PUBLICATIONS

Paper figs

 

Journal Papers

 

  1. Sekiguchi K, Medlock L, Dura-Bernal S, Prescott SA, Lytton WW (2021) Multiscale computer model of the spinal dorsal horn reveals changes in network processing associated with chronic pain. BioRxiv 2021.06.09.447785. Under review in Journal of Neuroscience. [PDF]
  1. Kelley C, Dura-Bernal S, Neymotin SA, Antic SD, Carnevale NT, Migliore M, Lytton WW (2021) Effects of Ih and TASK-like shunting current on dendritic impedance in layer 5 pyramidal-tract neurons. BioRxiv 2021.01.08.425962. Journal of Neurophysiology (Accepted). [PDF]
  1. Romaro C, Najman F, WW Lytton, Roque AC, Dura-Bernal S (2020) NetPyNE implementation and rescaling of the Potjans-Diesmann cortical microcircuit model. arXiv:2005.03764. Neural Computation (Accepted). [PDF]
  1. Neymotin SA, Barczak A, O'Connell MN, McGinnis T, Markowitz N, Espinal E, Griffith E, Anwar H, Dura-Bernal S, Lytton WW, Jones SR, Bickel S, Lakatos P. (2020) Taxonomy of neural oscillation events in primate auditory cortex. bioRxiv, 2020.04.16.045021. Under review in PLoS Biology. [PDF]
  1. Kuhl E, Alber M, Tepole BA, Cannon WR, De S, Dura-Bernal S, Garikipati K, Karniadakis GE, Lytton WW, Perdikaris P, Petzold L. (2019) Multiscale modeling meets machine learning: What can we learn? Archives of Computational Methods in Engineering, s11831-020-09405-5. [PDF]
  1. Gao P, Graham J, Zhou W, Jang J, Angulo S, Dura-Bernal S, Hines ML, Lytton WW, and Antic S (2020) Local Glutamate-Mediated Dendritic Plateau Potentials Change the State of the Cortical Pyramidal Neuron. Journal of Neurophysiology 2021 125:1, 23-42. [PDF]
  1. Dai K, Hernando J, Billeh JN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol J-D, Arkhipov A (2019). The SONATA Data Format for Efficient Description of Large-Scale Network Models. PLOS Computational Biology 16(2): e1007696. [PDF]
  1. Peng G, Alber M, Buganza A, Cannon W, De S, Dura-Bernal S, Garikipati K, Karmiadakis G, Lytton W, Perdikaris P, Petzold L, Kuhl E. (2019) Integrating Machine Learning and Multiscale Modeling: Perspectives, Challenges, and Opportunities in the Biological, Biomedical, and Behavioral Sciences. Nature Partner Journals (npj) Digital Medicine, 2, 115. [PDF]
  1. Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal R, Hines M, Shepherd GMG, Lytton WW. (2019) NetPyNE: a tool for data-driven multiscale modeling of brain circuits. eLife 2019;8:e44494. [PDF]
  1. Gleeson P, Cantarelli M, Quintana A, Earnsah M, Piasini E, Birgiolas J, Cannon RC, Cayco- Gajic A, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson S, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver A. (2019) Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits. Neuron 10.1016/j.neuron.2019.05.019. [PDF]
  1. Dura-Bernal S, Neymotin SA, Suter BA, Shepherd GMG, Lytton WW (2019) Multiscale dynamics and information flow in a data-driven model of the primary motor cortex microcircuit. bioRxiv 201707. [PDF]
  1. Cantarelli M, Marin B, Quintana A, Earnsah M, Court R, Gleeson P, Dura-Bernal S, Silver RA, Idili G (2018) Geppetto: a reusable modular open platform for exploring neuroscience data and models. Philos. Trans. Royal Soc. B 373: 20170380. [PDF]
  1. Kerr CC, Dura-Bernal S, Smolinski TG, Chadderdon GL, Wilson DP (2018) Optimization by Adaptive Stochastic Descent. PLoS ONE, 13(3):e0192944. [PDF]
  1. Neymotin SA, Dura-Bernal S, Moreno H, Lytton WW. (2017) Computer modeling for pharmacological treatments for dystonia. Drug Discovery Today: Disease Models, 19:51-57. [PDF]
  1. Dura-Bernal S, Neymotin SA, Kerr CC, Sivagnanam S, Majumdar A, Francis JT, Lytton WW (2017) Evolutionary algorithm optimization of biological learning parameters in a biomimetic neuroprosthesis. IBM Journal of Research and Development (Comp. Neuro. special issue), 61:2/3. [PDF]
  1. Neymotin SA, Suter BA, Dura-Bernal S, Shepherd GMG, Migliore M, Lytton WW (2017) Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. Journal of Neurophysiology, 117(1):148-162. [PDF]
  1. Neymotin SA, Dura-Bernal S, Lakatos P, Sanger TD, Lytton WW (2016) Multitarget multiscale simulation for pharmacological treatment of dystonia in motor cortex. Frontiers in Pharmacology, 7:157. [PDF]
  1. Lytton WW, Seidenstein AH, Dura-Bernal S, Schurmann F, McDougal RA, Hines ML (2016) Simulation neurotechnologies for advancing brain research: Parallelizing large networks in NEURON. Neural Computation, 28:2063-2090. [PDF]
  1. Dura-Bernal S, Li Kan, Neymotin SA, Francis JT, Principe JC, Lytton WW (2016) Restoring behavior via inverse controller in a lesioned cortical spiking model driving a virtual arm. Frontiers in Neuroscience (Neuroprosthetics), 10:28. [PDF]
  1. Dura-Bernal S, Zhou X, Neymotin SA, Przekwas A, Francis JT, Lytton WW (2016) Cortical spiking network interfaced with virtual musculoskeletal arm and robotic arm. Frontiers in Neurorobotics, 9:13. [PDF]
  1. Lee G, Matsunaga A, Dura-Bernal S, Zhang W, Lytton WW, Francis JT, Fortes AB (2014) Towards real-time communication between in vivo neurophysiological data sources and simulator-based brain biomimetic models. Journal of Computational Surgery, 3:12. [PDF]
  1. Dura-Bernal S, Chadderdon GL, Neymotin SA, Francis JT, Lytton WW (2014) Towards a real-time interface between a biomimetic model of sensorimotor cortex and a robotic arm. Pattern Recognition Letters, 36:204-212. [PDF]
  1. Dura-Bernal S, Garreau G, Georgiou J, Andreou A, Denham SL, Wennekers T (2013) Multimodal integration of micro-Doppler sonar and auditory signals for behaviour classification with convolutional networks. International Journal of Neural Systems, 23:1350021. [PDF]
  1. Dura-Bernal S, Wennekers T, Denham SL (2012) Top-Down Feedback in an HMAX-Like Cortical Model of Object Perception Based on Hierarchical Bayesian Networks and Belief Propagation. PLoS ONE, 7(11):e48216. [PDF]

 

Conference Papers and Book Chapters

 

  1. Lytton WW, Sherif MA, Dura-Bernal S, Neymotin S. (2020) Multiscale modeling of a “mental” disease. Virtual Physiological Human Conference, VHP2020
  1. Sivagnanam S, Gorman W, Doherty D, Neymotin S, Hovhannisyan H, Fang S, Lytton W, Dura-Bernal S (2020) Simulating large-scale models of brain neuronal circuits using Google Cloud Platform. Practice and Experience in Advanced Research Computing, PEARC2020. 10.1145/3311790.3399621 [PDF]
  1. Li K, Dura-Bernal S, Francis JT, Lytton WW, Principe JC (2015) Repairing lesions via kernel adaptive inverse control in a biomimetic model of sensorimotor cortex. In Neural Engineering (NER), 2015 7th International IEEE/EMBS Conference, pp. 478-481, IEEE.
  1. Dura-Bernal S, Chadderdon GL, Neymotin SA, Zhou X, Przekwas A, Francis JT, Lytton WW (2013) Virtual musculoskeletal arm and robotic arm driven by a biomimetic model of sensorimotor cortex with reinforcement learning. In Signal Processing in Medicine and Biology Symposium (SPMB), pp. 1-5, IEEE.
  1. Ramenahalli R, Mendat D, Dura-Bernal S, Culurciello E, Niebur E, Andreou AG (2013) Audio-Visual Saliency Map: Overview, Basic Models and Hardware Implementation. In Information Sciences and Systems (CISS), 2013 47th Annual Conference on, 2013 pp. 1-6, IEEE.
  1. Garreau G, Dura-Bernal S, Andreou C, Andreou A, Georgiou J, Wennekers T, Denham SL (2011) Gait-based person and gender recognition using micro-Doppler signatures. In Biomedical Circuits and Systems Conference (BioCAS), pp.444-7, IEEE.
  1. Dura-Bernal S, Garreau G, Andreou C, Andreou A, Georgiou J, Wennekers T, Denham SL (2011) Human action categorization using ultrasound micro-Doppler signatures. Human Behavior Understanding, In series: Lecture Notes in Computer Science Volume 7065, 2011 pp 18-28, Springer Berlin Heidelberg.
  1. Dura-Bernal S, Denham SL, Wennekers T (2011) The Role of Feedback in a Hierarchical Model of Object Perception. From Brains to Systems: Brain-Inspired Cognitive Systems, In series: Advances in Experimental Medicine and Biology, Volume 718, pp 165-79 Springer New York.
  1. Dura-Bernal S, Wennekers T, Denham SL (2011) Modelling object perception in cortex: hierarchical Bayesian networks and belief propagation. In Information Sciences and Systems (CISS), 45th Annual Conference on, 2011 pp.1-6, IEEE.
  1. Denham SL, Dura-Bernal S, Coath M, Balaguer-Ballester E (2010) Neurocomputational Models of Perceptual Organization Unconscious memory representation in perception  Processes and mechanisms in the brain, In series: Advances in Consciousness Research 78,Chapter 6. pp 147-177, John Benjamins Publishing.