Publications by authors named "P H Tonner"
Article Synopsis
- Current genomic variant calling pipelines are not one-size-fits-all, requiring developers and researchers to make subjective tradeoffs based on their specific applications.
- StratoMod is introduced as a machine-learning tool that predicts germline variant calling errors in a data-driven way, improving the accuracy of variant detection, especially in complex genomic regions.
- It offers insights into the impact of different reference methods on recall rates and helps identify clinically relevant variants that might be overlooked by existing pipelines, facilitating better decision-making in pipeline design.
Article Synopsis
- The text discusses the growing need for precise engineering of biological functions in synthetic biology, especially for programmed sensing that regulates gene expression based on stimuli.
- It introduces two innovative methods, in silico selection and machine-learning-enabled forward engineering, that leverage a comprehensive dataset to develop genetic sensors with specifically defined dose-response characteristics.
- The methods demonstrate the capability to fine-tune genetic sensors for various performance metrics, such as sensitivity and output, and to predictively engineer new sensor mutations beyond the existing dataset.
Method for reproducible automated bacterial cell culture and measurement.
Synth Biol (Oxf)
August 2022
Microbial cell culture is one of the most commonly performed protocols for synthetic biology, and laboratories are increasingly using 96-well plates and laboratory automation systems for cell culture. Here, we describe a method for reproducible microbial culture using laboratory automation systems, including automated liquid handling, automated plate sealing and de-sealing, automated incubation and measurement of growing cultures. We discuss the key considerations that, in our experience, are important for reproducibility and present statistical analyses of data from 150 automated microbial growth experiments performed over 27 months using our automated method.
View Article and Find Full Text PDF