# Publications Download 87 citations download- [BibTeX](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=bibtex) - [EndNote X3 XML](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=endnote8) - [EndNote 7 XML](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=endnote7) - [Endnote tagged](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=tagged) - [Marc](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=marc) - [PubMedId](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=pubmed_id) - [RIS](/bibcite/export?pager_style=show_more&number_of_items=12&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=ris) ### 2025 Yasha Ektefaie, Andrew Shen, Lavik Jain, Maha Farhat, and Marinka Zitnik. 2025. “[Sequence Modeling Is Not Evolutionary Reasoning](https://www.biorxiv.org/content/10.1101/2025.01.17.633626v2)”. BioRxiv Yasha Ektefaie, Andrew Shen, Lavik Jain, Maha Farhat, and Marinka Zitnik. 2025. “[Sequence Modeling Is Not Evolutionary Reasoning](https://www.biorxiv.org/content/10.1101/2025.01.17.633626v2)”. 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.](https://pubmed.ncbi.nlm.nih.gov/39964179/)”. 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.](https://pubmed.ncbi.nlm.nih.gov/39964179/)”. 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](https://pubmed.ncbi.nlm.nih.gov/39973802/)”. 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](https://pubmed.ncbi.nlm.nih.gov/39973802/)”. 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](/publication/genome-wide-association-study-identifies-locus-17p13-be-associated-intestinal)” Haytham Kaafarani and Maha R Farhat. 2025. “[Genome-Wide Association Study Identifies a Locus at 17p13 to Be Associated With Intestinal Malrotation](/publication/genome-wide-association-study-identifies-locus-17p13-be-associated-intestinal)” ### 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](/publications/estimation-country-specific-tuberculosis-antibiograms-using-genomic-data-0)”. 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](/publications/estimation-country-specific-tuberculosis-antibiograms-using-genomic-data-0)”. BMJ Global Health - [ descriptionPublisher's Version](https://www.medrxiv.org/content/10.1101/2021.09.23.21263991v1.full) - [ descriptionPublisher's Version](https://www.medrxiv.org/content/10.1101/2021.09.23.21263991v1.full) 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. ](/publications/identification-bacterial-determinants-tuberculosis-infection-and-treatment)”. 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. ](/publications/identification-bacterial-determinants-tuberculosis-infection-and-treatment)”. The Lancet Microbe. - [ descriptionPublisher's Version](https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(24)00022-3/fulltext) - [ descriptionPublisher's Version](https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(24)00022-3/fulltext) Maha Farhat and Karen Jacobson. 2024. “[For Tuberculosis, Not "To Screen or Not to Screen?" But "Who?" and ‘How?’](/publications/tuberculosis-not-screen-or-not-screen-who-and-how)”. PubMed Maha Farhat and Karen Jacobson. 2024. “[For Tuberculosis, Not "To Screen or Not to Screen?" But "Who?" and ‘How?’](/publications/tuberculosis-not-screen-or-not-screen-who-and-how)”. PubMed - [ descriptionPublisher's Version](https://pubmed.ncbi.nlm.nih.gov/38636953/) - [ descriptionPublisher's Version](https://pubmed.ncbi.nlm.nih.gov/38636953/) 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](https://journals.asm.org/doi/10.1128/mbio.03762-24)”. 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](https://journals.asm.org/doi/10.1128/mbio.03762-24)”. 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](https://pubmed.ncbi.nlm.nih.gov/38519618/)”. 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](https://pubmed.ncbi.nlm.nih.gov/38519618/)”. 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](https://pubmed.ncbi.nlm.nih.gov/38819323/)”. 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](https://pubmed.ncbi.nlm.nih.gov/38819323/)”. 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](https://pubmed.ncbi.nlm.nih.gov/38991722/)”. 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](https://pubmed.ncbi.nlm.nih.gov/38991722/)”. Eur Respir J Li H, Maximillian Marin, and Maha R. Farhat. 2024. “[Exploring Gene Content With Pangene Graphs](https://academic.oup.com/bioinformatics/article/40/7/btae456/7718494)”. Bioinformatics Li H, Maximillian Marin, and Maha R. Farhat. 2024. “[Exploring Gene Content With Pangene Graphs](https://academic.oup.com/bioinformatics/article/40/7/btae456/7718494)”. Bioinformatics Show morerefresh ### Bibliography [http://www.ncbi.nlm.nih.gov/sites/myncbi/1f5e\_XTK7evQc/bibliography/45264981/public/?sort=date&direction=ascending](http://www.ncbi.nlm.nih.gov/sites/myncbi/1f5e_XTK7evQc/bibliography/45264981/public/?sort=date&direction=ascending) ### News [Medical Xpress](https://medicalxpress.com/news/2024-07-links-tb-strain-infectivity-geographic.html) [Which Strains of Tuberculosis Are the Most Infectious? | Harvard Medical School](https://hms.harvard.edu/news/which-strains-tuberculosis-are-most-infectious) [Headtopics.com](https://headtopics.com/uk/study-reveals-how-geographic-origins-influence-tuberculosis-56779521) [Remdesivir-resistant COVID case sets off few alarms](https://news.harvard.edu/gazette/story/2021/12/few-alarms-over-cases-of-drug-resistant-covid/?utm_source=SilverpopMailing&utm_medium=email&utm_campaign=Daily%20Gazette%2020211214%20(1)) [Study identifies need to improve patient retention in the National TB Elimination Programme, highlights patients’ trust relation](https://indianexpress.com/article/cities/pune/national-tuberculosis-elimination-programme-study-patient-retention-7600067/) [Innovative tools take aim at antibiotic-resistant microbes](https://www.nature.com/articles/d41586-021-02292-1) [Study identifies concerning delays in TB diagnoses in the United States](https://www.sciencedaily.com/releases/2021/03/210322195840.htm) [AI model predicts TB resistance](https://news.harvard.edu/gazette/story/2019/05/harvard-undergrads-ai-model-predicts-tb-resistance/) [Big data targets drug resistance](https://news.harvard.edu/gazette/story/2018/06/ensuring-antibiotic-effectiveness-with-big-data/) [Predicting TB's behavior](https://www.eurekalert.org/pub_releases/2017-08/hms-ptb073117.php) [Genetic drug-sensitivity tests can predict response to tuberculosis treatment in hours](https://geneticliteracyproject.org/2017/08/08/genetic-drug-sensitivity-tests-can-predict-response-tuberculosis-treatment-hours/) [Resistance Fighters](https://hms.harvard.edu/news/resistance-fighters) [TB: Genetic drug resistance as good in gauging treatment outcome, death risk as traditional culture-based tests](https://medicalxpress.com/news/2017-08-tb-genetic-drug-resistance-good.html) [Molecular tests that detect drug-resistant TB may become faster alternative to traditional testing](https://www.news-medical.net/news/20170804/Molecular-tests-that-detect-drug-resistant-TBc2a0may-become-faster-alternative-to-traditional-testing.aspx)