Publications
2025
Yasha Ektefaie, Andrew Shen, Lavik Jain, Maha Farhat, and Marinka Zitnik. 2025. “Sequence Modeling Is Not Evolutionary Reasoning”. BioRxiv
Yasha Ektefaie, Andrew Shen, Lavik Jain, Maha Farhat, and Marinka Zitnik. 2025. “Sequence Modeling Is Not Evolutionary Reasoning”. BioRxiv
Maximilian Marin, Michael Chase, Natalia Quinones, Shoko Wakabayashi, Douaa Mugahid, Sarah Fortune, Maha Farhat Tara Ness Andrew DiNardo, and Michael Chao. 2025. “Complete Genome Sequence of a Virulent Barcoded Mycobacterium Tuberculosis Str. Erdman Commonly Used for Non-Human Primate Infection Studies.”. Microbiology Resource Announcements
Maximilian Marin, Michael Chase, Natalia Quinones, Shoko Wakabayashi, Douaa Mugahid, Sarah Fortune, Maha Farhat Tara Ness Andrew DiNardo, and Michael Chao. 2025. “Complete Genome Sequence of a Virulent Barcoded Mycobacterium Tuberculosis Str. Erdman Commonly Used for Non-Human Primate Infection Studies.”. Microbiology Resource Announcements
Christine A Tzelios, Samantha Malatesta, Tara Carney, Laura F White, Sarah E Weber, Sarah Thomson, Danie Theron, Bronwyn Myers, Charles D H Parry, Robin M Warren, Robert Horsburgh, Maha R Farhat, and Karen R Jacobson. 2025. “Patient Determinants and Effects on Adherence of Adverse Drug Reactions to Tuberculosis Treatment: A Prospective Cohort Analysis”. Clinical Infectious Diseases
Christine A Tzelios, Samantha Malatesta, Tara Carney, Laura F White, Sarah E Weber, Sarah Thomson, Danie Theron, Bronwyn Myers, Charles D H Parry, Robin M Warren, Robert Horsburgh, Maha R Farhat, and Karen R Jacobson. 2025. “Patient Determinants and Effects on Adherence of Adverse Drug Reactions to Tuberculosis Treatment: A Prospective Cohort Analysis”. Clinical Infectious Diseases
Haytham Kaafarani and Maha R Farhat. 2025. “Genome-Wide Association Study Identifies a Locus at 17p13 to Be Associated With Intestinal Malrotation”
Haytham Kaafarani and Maha R Farhat. 2025. “Genome-Wide Association Study Identifies a Locus at 17p13 to Be Associated With Intestinal Malrotation”
2024
Avika Dixit, Luca Freschi, Roger Vargas Jr, Matthias I. Groeschel, Sabira Tahseen, Masud Alam, Mostofa Kamal, Alena Skrahina, Alena Skrahina, Ramon P. Basilio, Dodge R. Lim, Nazir Ismail, and Maha R. Farhat. 2024. “Estimation of Country-Specific Tuberculosis Antibiograms Using Genomic Data”. BMJ Global Health
Avika Dixit, Luca Freschi, Roger Vargas Jr, Matthias I. Groeschel, Sabira Tahseen, Masud Alam, Mostofa Kamal, Alena Skrahina, Alena Skrahina, Ramon P. Basilio, Dodge R. Lim, Nazir Ismail, and Maha R. Farhat. 2024. “Estimation of Country-Specific Tuberculosis Antibiograms Using Genomic Data”. BMJ Global Health
Sydney Stanley, Caitlin Spaulding, Qingyun Liu, Michael Chase, Dang Thi Minh Ha, Phan Vuong Khac Thai, Nguyen Huu Lan, Do Dang Anh Thu, Nguyen Le Quang, Jessica Brown, Nathan Hicks, Xin Wang, Maximillian Marin, Nicole Howard, Andrew Vickers, Wiktor Karpinski, Michael Chao, and Maha Farhat. 2024. “Identification of Bacterial Determinants of Tuberculosis Infection and Treatment Outcomes: A Phenogenomic Analysis of Clinical Strains. ”. The Lancet Microbe.
Sydney Stanley, Caitlin Spaulding, Qingyun Liu, Michael Chase, Dang Thi Minh Ha, Phan Vuong Khac Thai, Nguyen Huu Lan, Do Dang Anh Thu, Nguyen Le Quang, Jessica Brown, Nathan Hicks, Xin Wang, Maximillian Marin, Nicole Howard, Andrew Vickers, Wiktor Karpinski, Michael Chao, and Maha Farhat. 2024. “Identification of Bacterial Determinants of Tuberculosis Infection and Treatment Outcomes: A Phenogenomic Analysis of Clinical Strains. ”. The Lancet Microbe.
Maha Farhat and Karen Jacobson. 2024. “For Tuberculosis, Not "To Screen or Not to Screen?" But "Who?" and ‘How?’”. PubMed
Maha Farhat and Karen Jacobson. 2024. “For Tuberculosis, Not "To Screen or Not to Screen?" But "Who?" and ‘How?’”. PubMed
Michael Luna, Peter Oluoch, Jia zheng Miao, Peter Culviner, Kadamba Papavinasasundaram, Eleni Jaecklein, Scarlet Shell, Thomas Ioerger, Sarah Fortune, Maha R Farhat, and Christopher Sassetti. 2024. “Frequently Arising ESX-1 Associated Phase Variants Influence Mycobacterium Tuberculosis Fitness in the Presence of Host and Antibiotic Pressures”. MBio
Michael Luna, Peter Oluoch, Jia zheng Miao, Peter Culviner, Kadamba Papavinasasundaram, Eleni Jaecklein, Scarlet Shell, Thomas Ioerger, Sarah Fortune, Maha R Farhat, and Christopher Sassetti. 2024. “Frequently Arising ESX-1 Associated Phase Variants Influence Mycobacterium Tuberculosis Fitness in the Presence of Host and Antibiotic Pressures”. MBio
Farhat M, Cox H, Ghanem M, Denkinger CM, Rodrigues C, Abd El Aziz MS, Enkh-Amgalan H, Vambe D, Ugarte-Gil C, Furin J, and Pai M. 2024. “Drug-Resistant Tuberculosis: A Persistent Global Health Concern”. Nat Rev Microbiol
Farhat M, Cox H, Ghanem M, Denkinger CM, Rodrigues C, Abd El Aziz MS, Enkh-Amgalan H, Vambe D, Ugarte-Gil C, Furin J, and Pai M. 2024. “Drug-Resistant Tuberculosis: A Persistent Global Health Concern”. Nat Rev Microbiol
Dixit A, Ektefaie Y, Kagal A, Freschi L, Karyakarte R, Lokhande R, Groschel M, Tornheim JA, Gupte N, Pradhan NN, Paradkar MS, Deshmukh S, Kadam D, Schito M, Engelthaler DM, Gupta A, Golub J, , and Maha Farhat. 2024. “Drug Resistance and Epidemiological Success of Modern Mycobacterium Tuberculosis Lineages in Western India”. J Infect Dis
Dixit A, Ektefaie Y, Kagal A, Freschi L, Karyakarte R, Lokhande R, Groschel M, Tornheim JA, Gupte N, Pradhan NN, Paradkar MS, Deshmukh S, Kadam D, Schito M, Engelthaler DM, Gupta A, Golub J, , and Maha Farhat. 2024. “Drug Resistance and Epidemiological Success of Modern Mycobacterium Tuberculosis Lineages in Western India”. J Infect Dis
Köser CU, Miotto P, Ismail N, Anthony RM, Utpatel C, Merker M, Niemann S, Tahseen S, Rigouts L, Rodrigues C, Omar SV, Maha R. Farhat, Antonenka U, Hoffmann H, Cirillo DM, and Schön T. 2024. “A Composite Reference Standard Is Needed for Bedaquiline Antimicrobial Susceptibility Testing for Mycobacterium Tuberculosis Complex”. Eur Respir J
Köser CU, Miotto P, Ismail N, Anthony RM, Utpatel C, Merker M, Niemann S, Tahseen S, Rigouts L, Rodrigues C, Omar SV, Maha R. Farhat, Antonenka U, Hoffmann H, Cirillo DM, and Schön T. 2024. “A Composite Reference Standard Is Needed for Bedaquiline Antimicrobial Susceptibility Testing for Mycobacterium Tuberculosis Complex”. Eur Respir J
Li H, Maximillian Marin, and Maha R. Farhat. 2024. “Exploring Gene Content With Pangene Graphs”. Bioinformatics
Li H, Maximillian Marin, and Maha R. Farhat. 2024. “Exploring Gene Content With Pangene Graphs”. Bioinformatics
Bibliography
News
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