Robert McDougal, PhD
Assistant Professor of Biostatistics; Co-Training Director, Health Informatics MS
Research & Publications
Biography
News
Locations
Coauthors
Selected Publications
- Reproducibility of biophysical in silico neuron states and spikes from event-based partial historiesCudone E, Lower A, McDougal R. Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories. PLOS Computational Biology 2023, 19: e1011548. PMID: 37824576, PMCID: PMC10597496, DOI: 10.1371/journal.pcbi.1011548.
- Tutorial: using NEURON for neuromechanical simulationsFietkiewicz C, McDougal R, Marco D, Chiel H, Thomas P. Tutorial: using NEURON for neuromechanical simulations. Frontiers In Computational Neuroscience 2023, 17: 1143323. PMID: 37583894, PMCID: PMC10424731, DOI: 10.3389/fncom.2023.1143323.
- A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signaturesNewton A, Chartash D, Kleinstein S, McDougal R. A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures. BMC Bioinformatics 2023, 24: 292. PMID: 37474900, PMCID: PMC10357743, DOI: 10.1186/s12859-023-05397-8.
- PLD3 affects axonal spheroids and network defects in Alzheimer’s diseaseYuan P, Zhang M, Tong L, Morse T, McDougal R, Ding H, Chan D, Cai Y, Grutzendler J. PLD3 affects axonal spheroids and network defects in Alzheimer’s disease. Nature 2022, 612: 328-337. PMID: 36450991, PMCID: PMC9729106, DOI: 10.1038/s41586-022-05491-6.
- Multiscale Computer Modeling of Spreading Depolarization in Brain SlicesKelley C, Newton AJH, Hrabetova S, McDougal RA, Lytton WW. Multiscale Computer Modeling of Spreading Depolarization in Brain Slices. ENeuro 2022, 9: eneuro.0082-22.2022. PMID: 35927026, PMCID: PMC9410770, DOI: 10.1523/eneuro.0082-22.2022.
- Modernizing the NEURON Simulator for Sustainability, Portability, and PerformanceAwile O, Kumbhar P, Cornu N, Dura-Bernal S, King JG, Lupton O, Magkanaris I, McDougal RA, Newton AJH, Pereira F, Săvulescu A, Carnevale NT, Lytton WW, Hines ML, Schürmann F. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Frontiers In Neuroinformatics 2022, 16: 884046. PMID: 35832575, PMCID: PMC9272742, DOI: 10.3389/fninf.2022.884046.
- ModelDBMcDougal R, Wang R, Morse T, Migliore M, Marenco L, Carnevale T, Hines M, Shepherd G. ModelDB. 2022, 2053-2056. DOI: 10.1007/978-1-0716-1006-0_158.
- Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and NetworksMcDougal RA, Conte C, Eggleston L, Newton AJH, Galijasevic H. Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks. Frontiers In Neuroinformatics 2022, 16: 847108. PMID: 35655652, PMCID: PMC9152282, DOI: 10.3389/fninf.2022.847108.
- BioSimulators: a central registry of simulation engines and services for recommending specific tools.Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research 2022 PMID: 35524558, PMCID: PMC9252793, DOI: 10.1093/nar/gkac331.
- Conditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity.Huertas MA, Newton AJH, McDougal RA, Sacktor TC, Shouval HZ. Conditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity. ENeuro 2022, 9: eneuro.0064-22.2022. PMID: 35443991, PMCID: PMC9087736, DOI: 10.1523/eneuro.0064-22.2022.
- Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG dataNeymotin SA, Daniels DS, Caldwell B, McDougal RA, Carnevale NT, Jas M, Moore CI, Hines ML, Hämäläinen M, Jones SR. Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data. ELife 2020, 9: e51214. PMID: 31967544, PMCID: PMC7018509, DOI: 10.7554/elife.51214.
- Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and CircuitsGleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron 2019, 103: 395-411.e5. PMID: 31201122, PMCID: PMC6693896, DOI: 10.1016/j.neuron.2019.05.019.
- NetPyNE, a tool for data-driven multiscale modeling of brain circuitsDura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ELife 2019, 8: e44494. PMID: 31025934, PMCID: PMC6534378, DOI: 10.7554/elife.44494.
- Neuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical NeuronsShepherd GM, Marenco L, Hines ML, Migliore M, McDougal RA, Carnevale NT, Newton AJH, Surles-Zeigler M, Ascoli GA. Neuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical Neurons. Frontiers In Neuroanatomy 2019, 13: 25. PMID: 30949034, PMCID: PMC6437103, DOI: 10.3389/fnana.2019.00025.
- Automated Metadata Suggestion During Repository SubmissionMcDougal RA, Dalal I, Morse TM, Shepherd GM. Automated Metadata Suggestion During Repository Submission. Neuroinformatics 2018, 17: 361-371. PMID: 30382537, PMCID: PMC6494730, DOI: 10.1007/s12021-018-9403-z.
- Optimizations for Neuron Time Warp(NTW) for Stochastic Reaction-Diffusion Models of NeuronsPatoary M, Tropper C, McDougal R, Lytton W. Optimizations for Neuron Time Warp(NTW) for Stochastic Reaction-Diffusion Models of Neurons. 2017, 1252-1263. DOI: 10.1109/wsc.2017.8247871.
- Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in NeuronPatoary M, Tropper C, McDougal RA, Lin Z, Lytton WW. Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2017, 16: 1007-1019. PMID: 28961124, PMCID: PMC5869087, DOI: 10.1109/tcbb.2017.2756930.
- Development of an on-line simulation environment for computational neuroscienceIKENO H, YAMAZAK T, KANNON T, OKUMURA Y, KAMIYAMA Y, ISHIHARA A, INAGAKI K, HIRATA Y, SATOH S, WAGATSUMA H, Yoshiyuki A, YAMAGUCHI Y, McDOUGAL R, Rixin W, MARENCO L, MORSE T, SHEPHERD G, Shiro U. Development of an on-line simulation environment for computational neuroscience. INCF Japan Node International Workshop Advances In Neuroinformatics 2017, Ⅳ: 53. DOI: 10.14931/aini2016.ps.17.
- Multithreaded Stochastic PDES for Reactions and Diffusions in NeuronsLin Z, Tropper C, McDougal RA, Patoary MNI, Lytton WW, Yao Y, Hines ML. Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons. ACM Transactions On Modeling And Computer Simulation 2016, 27: 1-27. PMID: 28943743, PMCID: PMC5604336, DOI: 10.1145/2987373.
- ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactionsMarenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database 2016, 2016: baw132. PMID: 27694208, PMCID: PMC5045865, DOI: 10.1093/database/baw132.
- Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscienceMcDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. Journal Of Computational Neuroscience 2016, 42: 1-10. PMID: 27629590, PMCID: PMC5279891, DOI: 10.1007/s10827-016-0623-7.
- Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURONLytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML. Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Computation 2016, 28: 2063-2090. PMID: 27557104, PMCID: PMC5295685, DOI: 10.1162/neco_a_00876.
- Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortexNeymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW. Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 2015, 316: 344-366. PMID: 26746357, PMCID: PMC4724569, DOI: 10.1016/j.neuroscience.2015.12.043.
- Parallelizing large networks using NEURON-PythonSeidenstein A, McDougal R, Hines M, Lytton W. Parallelizing large networks using NEURON-Python. BMC Neuroscience 2015, 16: p151. PMCID: PMC4697477, DOI: 10.1186/1471-2202-16-s1-p151.
- 3D-printer visualization of neuron modelsMcDougal RA, Shepherd GM. 3D-printer visualization of neuron models. Frontiers In Neuroinformatics 2015, 9: 18. PMID: 26175684, PMCID: PMC4485057, DOI: 10.3389/fninf.2015.00018.
- NTW-MTLin Z, Tropper C, Patoary M, McDougal R, Lytton W, Hines M. NTW-MT. 2015, 157-167. DOI: 10.1145/2769458.2769459.
- ModelView for ModelDB: Online Presentation of Model StructureMcDougal RA, Morse TM, Hines ML, Shepherd GM. ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 2015, 13: 459-470. PMID: 25896640, PMCID: PMC4618280, DOI: 10.1007/s12021-015-9269-2.
- Deterministic Reaction-Diffusion SimulatorsLytton W, McDougal R. Deterministic Reaction-Diffusion Simulators. 2015, 1016-1018. DOI: 10.1007/978-1-4614-6675-8_185.
- ModelDBMcDougal R, Wang R, Morse T, Migliore M, Marenco L, Carnevale T, Hines M, Shepherd G. ModelDB. 2015, 1727-1730. DOI: 10.1007/978-1-4614-6675-8_158.
- SenseLab: Integration of Multidisciplinary Neuroscience DataShepherd G, Morse T, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines M, Miller P. SenseLab: Integration of Multidisciplinary Neuroscience Data. 2015, 2655-2657. DOI: 10.1007/978-1-4614-6675-8_497.
- Neuronal Calcium Wave Propagation Varies with Changes in Endoplasmic Reticulum Parameters: A Computer ModelNeymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW. Neuronal Calcium Wave Propagation Varies with Changes in Endoplasmic Reticulum Parameters: A Computer Model. Neural Computation 2015, 27: 898-924. PMID: 25734493, PMCID: PMC4386758, DOI: 10.1162/neco_a_00712.
- NTW-MT: a Multi-threaded Simulator for Reaction Diffusion Simulations in NEURONLin, Z., Tropper, C., Ishlam Patoary, M. N., McDougal, R. A., Lytton, W. W., & Hines, M. L. (2015, June). NTW-MT: a Multi-threaded Simulator for Reaction Diffusion Simulations in NEURON. In Proceedings of the 3rd ACM Conference on SIGSIM-Principles of Advanced Discrete Simulation (pp. 157-167). ACM.
- Neuron Time WarpPatoary M, Lin Z, Tropper C, McDougal R, Lytton W. Neuron Time Warp. 2014, 3447-3458. DOI: 10.1109/wsc.2014.7020177.
- Calcium regulation of HCN supports persistent activity associated with working memory: a multiscale model of prefrontal cortexNeymotin S, McDougal R, Hines M, Lytton W. Calcium regulation of HCN supports persistent activity associated with working memory: a multiscale model of prefrontal cortex. BMC Neuroscience 2014, 15: p108. PMCID: PMC4124985, DOI: 10.1186/1471-2202-15-s1-p108.
- Integrating Systems Biology Markup Language(SBML) with NEURONBulanova A, McDougal R, Neymotin S, Mutai V, Lytton W, Hines M. Integrating Systems Biology Markup Language(SBML) with NEURON. BMC Neuroscience 2014, 15: p144. PMCID: PMC4125051, DOI: 10.1186/1471-2202-15-s1-p144.
- A method for multi-simulator reaction-diffusion with NEURONMcDougal R, Hines M, Lytton W. A method for multi-simulator reaction-diffusion with NEURON. BMC Neuroscience 2014, 15: p109. PMCID: PMC4124986, DOI: 10.1186/1471-2202-15-s1-p109.
- Neuron time warpPatoary, M. N. I., Tropper, C., Lin, Z., McDougal, R., & Lytton, W. W. (2014, December). Neuron time warp. In Proceedings of the 2014 Winter Simulation Conference (pp. 3447-3458). IEEE Press.
- Water-tight membranes from neuronal morphology filesMcDougal RA, Hines ML, Lytton WW. Water-tight membranes from neuronal morphology files. Journal Of Neuroscience Methods 2013, 220: 167-178. PMID: 24091136, PMCID: PMC4197804, DOI: 10.1016/j.jneumeth.2013.09.011.
- Deterministic Reaction-Diffusion SimulatorsLytton W, McDougal R. Deterministic Reaction-Diffusion Simulators. 2013, 1-3. DOI: 10.1007/978-1-4614-7320-6_185-2.
- ModelDBMcDougal R, Wang R, Morse T, Migliore M, Marenco L, Carnevale T, Hines M, Shepherd G. ModelDB. 2013, 1-4. DOI: 10.1007/978-1-4614-7320-6_158-1.
- SenseLab: Integration of Multidisciplinary Neuroscience DataShepherd G, Morse T, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines M, Miller P. SenseLab: Integration of Multidisciplinary Neuroscience Data. 2013, 1-3. DOI: 10.1007/978-1-4614-7320-6_497-1.
- Reaction-diffusion in the NEURON simulatorMcDougal RA, Hines ML, Lytton WW. Reaction-diffusion in the NEURON simulator. Frontiers In Neuroinformatics 2013, 7: 28. PMID: 24298253, PMCID: PMC3828620, DOI: 10.3389/fninf.2013.00028.
- Reaction-diffusion modeling in the NEURON simulatorMcDougal R, Skolnick Y, Schaff J, Lytton W, Hines M. Reaction-diffusion modeling in the NEURON simulator. BMC Neuroscience 2012, 13: p119. PMCID: PMC3403371, DOI: 10.1186/1471-2202-13-s1-p119.
- Alternative splicing regulates kv3.1 polarized targeting to adjust maximal spiking frequency.Gu Y, Barry J, McDougel R, Terman D, Gu C. Alternative splicing regulates kv3.1 polarized targeting to adjust maximal spiking frequency. The Journal Of Biological Chemistry 2012, 287: 1755-69. PMID: 22105078, PMCID: PMC3265858, DOI: 10.1074/jbc.M111.299305.
- A working memory model based on excitatory-inhibitory interactions and calcium dynamicsLyman K, McDougal R, Myers B, Tien J, Zeki M, Fall C, Terman D. A working memory model based on excitatory-inhibitory interactions and calcium dynamics. BMC Neuroscience 2010, 11: p32. PMCID: PMC3090918, DOI: 10.1186/1471-2202-11-s1-p32.