Maha Farhat
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View article: The structural context of mutations in proteins predicts their effect on antibiotic resistance
The structural context of mutations in proteins predicts their effect on antibiotic resistance Open
In Mycobacterium tuberculosis, a prevalent and deadly pathogen, resistance to antibiotics evolves primarily through non-synonymous mutations in proteins. Sequence-based analyses are currently used to understand the genetic basis of antibio…
View article: The structural context of mutations in proteins predicts their effect on antibiotic resistance
The structural context of mutations in proteins predicts their effect on antibiotic resistance Open
In Mycobacterium tuberculosis, a prevalent and deadly pathogen, resistance to antibiotics evolves primarily through non-synonymous mutations in proteins. Sequence-based analyses are currently used to understand the genetic basis of antibio…
View article: An Integrated Data-Driven Model for Clinical Phenotyping of Tuberculosis Disease Severity
An Integrated Data-Driven Model for Clinical Phenotyping of Tuberculosis Disease Severity Open
A common approach to describing tuberculosis (TB) disease severity is to use a binary classification such as “advanced” and “minimal or early disease,” though this may not fully capture the range of clinical presentations. As individuals t…
View article: Insights into the Role of Rifampicin Exposure and Clinical Baseline Covariates on the Response to Pulmonary Tuberculosis Treatment
Insights into the Role of Rifampicin Exposure and Clinical Baseline Covariates on the Response to Pulmonary Tuberculosis Treatment Open
Background Quantitative markers of tuberculosis disease burden are essential for assessing treatment response and optimizing therapeutic strategies. This study evaluated the impact of antimicrobial plasma drug levels on time-to-positivity …
View article: The structural context of mutations in proteins predicts their effect on antibiotic resistance
The structural context of mutations in proteins predicts their effect on antibiotic resistance Open
In Mycobacterium tuberculosis , a prevalent and deadly pathogen, resistance to antibiotics evolves primarily through non-synonymous mutations in proteins. Sequence-based analyses are currently used to understand the genetic basis of antibi…
View article: Awareness of management of pulmonary multidrug-resistant tuberculosis (MDR-TB) among private practitioners in suburban areas of Pune city, India: Input for developing an educational tool
Awareness of management of pulmonary multidrug-resistant tuberculosis (MDR-TB) among private practitioners in suburban areas of Pune city, India: Input for developing an educational tool Open
Private practitioners (PPs) play a major role in caring for people with tuberculosis (TB) in India. At the same time, PPs have limited access to continuing medical education and oversight especially with regards to recent changes in the ma…
View article: Author response: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
Author response: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference Open
View article: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference Open
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulenc…
View article: Contamination rates in serially sampled sputum specimens obtained during tuberculosis treatment to capture culture conversion
Contamination rates in serially sampled sputum specimens obtained during tuberculosis treatment to capture culture conversion Open
Sputum cultures are the gold standard for tuberculosis (TB) diagnosis and treatment monitoring. However, cultures in MGIT liquid media are susceptible to microbial contamination, often rendering them uninterpretable. Research has shown tha…
View article: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference Open
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulenc…
View article: Author response: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
Author response: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference Open
View article: Convolutional neural networks quantify antibiotic resistance in <i>Mycobacterium tuberculosis</i> with diagnostic grade accuracy and predict treatment response
Convolutional neural networks quantify antibiotic resistance in <i>Mycobacterium tuberculosis</i> with diagnostic grade accuracy and predict treatment response Open
There is considerable interest in training machine learning (ML) models on genomic data that achieve clinical grade diagnostic accuracy. Many successful ML models have been trained and validated on binary tasks because predicting biomedica…
View article: Author response: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
Author response: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference Open
View article: The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference Open
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulenc…
View article: Pitfalls of bacterial pan-genome analysis approaches: a case study of <i>Mycobacterium tuberculosis</i> and two less clonal bacterial species
Pitfalls of bacterial pan-genome analysis approaches: a case study of <i>Mycobacterium tuberculosis</i> and two less clonal bacterial species Open
Summary Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using M…
View article: Fleming: An AI Agent for Antibiotic Discovery in Mycobacterium tuberculosis
Fleming: An AI Agent for Antibiotic Discovery in Mycobacterium tuberculosis Open
Tuberculosis (TB) remains a critical public health challenge, causing over 1.5 million deaths annually. Rising resistance to existing TB antibiotics threatens to reverse decades of progress in combating the disease. Developing new antibiot…
View article: Contamination rates in serially sampled sputum specimens obtained during tuberculosis treatment to capture culture conversion
Contamination rates in serially sampled sputum specimens obtained during tuberculosis treatment to capture culture conversion Open
Sputum cultures are the gold standard for tuberculosis (TB) diagnosis and treatment monitoring. However, cultures in MGIT liquid media are susceptible to microbial contamination, often rendering them uninterpretable. Research has shown tha…
View article: Multivariable regression models improve accuracy and sensitive grading of antibiotic resistance mutations in Mycobacterium tuberculosis
Multivariable regression models improve accuracy and sensitive grading of antibiotic resistance mutations in Mycobacterium tuberculosis Open
Rapid genotype-based drug susceptibility testing for the Mycobacterium tuberculosis complex (MTBC) relies on a comprehensive knowledgebase of the genetic determinants of resistance. Here we present a catalogue of resistance-associated muta…
View article: Complete genome sequence of a virulent barcoded <i>Mycobacterium tuberculosis</i> str. Erdman commonly used for non-human primate infection studies
Complete genome sequence of a virulent barcoded <i>Mycobacterium tuberculosis</i> str. Erdman commonly used for non-human primate infection studies Open
Mycobacterium tuberculosis is the etiologic agent of tuberculosis (TB), which claims over a million lives per year. Here, we report the complete genome sequence of a virulent barcoded M. tuberculosis Erdman strain that has been used extens…
View article: Frequently arising ESX-1-associated phase variants influence <i>Mycobacterium tuberculosis</i> fitness in the presence of host and antibiotic pressures
Frequently arising ESX-1-associated phase variants influence <i>Mycobacterium tuberculosis</i> fitness in the presence of host and antibiotic pressures Open
Mycobacterium tuberculosis (Mtb) exhibits an impressive ability to adapt to rapidly changing environments, despite its genome’s apparent stability. Recently, phase variation through indel formation in homopolymeric tracts (HT) has emerged …
View article: Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models
Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models Open
Protein language models (PLMs) are often assumed to capture evolutionary information by training on large protein sequence datasets. Yet it remains unclear whether PLMs can reason about evolution—that is, infer evolutionary relationships b…
View article: Systematic review and meta-analysis of protocols and yield of direct from sputum sequencing of<i>Mycobacterium tuberculosis</i>
Systematic review and meta-analysis of protocols and yield of direct from sputum sequencing of<i>Mycobacterium tuberculosis</i> Open
Direct sputum whole genome sequencing (dsWGS) can revolutionize Mycobacterium tuberculosis ( Mtb ) diagnosis by enabling rapid detection of drug resistance and strain diversity without the biohazard of culture. We searched PubMed, Web of S…
View article: Precision phenotyping for curating research cohorts of patients with unexplained post-acute sequelae of COVID-19
Precision phenotyping for curating research cohorts of patients with unexplained post-acute sequelae of COVID-19 Open
This research was funded by the US National Institute of Allergy and Infectious Diseases (NIAID).
View article: Erratum for Poonawala et al., “Transcriptomic responses to antibiotic exposure in <i>Mycobacterium tuberculosis</i> ”
Erratum for Poonawala et al., “Transcriptomic responses to antibiotic exposure in <i>Mycobacterium tuberculosis</i> ” Open
View article: Beyond diagnostic connectivity: Leveraging digital health technology for the real-time collection and provision of high-quality actionable data on infectious diseases in Uganda
Beyond diagnostic connectivity: Leveraging digital health technology for the real-time collection and provision of high-quality actionable data on infectious diseases in Uganda Open
Automated data transmission from diagnostic instrument networks to a central database at the Ministries of Health has the potential of providing real-time quality data not only on diagnostic instrument performance, but also continuous dise…
View article: Author response: The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
Author response: The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference Open
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulenc…
View article: Reviewer #2 (Public Review): The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
Reviewer #2 (Public Review): The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference Open
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulenc…
View article: The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference Open
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulenc…
View article: Exploring gene content with pangene graphs
Exploring gene content with pangene graphs Open
Motivation The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is appl…
View article: A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for<i>Mycobacterium tuberculosis</i>complex
A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for<i>Mycobacterium tuberculosis</i>complex Open
A composite reference standard minimises false-susceptible AST results for bedaquiline https://bit.ly/3wAVvFm