Harvard Catalyst Profiles

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Maha Reda Farhat, M.D.,C.M., M.D.

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  1. K01ES026835 (FARHAT, MAHA) Sep 30, 2015 - Jul 31, 2020
    NIH/NIEHS
    New Tools for the interpretation of Pathogen Genomic Data with a focus on Mycobacterium tuberculosis
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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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. Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol. 2019 Jun 17. PMID: 31209399.
    Citations:    
  2. Farhat MR, Sixsmith J, Calderon R, Hicks ND, Fortune SM, Murray M. Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates. J Antimicrob Chemother. 2019 Jun 01; 74(6):1477-1483. PMID: 30793747.
    Citations:    
  3. Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat Commun. 2019 05 13; 10(1):2128. PMID: 31086182.
    Citations:    
  4. Chen ML, Doddi A, Royer J, Freschi L, Schito M, Ezewudo M, Kohane IS, Beam A, Farhat M. Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction. EBioMedicine. 2019 May; 43:356-369. PMID: 31047860.
    Citations:    
  5. Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci Rep. 2019 Apr 03; 9(1):5602. PMID: 30944370.
    Citations:    
  6. Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS. Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings. Nat Microbiol. 2019 02; 4(2):328-338. PMID: 30510172.
    Citations:    Fields:    
  7. Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med. 2018 10 11; 379(15):1403-1415. PMID: 30280646.
    Citations:    Fields:    Translation:HumansCells
  8. Pollock N, Dhiman R, Daifalla N, Farhat M, Campos-Neto A. Discovery of a unique Mycobacterium tuberculosis protein through proteomic analysis of urine from patients with active tuberculosis. Microbes Infect. 2018 04; 20(4):228-235. PMID: 29306028.
    Citations:    Fields:    
  9. Farhat MR, Jacobson KR, Franke MF, Kaur D, Murray M, Mitnick CD. Fluoroquinolone Resistance Mutation Detection Is Equivalent to Culture-Based Drug Sensitivity Testing for Predicting Multidrug-Resistant Tuberculosis Treatment Outcome: A Retrospective Cohort Study. Clin Infect Dis. 2017 Oct 15; 65(8):1364-1370. PMID: 29017248.
    Citations:    Fields:    Translation:HumansCells
  10. Nebenzahl-Guimaraes H, van Laarhoven A, Farhat MR, Koeken VACM, Mandemakers JJ, Zomer A, van Hijum SAFT, Netea MG, Murray M, van Crevel R, van Soolingen D. Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. Am J Respir Crit Care Med. 2017 06 01; 195(11):1519-1527. PMID: 27997216.
    Citations: 3     Fields:    Translation:Cells
  11. Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med. 2016 09 01; 194(5):621-30. PMID: 26910495.
    Citations: 14     Fields:    Translation:HumansCells
  12. Andre E, Isaacs C, Affolabi D, Alagna R, Brockmann D, de Jong BC, Cambau E, Churchyard G, Cohen T, Delmee M, Delvenne JC, Farhat M, Habib A, Holme P, Keshavjee S, Khan A, Lightfoot P, Moore D, Moreno Y, Mundade Y, Pai M, Patel S, Nyaruhirira AU, Rocha LE, Takle J, Trébucq A, Creswell J, Boehme C. Connectivity of diagnostic technologies: improving surveillance and accelerating tuberculosis elimination. Int J Tuberc Lung Dis. 2016 08; 20(8):999-1003. PMID: 27393530.
    Citations: 7     Fields:    Translation:HumansPHPublic Health
  13. Farhat MR, Jacobson KR, Franke MF, Kaur D, Sloutsky A, Mitnick CD, Murray M. Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis. J Clin Microbiol. 2016 Mar; 54(3):727-33. PMID: 26763957.
    Citations: 8     Fields:    Translation:HumansCells
  14. Ramly EP, Bohnen JD, Farhat MR, Razmdjou S, Mavros MN, Yeh DD, Lee J, Butler K, De Moya M, Velmahos GC, Kaafarani HM. The nature, patterns, clinical outcomes, and financial impact of intraoperative adverse events in emergency surgery. Am J Surg. 2016 Jul; 212(1):16-23. PMID: 26601649.
    Citations: 1     Fields:    Translation:Humans
  15. Farhat MR, Mitnick CD, Franke MF, Kaur D, Sloutsky A, Murray M, Jacobson KR. Concordance of Mycobacterium tuberculosis fluoroquinolone resistance testing: implications for treatment. Int J Tuberc Lung Dis. 2015 Mar; 19(3):339-41. PMID: 25686144.
    Citations: 4     Fields:    Translation:HumansCells
  16. Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M. A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Med. 2014; 6(11):101. PMID: 25484920.
    Citations: 7     Fields:    
  17. Nebenzahl-Guimaraes H, Jacobson KR, Farhat MR, Murray MB. Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2014 Feb; 69(2):331-42. PMID: 24055765.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  18. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013 Oct; 45(10):1183-9. PMID: 23995135.
    Citations: 91     Fields:    Translation:Cells
  19. Farhat MR, Loring SH, Riskind P, Weinhouse G. Disturbance of respiratory muscle control in a patient with early-stage multiple sclerosis. Eur Respir J. 2013 Jun; 41(6):1454-6. PMID: 23728406.
    Citations: 2     Fields:    Translation:Humans
  20. Karvellas CJ, Farhat MR, Sajjad I, Mogensen SS, Leung AA, Wald R, Bagshaw SM. 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. Crit Care. 2011; 15(1):R72. PMID: 21352532.
    Citations: 87     Fields:    Translation:Humans
  21. Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol. 2009 Aug; 5(8):e1000489. PMID: 19714220.
    Citations: 115     Fields:    Translation:Cells
  22. Menzies D, Gardiner G, Farhat M, Greenaway C, Pai M. Thinking in three dimensions: a web-based algorithm to aid the interpretation of tuberculin skin test results. Int J Tuberc Lung Dis. 2008 May; 12(5):498-505. PMID: 18419884.
    Citations: 19     Fields:    Translation:Humans
  23. Cobelens FG, Menzies D, Farhat M. False-positive tuberculin reactions due to non-tuberculous mycobacterial infections. Int J Tuberc Lung Dis. 2007 Aug; 11(8):934-5;author reply 935. PMID: 17705966.
    Citations: 3     Fields:    Translation:HumansCells
  24. Farhat M, Greenaway C, Pai M, Menzies D. False-positive tuberculin skin tests: what is the absolute effect of BCG and non-tuberculous mycobacteria? Int J Tuberc Lung Dis. 2006 Nov; 10(11):1192-204. PMID: 17131776.
    Citations: 146     Fields:    Translation:HumansCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.