Maha Farhat

Maha Farhat, MD, MSc

Gilbert S. Omenn Associate Professor of Biomedical Informatics
Associate Director, Bioinformatics and Integrative Genomics (BIG) PhD Track

10 Shattuck Street #307, Boston, MA 02115

Farhat Lab

Maha Farhat  holds an MD from the McGill University Faculty of Medicine and a MSc in biostatistics from the Harvard Chan School of Public Health. She is also a practicing physician at the Massachusetts General Hospital Division of Pulmonary and Critical Care Medicine.

Dr. Farhat's research focuses on the development and application of methods for associating genotype and phenotype in infectious disease pathogens, with a strong emphasis on translation to better diagnostics and surveillance in resource-poor settings. To date, Farhat's work has focused on the pathogen Mycobacterium tuberculosis and spans the spectrum from computational analysis to field studies. She is PI and Co-Investigator on several large projects funded by NIH including the NIAID and the BD2K initiative.


DBMI Research Areas
Whole Genome Sequencing Assessing Impact of Diabetes Mellitus on Tuberculosis Mutations and Type of Recurrence in India.
Authors: Mave V, Chen L, Ranganathan UD, Kadam D, Vishwanathan V, Lokhande R, S SK, Kagal A, Pradhan NN, Shivakumar SVBY, Paradkar MS, Deshmukh S, Tornheim JA, Kornfeld H, Farhat M, Gupta A, Padmapriyadarsini C, Gupte N, Golub JE, Mathema B, Kreiswirth BN.
Clin Infect Dis
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A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis.
Authors: Green AG, Yoon CH, Chen ML, Ektefaie Y, Fina M, Freschi L, Gröschel MI, Kohane I, Beam A, Farhat M.
Nat Commun
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The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis.
Authors: Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey J, Omar SV, Peto TE, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS, Crook DW, Ismail N, Rodwell TC.
Lancet Microbe
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Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome.
Authors: Marin M, Vargas R, Harris M, Jeffrey B, Epperson LE, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Crudu V, Rosenthal A, Farhat MR.
Bioinformatics
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Tuberculosis Pathways to Care and Transmission of Multidrug-Resistance in India.
Authors: Atre SR, Jagtap JD, Faqih MI, Dumbare YK, Sawant TU, Ambike SL, Bhawalkar JS, Bharaswadkar SK, Jogewar PK, Adkekar RS, Hodgar BP, Jadhav V, Mokashi ND, Golub JE, Dixit A, Farhat MR.
Am J Respir Crit Care Med
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Population structure, biogeography and transmissibility of Mycobacterium tuberculosis.
Authors: Freschi L, Vargas R, Husain A, Kamal SMM, Skrahina A, Tahseen S, Ismail N, Barbova A, Niemann S, Cirillo DM, Dean AS, Zignol M, Farhat MR.
Nat Commun
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Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex.
Authors: Vargas R, Freschi L, Spitaleri A, Tahseen S, Barilar I, Niemann S, Miotto P, Cirillo DM, Köser CU, Farhat MR.
Antimicrob Agents Chemother
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Association Between NEDD4L Variation and the Genetic Risk of Acute Appendicitis: A Multi-institutional Genome-Wide Association Study.
Authors: Gaitanidis A, Kaafarani HMA, Christensen MA, Breen K, Mendoza A, Fagenholz PJ, Velmahos GC, Farhat MR.
JAMA Surg
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Fecal microbiota transplantation and Clostridioides difficile infection among privately insured patients in the United States.
Authors: El Halabi J, Palmer N, Fox K, Kohane I, Farhat MR.
J Gastroenterol
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GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.
Authors: Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR.
Genome Med
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