| An atlas of human metabolism JL Robinson, P Kocabaş, H Wang, PE Cholley, D Cook, A Nilsson, ... Science signaling 13 (624), eaaz1482, 2020 | 351 | 2020 |
| Genome‐scale metabolic models applied to human health and disease DJ Cook, J Nielsen Wiley Interdisciplinary Reviews: Systems Biology and Medicine 9 (6), e1393, 2017 | 56 | 2017 |
| An agent-based modeling framework for evaluating hypotheses on risks for developing autism: Effects of the gut microbial environment B Weston, B Fogal, D Cook, P Dhurjati Medical Hypotheses 84 (4), 395-401, 2015 | 39 | 2015 |
| Metastatic triple negative breast cancer adapts its metabolism to destination tissues while retaining key metabolic signatures F Roshanzamir, JL Robinson, D Cook, MH Karimi-Jafari, J Nielsen Proceedings of the National Academy of Sciences 119 (35), e2205456119, 2022 | 38 | 2022 |
| Model-based hypothesis of gut microbe populations and gut/brain barrier permeabilities in the development of regressive autism R Downs, J Perna, A Vitelli, D Cook, P Dhurjati Medical hypotheses 83 (6), 649-655, 2014 | 35 | 2014 |
| Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes D Cook, BA Ogunnaike, R Vadigepalli BMC systems biology 9, 1-24, 2015 | 34 | 2015 |
| Maximum recommended dosage of lithium for pregnant women based on a PBPK model for lithium absorption S Horton, A Tuerk, D Cook, J Cook, P Dhurjati Advances in bioinformatics 2012 (1), 352729, 2012 | 33 | 2012 |
| Adiponectin fine‐tuning of liver regeneration dynamics revealed through cellular network modelling JM Correnti, D Cook, E Aksamitiene, A Swarup, B Ogunnaike, ... The Journal of Physiology 593 (2), 365-383, 2015 | 23 | 2015 |
| Systems biology investigation of cAMP modulation to increase SMN levels for the treatment of spinal muscular atrophy SG Mack, DJ Cook, P Dhurjati, MER Butchbach PLoS One 9 (12), e115473, 2014 | 15 | 2014 |
| Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics D Cook, S Achanta, JB Hoek, BA Ogunnaike, R Vadigepalli BMC Systems Biology 12, 1-29, 2018 | 13 | 2018 |
| A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes DJ Cook, B Patra, L Kuttippurathu, JB Hoek, R Vadigepalli Frontiers in physiology 6, 189, 2015 | 10 | 2015 |
| Molecular natural history of breast cancer: Leveraging transcriptomics to predict breast cancer progression and aggressiveness DJ Cook, J Kallus, R Jörnsten, J Nielsen Cancer Medicine 9 (10), 3551-3562, 2020 | 9 | 2020 |
| Pattern analysis uncovers a chronic ethanol-induced disruption of the switch-like dynamics of C/EBP-β and C/EBP-α genome-wide binding during liver regeneration L Kuttippurathu, B Patra, D Cook, JB Hoek, R Vadigepalli Physiological Genomics 49 (1), 11-26, 2017 | 6 | 2017 |
| Computational Modeling as an Approach to Study the Cellular and Molecular Regulatory Networks Driving Liver Regeneration D Cook, R Vadigepalli Liver Regeneration, 185-198, 2015 | 5 | 2015 |
| Next generation immuno-oncology tumor profiling using a rapid, non-invasive, computational biophysics biomarker in early-stage breast cancer D Cook, M Biancalana, N Liadis, D Lopez Ramos, Y Zhang, S Patel, ... Frontiers in Artificial Intelligence 6, 1153083, 2023 | 3 | 2023 |
| Elucidating the Mechanisms of Dynamic and Robust Control of the Liver Homeostatic Renewal Process: Cell Network Modeling and Analysis D Cook, A Manchel, BA Ogunnaike, R Vadigepalli Industrial & Engineering Chemistry Research 62 (5), 2275-2287, 2023 | 2 | 2023 |
| Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format A Mutsuddy, C Erdem, JR Huggins, M Salim, D Cook, N Hobbs, FA Feltus, ... Bioinformatics Advances 3 (1), vbad039, 2023 | 2 | 2023 |
| Accurate prediction of tumor growth and doubling times for triple negative breast cancer (TNBC) allows for patient-specific assessment of tumor aggressiveness J Whitman, D Cook, S Patel, L Munn, JA Cole, SimBioSys Team Cancer Research 82 (12_Supplement), 2721-2721, 2022 | 1 | 2022 |
| 45P Spatially-resolved single-cell HER2 tumor heterogeneity captured by biophysical modeling D Cook, N Hobbs, D Lopez-Ramos, J Cole, S Patel Annals of Oncology 33, S142, 2022 | 1 | 2022 |
| Abstract P1-08-31: Simbiosys tumorscope: Biophysical modeling of patient-specific response to chemotherapy JA Cole Jr, JR Peterson, TM Earnest, MJ Hallock, DJ Cook, E Braun, ... Cancer Research 82 (4_Supplement), P1-08-31-P1-08-31, 2022 | 1 | 2022 |