| Detecting differential growth of microbial populations with Gaussian process regression PD Tonner, CL Darnell, BE Engelhardt, AK Schmid Genome research 27 (2), 320-333, 2017 | 78 | 2017 |
| Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model … FML Bushell, PD Tonner, S Jabbari, AK Schmid, PA Lund Frontiers in Microbiology 9, 3196, 2019 | 65 | 2019 |
| The genotype‐phenotype landscape of an allosteric protein DS Tack, PD Tonner, A Pressman, ND Olson, SF Levy, EF Romantseva, ... Molecular systems biology 17 (3), e10179, 2021 | 57 | 2021 |
| Transcriptional regulation in archaea: from individual genes to global regulatory networks M Martinez-Pastor, PD Tonner, CL Darnell, AK Schmid Annual review of genetics 51 (1), 143-170, 2017 | 45 | 2017 |
| Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data P Tonner, V Srinivasasainagendra, S Zhang, D Zhi BMC genomics 13, 1-10, 2012 | 43 | 2012 |
| A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea PD Tonner, AMC Pittman, JG Gulli, K Sharma, AK Schmid PLoS Genetics 11 (1), e1004912, 2015 | 40 | 2015 |
| Systematic discovery of archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis CL Darnell, PD Tonner, JG Gulli, SC Schmidler, AK Schmid MSystems 2 (5), 10.1128/msystems. 00032-17, 2017 | 29 | 2017 |
| Geppetto: An environment for the efficient control and transmission of digital puppetry DP Mapes, P Tonner, CE Hughes Virtual and Mixed Reality-Systems and Applications: International Conference …, 2011 | 27 | 2011 |
| Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power PD Tonner, A Pressman, D Ross Proceedings of the National Academy of Sciences 119 (26), e2114021119, 2022 | 26 | 2022 |
| Predicted coronavirus Nsp5 protease cleavage sites in the human proteome BM Scott, V Lacasse, DG Blom, PD Tonner, NS Blom BMC Genomic Data 23 (1), 25, 2022 | 25 | 2022 |
| A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea M Martinez-Pastor, WA Lancaster, PD Tonner, MWW Adams, AK Schmid Nucleic Acids Research 45 (17), 9990-10001, 2017 | 22 | 2017 |
| A Bayesian non-parametric mixed-effects model of microbial growth curves PD Tonner, CL Darnell, FML Bushell, PA Lund, AK Schmid, SC Schmidler PLOS Computational Biology 16 (10), e1008366, 2020 | 17 | 2020 |
| Application of bayesian optimization and regression analysis to ferromagnetic materials development AR Will-Cole, AG Kusne, P Tonner, C Dong, X Liang, H Chen, NX Sun IEEE transactions on magnetics 58 (1), 1-8, 2021 | 11 | 2021 |
| Method for reproducible automated bacterial cell culture and measurement D Ross, PD Tonner, OB Vasilyeva Synthetic Biology 7 (1), ysac013, 2022 | 8 | 2022 |
| Systematic discovery of archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis. mSystems 2: e00032-17 CL Darnell, PD Tonner, JG Gulli, SC Schmidler, AK Schmid Web of Science, 2017 | 6 | 2017 |
| StratoMod: Predicting sequencing and variant calling errors with interpretable machine learning N Dwarshuis, P Tonner, ND Olson, FJ Sedlazeck, J Wagner, JM Zook Communications Biology 7 (1), 1316, 2024 | 3 | 2024 |
| Precision engineering of biological function with large-scale measurements and machine learning DS Tack, PD Tonner, A Pressman, ND Olson, SF Levy, EF Romantseva, ... PloS one 18 (3), e0283548, 2023 | 2 | 2023 |
| Improved stability of an engineered function using adapted bacterial strains DS Tack, PD Tonner, E Musteata, V Paralanov, D Ross bioRxiv, 2020.03. 05.979385, 2020 | 1 | 2020 |
| Interpretable modeling of genotype–phenotype landscapes withstate-of-the-art predictive power P Tonner, A Pressman, DJ Ross Peter Tonner, Abe Pressman, David J. Ross 119 (26), 2022 | | 2022 |
| Measurements drive progress in directed evolution for precise engineering of biological systems DS Tack, EF Romantseva, PD Tonner, A Pressman, J Rammohan, ... Current opinion in systems biology 23, 32-37, 2020 | | 2020 |