Maha Reda Farhat (Maha Farhat, Maha R Farhat)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 41

Top Topics

Convolutional Neural Network

Pulmonary Tuberculosis

Top Venues

bioRxiv : the preprint server for biology

Antimicrobial agents and chemotherapy

Nature microbiology

This page only lists publications with an associated author ORCID identifier.

Publications

Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Matthias I Gröschel, Francy J Pérez-Llanos, Roland Diel, Roger Vargas, Vincent Escuyer, Kimberlee Musser, Lisa Trieu, Jeanne Sullivan Meissner, Jillian Knorr, Don Klinkenberg, Peter Kouw, Susanne Homolka, Wojciech Samek, Barun Mathema, Dick van Soolingen, Stefan Niemann, Shama Desai Ahuja, Maha Reda Farhat
Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry. Nature microbiology 9 (8) (2024)
Avika Dixit, Yasha Ektefaie, Anju Kagal, Luca Freschi, Rajesh Karyakarte, Rahul Lokhande, Matthias Groschel, Jeffrey A Tornheim, Nikhil Gupte, Neeta N Pradhan, Mandar S Paradkar, Sona Deshmukh, Dileep Kadam, Marco Schito, David M Engelthaler, Amita Gupta, Jonathan Golub, Vidya Mave, Maha Reda Farhat
Drug resistance and epidemiological success of modern Mycobacterium tuberculosis lineages in western India. The Journal of infectious diseases (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Claudio Umberto Köser, Paolo Miotto, Nabila Ismail, Richard M Anthony, Christian Utpatel, Matthias Merker, Stefan Niemann, Sabira Tahseen, Leen Rigouts, Camilla Rodrigues, Shaheed Vally Omar, Maha Reda Farhat, Uladzimir Antonenka, Harald Hoffmann, Daniela Maria Cirillo, Thomas Schön
A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for Mycobacterium tuberculosis complex. The European respiratory journal 64 (1) (2024)
Maha Reda Farhat, Helen Cox, Marwan Ghanem, Claudia M Denkinger, Camilla Rodrigues, Mirna S Abd El Aziz, Handaa Enkh-Amgalan, Debrah Vambe, Cesar Ugarte-Gil, Jennifer Furin, Madhukar Pai
Drug-resistant tuberculosis: a persistent global health concern. Nature reviews. Microbiology (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Husain Poonawala, Yu Zhang, Sravya Kuchibhotla, Anna G Green, Daniela Maria Cirillo, Federico Di Marco, Andrea Spitlaeri, Paolo Miotto, Maha Reda Farhat
Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis . Antimicrobial agents and chemotherapy 68 (5) (2024)
Claudio Umberto Köser, Paolo Miotto, Nabila Ismail, Richard M Anthony, Christian Utpatel, Matthias Merker, Stefan Niemann, Sabira Tahseen, Leen Rigouts, Camilla Rodrigues, Shaheed Vally Omar, Maha Reda Farhat, Uladzimir Antonenka, Harald Hoffmann, Daniela Maria Cirillo, Thomas Schön
A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for Mycobacterium tuberculosis complex. The European respiratory journal 64 (1) (2024)
Heng Li, Maximillian G Marin, Maha Reda Farhat
Exploring gene content with pangene graphs. ArXiv (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Heng Li, Maximillian G Marin, Maha Reda Farhat
Exploring gene content with pangene graphs. ArXiv (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Husain Poonawala, Yu Zhang, Sravya Kuchibhotla, Anna G Green, Daniela Maria Cirillo, Federico Di Marco, Andrea Spitaleri, Paolo Miotto, Maha Reda Farhat
Erratum for Poonawala et al., "Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis ". Antimicrobial agents and chemotherapy (2024)
Matthias I Gröschel, Francy J Pérez-Llanos, Roland Diel, Roger Vargas, Vincent Escuyer, Kimberlee Musser, Lisa Trieu, Jeanne Sullivan Meissner, Jillian Knorr, Don Klinkenberg, Peter Kouw, Susanne Homolka, Wojciech Samek, Barun Mathema, Dick van Soolingen, Stefan Niemann, Shama Desai Ahuja, Maha Reda Farhat
Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry. Nature microbiology (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Husain Poonawala, Yu Zhang, Sravya Kuchibhotla, Anna G Green, Daniela Maria Cirillo, Federico Di Marco, Andrea Spitlaeri, Paolo Miotto, Maha Reda Farhat
Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis . Antimicrobial agents and chemotherapy (2024)
Matthias I Gröschel, Francy J Pérez-Llanos, Roland Diel, Roger Vargas, Vincent Escuyer, Kimberlee Musser, Lisa Trieu, Jeanne Sullivan Meissner, Jillian Knorr, Don Klinkenberg, Peter Kouw, Susanne Homolka, Wojciech Samek, Barun Mathema, Dick van Soolingen, Stefan Niemann, Shama Desai Ahuja, Maha Reda Farhat
Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry. Nature microbiology 9 (8) (2024)
Husain Poonawala, Yu Zhang, Sravya Kuchibhotla, Anna G Green, Daniela Maria Cirillo, Federico Di Marco, Andrea Spitlaeri, Paolo Miotto, Maha Reda Farhat
Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis . Antimicrobial agents and chemotherapy 68 (5) (2024)
Heng Li, Maximillian G Marin, Maha Reda Farhat
Exploring gene content with pangene graphs. ArXiv (2024)
Maximillian G Marin, Christoph Wippel, Natalia Quinones-Olvera, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen Rita Jacobson, Robin Mark Warren, Heng Li, Conor Joseph Meehan, Maha Reda Farhat
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches. bioRxiv : the preprint server for biology (2024)
Husain Poonawala, Yu Zhang, Sravya Kuchibhotla, Anna G Green, Daniela Maria Cirillo, Federico Di Marco, Andrea Spitlaeri, Paolo Miotto, Maha Reda Farhat
Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis . Antimicrobial agents and chemotherapy 68 (5) (2024)
Heng Li, Maximillian G Marin, Maha Reda Farhat
Exploring gene content with pangenome gene graphs. ArXiv (2024)
Husain Poonawala, Yu Zhang, Sravya Kuchibhotla, Anna G Green, Daniela Maria Cirillo, Federico Di Marco, Andrea Spitlaeri, Paolo Miotto, Maha Reda Farhat
Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis . Antimicrobial agents and chemotherapy (2024)
Heng Li, Maximillian G Marin, Maha Reda Farhat
Exploring gene content with pangene graphs. ArXiv (2024)
Avika Dixit, Yasha Ektefaie, Anju Kagal, Luca Freschi, Rajesh Karyakarte, Rahul Lokhande, Matthias Groschel, Jeffrey A Tornheim, Nikhil Gupte, Neeta N Pradhan, Mandar S Paradkar, Sona Deshmukh, Dileep Kadam, Marco Schito, David M Engelthaler, Amita Gupta, Jonathan Golub, Vidya Mave, Maha Reda Farhat
Drug resistance and epidemiological success of modern Mycobacterium tuberculosis lineages in western India. The Journal of infectious diseases (2024)
Heng Li, Maximillian G Marin, Maha Reda Farhat
Exploring gene content with pangene graphs. ArXiv (2024)
Nicoletta Commins, Mark R Sullivan, Kerry McGowen, Evan M Koch, Eric J Rubin, Maha Reda Farhat
Mutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus . Proceedings of the National Academy of Sciences of the United States of America 120 (22) (2023)
Roger Vargas, Michael J Luna, Luca Freschi, Maximillian G Marin, Ruby Froom, Kenan C Murphy, Elizabeth A Campbell, Thomas R Ioerger, Christopher M Sassetti, Maha Reda Farhat
Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex. Proceedings of the National Academy of Sciences of the United States of America 120 (28) (2023)
Sydney Stanley, Caitlin N Spaulding, Qingyun Liu, Michael R Chase, Dang Thi Minh Ha, Phan Vuong Khac Thai, Nguyen Huu Lan, Do Dang Anh Thu, Nguyen Le Quang, Jessica Brown, Nathan D Hicks, Xin Wang, Maximillian G Marin, Nicole C Howard, Andrew J Vickers, Wiktor M Karpinski, Michael C Chao, Maha Reda Farhat, Maxine Caws, Sarah J Dunstan, Nguyen Thuy Thuong Thuong, Sarah M Fortune
High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes. bioRxiv : the preprint server for biology (2023)
Sydney Stanley, Caitlin N Spaulding, Qingyun Liu, Michael R Chase, Dang Thi Minh Ha, Phan Vuong Khac Thai, Nguyen Huu Lan, Do Dang Anh Thu, Nguyen Le Quang, Jessica Brown, Nathan D Hicks, Xin Wang, Maximillian G Marin, Nicole C Howard, Andrew J Vickers, Wiktor M Karpinski, Michael C Chao, Maha Reda Farhat, Maxine Caws, Sarah J Dunstan, Nguyen Thuy Thuong Thuong, Sarah M Fortune
High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes. bioRxiv : the preprint server for biology (2023)
Sydney Stanley, Caitlin N Spaulding, Qingyun Liu, Michael R Chase, Dang Thi Minh Ha, Phan Vuong Khac Thai, Nguyen Huu Lan, Do Dang Anh Thu, Nguyen Le Quang, Jessica Brown, Nathan D Hicks, Xin Wang, Maximillian G Marin, Nicole C Howard, Andrew J Vickers, Wiktor M Karpinski, Michael C Chao, Maha Reda Farhat, Maxine Caws, Sarah J Dunstan, Nguyen Thuy Thuong Thuong, Sarah M Fortune
High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes. bioRxiv : the preprint server for biology (2023)
Anna G Green, Chang Ho Yoon, Michael L Chen, Yasha Ektefaie, Mack Fina, Luca Freschi, Matthias I Gröschel, Isaac Kohane, Andrew Beam, Maha Reda Farhat
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis. Nature communications 13 (1) (2022)
Jessica El Halabi, Nathan Palmer, Kathe Fox, Isaac Kohane, Maha Reda Farhat
Fecal microbiota transplantation and Clostridioides difficile infection among privately insured patients in the United States. Journal of gastroenterology (2021)
Roger Vargas, Luca Freschi, Andrea Spitaleri, Sabira Tahseen, Ivan Barilar, Stefan Niemann, Paolo Miotto, Daniela Maria Cirillo, Claudio Umberto Köser, Maha Reda Farhat
Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex. Antimicrobial agents and chemotherapy 65 (11) (2021)
Luca Freschi, Roger Vargas, Ashaque Husain, S M Mostofa Kamal, Alena Skrahina, Sabira Tahseen, Nazir Ismail, Anna Barbova, Stefan Niemann, Daniela Maria Cirillo, Anna S Dean, Matteo Zignol, Maha Reda Farhat
Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. Nature communications 12 (1) (2021)
Jacob E Lemieux, Katherine J Siddle, Bennett M Shaw, Christine Loreth, Stephen F Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H Tomkins-Tinch, Lydia A Krasilnikova, Katherine C DeRuff, Melissa A Rudy, Matthew R Bauer, Kim A Lagerborg, Erica Normandin, Sinéad B Chapman, Steven K Reilly, Melis N Anahtar, Aaron E Lin, Amber Carter, Cameron A Myhrvold, Molly E Kemball, Sushma Chaluvadi, Caroline N Cusick, Katelyn Flowers, Anna E Neumann, Felecia Cerrato, Maha Reda Farhat, Damien Slater, Jason B Harris, John A Branda, David Hooper, Jessie M Gaeta, Travis P Baggett, James O'Connell, Andreas Gnirke, Tami D Lieberman, Anthony Philippakis, Meagan Burns, Catherine M Brown, Jeremy Luban, Edward T Ryan, Sarah E Turbett, Regina C LaRocque, William P Hanage, Glen R Gallagher, Lawrence C Madoff, Sandra Smole, Virginia M Pierce, Eric D Rosenberg, Pardis C Sabeti, Daniel J Park, Bronwyn L MacInnis
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science (New York, N.Y.) 371 (6529) (2020)
Matthias I Gröschel, Conor Joseph Meehan, Ivan Barilar, Margo Diricks, Aitor Gonzaga, Matthias Steglich, Oscar Conchillo-Solé, Isabell-Christin Scherer, Uwe Mamat, Christian Friedemann Luz, Katrien De Bruyne, Christian Utpatel, Daniel Yero, Isidre Gibert, Xavier Daura, Stefanie Kampmeier, Nurdyana Abdul Rahman, Michael Kresken, Tjip S van der Werf, Ifey Alio, Wolfgang J Streit, Kai Zhou, Thomas Schwartz, John W A Rossen, Maha Reda Farhat, Ulrich E Schaible, Ulrich Nübel, Jan Rupp, Joerg Steinmann, Stefan Niemann, Thomas Andreas Kohl
The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nature communications 11 (1) (2020)
Conor Joseph Meehan, Galo A Goig, Thomas A Kohl, Lennert Verboven, Anzaan Dippenaar, Matthew Ezewudo, Maha Reda Farhat, Jennifer L Guthrie, Kris Laukens, Paolo Miotto, Boatema Ofori-Anyinam, Viola Dreyer, Philip Supply, Anita Suresh, Christian Utpatel, Dick van Soolingen, Yang Zhou, Philip M Ashton, Daniela Brites, Andrea Maurizio Cabibbe, Bouke C de Jong, Margaretha de Vos, Fabrizio Menardo, Sebastien Gagneux, Qian Gao, Tim H Heupink, Qingyun Liu, Chloé Loiseau, Leen Rigouts, Timothy C Rodwell, Elisa Tagliani, Timothy M Walker, Robin M Warren, Yan-Lin Zhao, Matteo Zignol, Marco Schito, Jennifer L Gardy, Daniela M Cirillo, Stefan Niemann, Iñaki Comas, Annelies Van Rie
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature reviews. Microbiology 17 (9) (2020)
Maha Reda Farhat, Razvan Sultana, Oleg Iartchouk, Sam Bozeman, James Galagan, Peter Sisk, Christian Stolte, Hanna Nebenzahl-Guimaraes, Karen Jacobson, Alexander Sloutsky, Devinder Kaur, James Posey, Barry N Kreiswirth, Natalia Kurepina, Leen Rigouts, Elizabeth M Streicher, Tommie C Victor, Robin M Warren, Dick van Soolingen, Megan Murray
Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. American journal of respiratory and critical care medicine 194 (5) (2017)