Related papers: Antibiotic resistant characteristics from 16S rRNA
Molecular communication promises to enable communication between nanomachines with a view to increasing their functionalities and open up new possible applications. Due to some of the biological properties, bacteria have been proposed as a…
The tolerance of bacterial populations to biocidal or antibiotic treatment has been well documented in both biofilm and planktonic settings. However, there is still very little known about the mechanisms that produce this tolerance.…
Antibiotics resistance has caused much complication in the treatment of diseases, where the pathogen is no longer susceptible to specific antibiotics and the use of such antibiotics are no longer effective for treatment. A recent study that…
Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate…
Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis. Prediction of transcription…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
Targeting RNA with small molecules offers significant therapeutic potential. Machine learning could substantially accelerate preclinical drug discovery, from hit identification to lead optimization. Yet a fundamental limitation emerges:…
RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly…
Bacterial communities such as biofilms are widely recognised as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can…
Cell growth is determined by substrate availability and the cell's metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can…
A Recurrent Neural Network (RNN) was used to perform video frame prediction of microbial growth for a population of two mutants of Pseudomonas aeruginosa. The RNN was trained on videos of 20 frames that were acquired using fluorescence…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
We introduce a new version of forward stepwise regression. Our modification finds solutions to regression problems where the selected predictors appear in a structured pattern, with respect to a predefined distance measure over the…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
Antimicrobial resistance is a threat to public health with millions of deaths linked to drug resistant infections every year. To mitigate resistance, common strategies that are used are combination therapies and therapy switching. However,…
A fundamental step in the race to design a rapid diagnostic test for antimicrobial resistance is the separation of bacteria from their matrix. Many recent studies have been focused on the development of systems capable of separating and…
Rapid detection of foodborne bacteria is critical for food safety and quality, yet traditional culture-based methods require extended incubation and specialized sample preparation. This study addresses these challenges by i) enhancing the…
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…
Communication and coordination play a major role in the ability of bacterial cells to adapt to ever changing environments and conditions. Recent work has shown that such coordination underlies several aspects of bacterial responses…