxiv · Dec 8, 2022 · PreprintMicrobiology

Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex

R. Vargas, M. J. Luna, L. Freschi, K. C. Murphy, T. R. Ioerger, C. M. Sassetti, M. R. Farhat

The paper identifies phase variation in Mycobacterium tuberculosis complex as an adaptive mechanism, showing it alters gene expression and virulence.

bioRxiv · Jun 10, 2022Microbiology

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

L. Freschi, R. Vargas, A. Hussain, S. M. Mostofa Kamal, A. Skrahina, S. Tahseen, N. Ismail, A. Barbova, S. Niemann, D. M. Cirillo, A. S. Dean, M. Zignol, M. R. Farhat

This study analyzes the population structure, biogeography, and transmissibility of Mycobacterium tuberculosis using genomic data from thousands of strains, identifying new clades and sub-lineages.

bioRxiv · Sep 29, 2020Microbiology

Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions

M. R. Farhat, L. Freschi, R. Calderon, T. Ioerger, M. Snyder, C. J. Meehan, B. de Jong, L. Rigouts, A. Sloutsky, D. Kaur, S. Sunyaev, D. van Soolingen, J. Shendure, J. Sacchettini, M. Murray

This study identifies novel resistance genes and regulatory regions in Mycobacterium tuberculosis using genome-wide association analysis of drug resistance phenotypes.

bioRxiv · Oct 1, 2018Evolutionary Biology

Rifampicin and rifabutin resistance in 1000 Mycobacterium tuberculosis clinical isolates

M. R. Farhat, J. Sixsmith, R. Calderon, N. Hicks, S. Fortune, M. Murray

The paper investigates rifamycin resistance in Mycobacterium tuberculosis isolates, finding that the D435V rpoB mutation increases IC50 for both rifampicin and rifabutin, suggesting the need to revise RFB testing concentrations.

bioRxiv · Sep 25, 2018Evolutionary Biology

Genotypic clustering does not imply recent tuberculosis transmission in a high prevalence setting: A genomic epidemiology study in Lima, Peru

A. Dixit, L. Freschi, R. Vargas, R. Calderon, J. Sacchettini, F. Drobniewski, J. T. Galea, C. Contreras, R. Yataco, Z. Zhang, L. Lecca, S.-O. Kolokotronis, B. Mathema, M. R. Farhat

This study uses genomic data to show that TB clusters identified by traditional methods may persist for decades, and WGS reveals genetic factors that may enhance transmissibility.

bioRxiv · Sep 16, 2018Microbiology