Related papers: Antibiotic resistant characteristics from 16S rRNA
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Ribosomal protein S30 (RS30) exhibits potent antimicrobial activity against a broad spectrum of bacteria. Despite its efficacy, the underlying action mechanism remained elusive. In this study, we unravel the fundamental mechanism by which…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…
We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…
Cross-species antimicrobial resistance (AMR) prediction is fundamentally an out-of-distribution (OOD) generalization problem: models trained on one set of bacterial taxa must transfer to phylogenetically distinct genomes that may rely on…
Synthetic microbiomes offer new possibilities for modulating microbiota, to address the barriers in multidtug resistance (MDR) research. We present a Bayesian optimization approach to enable efficient searching over the space of synthetic…
The global surge in the cases of gastric cancer has prompted an investigation into the potential of gut microbiota as a predictive marker for the disease. The alterations in gut diversity are suspected to be associated with an elevated risk…
Antibiotic resistance poses a significant threat in in-patient settings with high mortality. Using MIMIC-III data, we generated Sentence-BERT embeddings from clinical notes and applied Neural Networks and XGBoost to predict antibiotic…
We propose a mathematical model of Antimicrobial Resistance in the host to predict the failure of two antagonists of bacterial growth: the immune response and a single-antibiotic therapy. After characterising the initial bacterial load that…
Quantification of microbial interactions from 16S rRNA and meta-genomic sequencing data is difficult due to their sparse nature, as well as the fact that the data only provides measures of relative abundance. In this paper, we propose using…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Antimicrobial resistance (AMR) poses a global health threat, reducing the effectiveness of antibiotics and complicating clinical decision-making. To address this challenge, we introduce abx_amr_simulator, a Python-based simulation package…
Antibiotic resistance presents a growing global health crisis, demanding new therapeutic strategies that target novel bacterial mechanisms. Recent advances in protein structure prediction and machine learning-driven molecule generation…
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…