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
Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement.
Authors: Domínguez J, Boeree MJ, Cambau E, Chesov D, Conradie F, Cox V, Dheda K, Dudnyk A, Farhat MR, Gagneux S, Grobusch MP, Gröschel MI, Guglielmetti L, Kontsevaya I, Lange B, van Leth F, Lienhardt C, Mandalakas AM, Maurer FP, Merker M, Miotto P, Molina-Moya B, Morel F, Niemann S, Veziris N, Whitelaw A, Horsburgh CR, Lange C.
Lancet Infect Dis
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Optimizing DNA Extraction from Pediatric Stool for Diagnosis of Tuberculosis and Use in Next-Generation Sequencing Applications.
Authors: Ness TE, Meiwes L, Kay A, Mejia R, Lange C, Farhat M, Mandalakas A, DiNardo A.
Microbiol Spectr
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Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations.
Authors: Koch EM, Du J, Dressner M, Alwasti HE, Taif ZA, Shehab F, Mohamed AM, Ghanem A, Haghighi A, Sunyaev S, Farhat M.
medRxiv
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COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation.
Authors: Patton MJ, Orihuela CJ, Harrod KS, Bhuiyan MAN, Dominic P, Kevil CG, Fort D, Liu VX, Farhat M, Koff JL, Lal CV, Gaggar A, Richter RP, Erdmann N, Might M, Gaggar A.
Crit Care
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COVID-19 and global childhood tuberculosis notifications.
Authors: Atre S, Chatterjee A, Farhat M.
Lancet Glob Health
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High Throughput Sequencing for Clinical Tuberculosis: An Overview.
Authors: Ness TE, DiNardo A, Farhat MR.
Pathogens
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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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