Peter D. Tonner
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View article: Epistasis in Allosteric Proteins: Can Biophysical Models Provide a Better Framework for Prediction and Understanding?
Epistasis in Allosteric Proteins: Can Biophysical Models Provide a Better Framework for Prediction and Understanding? Open
The prediction of epistasis, or the interaction between mutations, is a complex challenge impacting protein science, healthcare, and biotechnology. For allosteric proteins, the prediction of epistatic effects is further complicated by the …
View article: StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
StratoMod: predicting sequencing and variant calling errors with interpretable machine learning Open
Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for…
View article: StratoMod: Predicting sequencing and variant calling errors with interpretable machine learning
StratoMod: Predicting sequencing and variant calling errors with interpretable machine learning Open
Repetitive structures in the genome often lead to difficulty in accurately characterizing variation across a variety of sequencing technologies and variant detection methods. To address this, the Genome in a Bottle consortium maintains “st…
View article: Precision engineering of biological function with large-scale measurements and machine learning
Precision engineering of biological function with large-scale measurements and machine learning Open
As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require progr…
View article: StratoMod: Predicting sequencing and variant calling errors with interpretable machine learning
StratoMod: Predicting sequencing and variant calling errors with interpretable machine learning Open
Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for…
View article: Precision engineering of biological function with large-scale measurements and machine learning
Precision engineering of biological function with large-scale measurements and machine learning Open
As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require progr…
View article: Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power
Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power Open
Large-scale measurements linking genetic background to biological function have driven a need for models that can incorporate these data for reliable predictions and insight into the underlying biophysical system. Recent modeling efforts, …
View article: Method for reproducible automated bacterial cell culture and measurement
Method for reproducible automated bacterial cell culture and measurement Open
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 reprodu…
View article: Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures Open
Additional File 1: This includes Supplementary Tables S1-S16 Additional File 2: human_all_proteins_netcorona.txt (108MB) This is the raw data output by NetCorona following analysis of the “All Human Proteins” dataset Additional File 3: h…
View article: Additional file 6 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome
Additional file 6 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome Open
Additional file 6. Raw data displaying how predicted cleaved motifs were matched to a PDB file.
View article: Additional file 2 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome
Additional file 2 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome Open
Additional file 2. This is the raw data output by NetCorona following analysis of the “All Human Proteins” dataset.
View article: Additional file 1 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome
Additional file 1 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome Open
Additional file 1. Supplementary Tables S1-S16
View article: Additional file 3 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome
Additional file 3 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome Open
Additional file 3. This is the raw data output by NetCorona following analysis of the “One Protein Per Gene” dataset.
View article: Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures Open
Additional File 1: This includes Supplementary Tables S1-S16 Additional File 2: human_all_proteins_netcorona.txt (108MB) This is the raw data output by NetCorona following analysis of the “All Human Proteins” dataset Additional File 3: h…
View article: Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures Open
Additional File 1: This includes Supplementary Tables S1-S16 Additional File 2: human_all_proteins_netcorona.txt (108MB) This is the raw data output by NetCorona following analysis of the “All Human Proteins” dataset Additional File 3: h…
View article: Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome - supplementary data, tables, and figures Open
Additional File 1: This includes Supplementary Tables S1-S16 Additional File 2: human_all_proteins_netcorona.txt (108MB) This is the raw data output by NetCorona following analysis of the “All Human Proteins” dataset Additional File 3: h…
View article: Additional file 4 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome
Additional file 4 of Predicted coronavirus Nsp5 protease cleavage sites in the human proteome Open
Additional file 4. This is the raw data output by NetCorona following analysis of the “Proteins With PDB” dataset.
View article: Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research Open
Background The coronavirus nonstructural protein 5 (Nsp5) is a cysteine protease required for processing the viral polyprotein and is therefore crucial for viral replication. Nsp5 from several coronaviruses have also been found to cleave h…
View article: The genotype‐phenotype landscape of an allosteric protein
The genotype‐phenotype landscape of an allosteric protein Open
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale m…
View article: Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research - supplementary data, tables, and figures
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research - supplementary data, tables, and figures Open
Additional File 1: This includes Supplementary Tables S1-S15 Additional File 2: human_all_proteins_netcorona.txt (108MB) This is the raw data output by NetCorona following analysis of the “All Human Proteins” dataset Additional File 3: h…
View article: A Bayesian non-parametric mixed-effects model of microbial growth curves
A Bayesian non-parametric mixed-effects model of microbial growth curves Open
Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and fo…
View article: The genotype-phenotype landscape of an allosteric protein
The genotype-phenotype landscape of an allosteric protein Open
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here we report the large-scale me…
View article: The genotype-phenotype landscape of an allosteric protein
The genotype-phenotype landscape of an allosteric protein Open
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Quantitative methods to characterize the genotype-phenotype relationships for allosteric proteins would provide data needed to imp…
View article: Improved stability of an engineered function using adapted bacterial strains
Improved stability of an engineered function using adapted bacterial strains Open
Engineering useful functions into cells is one of the primary goals of synthetic biology. However, engineering novel functions that remain stable for multiple generations remains a significant challenge. Here we report the importance of ho…
View article: Designing over uncertain outcomes with stochastic sampling Bayesian optimization
Designing over uncertain outcomes with stochastic sampling Bayesian optimization Open
Optimization is becoming increasingly common in scientific and engineering domains. Oftentimes, these problems involve various levels of stochasticity or uncertainty in generating proposed solutions. Therefore, optimization in these scenar…
View article: A Bayesian Non-parametric Mixed-Effects Model of Microbial Phenotypes
A Bayesian Non-parametric Mixed-Effects Model of Microbial Phenotypes Open
Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and fo…
View article: Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth
Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth Open
Different weak organic acids have significant potential as topical treatments for wounds infected by opportunistic pathogens that are recalcitrant to standard treatments. These acids have long been used as bacteriostatic compounds in the f…