| Learning mixed graphical models with separate sparsity parameters and stability-based model selection AJ Sedgewick, I Shi, RM Donovan, PV Benos BMC bioinformatics 17, 307-318, 2016 | 94 | 2016 |
| Integrated intracellular organization and its variations in human iPS cells MP Viana, J Chen, TA Knijnenburg, R Vasan, C Yan, JE Arakaki, M Bailey, ... Nature 613 (7943), 345-354, 2023 | 91 | 2023 |
| Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories RM Donovan, AJ Sedgewick, JR Faeder, DM Zuckerman The Journal of chemical physics 139 (11), 2013 | 65 | 2013 |
| Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes KA Gerbin, T Grancharova, RM Donovan-Maiye, MC Hendershott, ... Cell Systems 12 (6), 670-687. e10, 2021 | 52 | 2021 |
| Building a 3d integrated cell GR Johnson, RM Donovan-Maiye, MM Maleckar BioRxiv, 238378, 2017 | 51 | 2017 |
| A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes T Grancharova, KA Gerbin, AB Rosenberg, CM Roco, JE Arakaki, ... Scientific Reports 11 (1), 15845, 2021 | 48 | 2021 |
| Unbiased rare event sampling in spatial stochastic systems biology models using a weighted ensemble of trajectories RM Donovan, JJ Tapia, DP Sullivan, JR Faeder, RF Murphy, M Dittrich, ... PLoS computational biology 12 (2), e1004611, 2016 | 45 | 2016 |
| Atlas of transcription factor binding sites from ENCODE DNase hypersensitivity data across 27 tissue types CC Funk, AM Casella, S Jung, MA Richards, A Rodriguez, P Shannon, ... Cell reports 32 (7), 2020 | 40 | 2020 |
| Degradation of MgB/sub 2/thin films in water Y Cui, JE Jones, A Beckley, R Donovan, D Lishego, E Maertz, ... IEEE transactions on applied superconductivity 15 (2), 224-227, 2005 | 30 | 2005 |
| A deep generative model of 3D single-cell organization RM Donovan-Maiye, JM Brown, CK Chan, L Ding, C Yan, N Gaudreault, ... PLoS computational biology 18 (1), e1009155, 2022 | 28 | 2022 |
| Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process R Anandakrishnan, Z Zhang, R Donovan-Maiye, DM Zuckerman Proceedings of the National Academy of Sciences 113 (40), 11220-11225, 2016 | 27 | 2016 |
| Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable MP Viana, J Chen, TA Knijnenburg, R Vasan, C Yan, JE Arakaki, M Bailey, ... BioRxiv, 2020.12. 08.415562, 2020 | 22 | 2020 |
| Enhancing generative perturbation models with llm-informed gene embeddings K Märtens, R Donovan-Maiye, J Ferkinghoff-Borg ICLR 2024 Workshop on Machine Learning for Genomics Explorations, 2024 | 7 | 2024 |
| BDQC: a general-purpose analytics tool for domain-blind validation of Big Data EW Deutsch, R Kramer, J Ames, A Bauman, DS Campbell, K Chard, ... bioRxiv, 258822, 2018 | 6 | 2018 |
| Systematic testing of belief-propagation estimates for absolute free energies in atomistic peptides and proteins RM Donovan-Maiye, CJ Langmead, DM Zuckerman Journal of chemical theory and computation 14 (1), 426-443, 2018 | 5 | 2018 |
| Studying stem cell organization using “label-free” methods and a novel generative adversarial model G Johnson, R Donovan-Maiye, C Ounkomol, MM Maleckar Biophysical Journal 114 (3), 43a, 2018 | 4 | 2018 |
| Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes. Cell Syst. 2021; 12 (6): 670–687. e10 KA Gerbin, T Grancharova, RM Donovan-Maiye, MC Hendershott, ... | 4 | |
| O3‐03‐01: MECHANISTIC AND DIRECTIONAL TRANSCRIPTIONAL REGULATORY NETWORKS IN ALZHEIMER'S DISEASE CC Funk, MA Richards, P Shannon, R Donovan-Maiye, N Rappaport, ... Alzheimer's & Dementia 14 (7S_Part_19), P1014-P1015, 2018 | | 2018 |
| A novel conditional model of cell organization: building an integrated cell GR Johnson, R Donovan-Maiye, MM Maleckar, CD Williams INTEGRATIVE AND COMPARATIVE BIOLOGY 58, E109-E109, 2018 | | 2018 |
| Efficient sampling in stochastic biological models R Donovan-Maiye University of Pittsburgh, 2016 | | 2016 |
Daniel M. ZuckermanProfessor of Biomedical Engineering. Oregon Health & Science UniversityEmail verificata su ohsu.edu