Publications

Papers in international scientific journals with referees

[36] Conde-Sousa E, Szücs P, Peng H, Aguiar P*, "N3DFix: An algorithm for automatic removal of swelling artifacts in neuronal reconstructions.", (2017) Neuroinformatics, 15(1):5-12

[35] Lopes CD, Gomes CP, Neto E, Sampaio P, Aguiar P, Pêgo AP, "Microfluidic-based platform to mimic the in vivo peripheral administration of neurotropic nanoparticles", (2016) Nanomedicine, 11(24):3205-3221

[34] Neto E, Leitão L, Sousa D, Alves CJ, Alencastre IS, Aguiar P, Lamghari M, "Compartmentalized microfluidic platforms - the unrivaled refresh of in vitro tools for neurobiological research", (2016) JNeuroscience, 36(46):11573-11584

[33] Pereira CL, Teixeira GQ, Ribeiro-Machado C, Caldeira J, Costa M, Figueiredo F, Fernandes R, Aguiar P, Grad S, Barbosa MA, Gonçalves RM, "Mesenchymal Stem/Stromal Cells seeded on cartilaginous endplates promote Intervertebral Disc Regeneration through Extracellular Matrix Remodeling", (2016) Scientific Reports, 6,33836

[32] Sousa DM, Conceição F, Silva D, Leitão L, Neto E, Alves CJ, Alencastre IS, Herzog H, Aguiar P, Lamghari M, "Ablation of Y1 receptor impairs osteoclast bone-resorbing activity", (2016) Scientific Reports, 6,33470

[31] Teixeira G, Pereira C, Castro F, Ferreira J, Lázaro M, Aguiar P, Wilke H, Ignatius A, Barbosa M, Neidlinger-Wilke C, Gonçalves R, “Anti-inflammatory Chitosan/Poly-ɣ-glutamic acid nanoparticles control inflammation while remodeling extracellular matrix in degenerated intervertebral disc”, (2016) Acta Biomaterialia, 42:168-179

[30] Alencastre I, Sousa D, Alves C, Leitão L, Neto E, Aguiar P, Lamghari M, "Delivery of pharmaceutics to bone: Nanotechnologies, High-throughput processing and in silico mathematical models.", (2016) e Cells and Materials Journal, 31: 355-381

[29] Gerós A, Horta R, Aguiar P*, "Facegram - Objective quantitative analysis in facial reconstructive surgery", (2016) Journal of Biomedical Informatics, 61:1-9

[28] Pereira AJ, Aguiar P, Belsley M, Maiato H, "Inducible fluorescent speckle microscopy", (2016) Journal of Cell Biology, 212 (2), 245-255

[27] Dias C, Guerra M, Ventura J*, Aguiar P*, "Memristor-based Willshaw network: capacity and robustness to noise in the presence of defects", (2015) Applied Physics Letters, 106, 223505

[26] Neto E, Paramos-de-Carvalho D, Lourenco A, Aguiar P, Lamghari M, "Compartmentalized microfluidic platforms as tool of choice to study the interaction between neurons and osteoblasts", (2015) Neuromethods, 103:161-179

[25] Barisic M, Aguiar P, Geley S, Maiato H, "Kinetochore motors drive congression of peripheral polar chromosomes by overcoming random arm-ejection forces", (2014) Nature Cell Biology, 16(12):1249-56

[24] Silva P, Travassos B, Vilar L, Aguiar P, Davids K, Araujo D, Garganta J, "Numerical relations and skill level constrain co-adaptive behaviors of agents in sports teams", (2014) PLoS ONE, 9(9), Article number e107112

[23] Silva , Duarte R, Sampaio J, Aguiar P, Davids K, Araujo D, Garganta J, "Field dimension and skill level constrain team tactical behaviours in small-sided and conditioned games in football", (2014) Journal of Sports Sciences, 32(20):1888-1896

[22] Sousa M, Szucs P, Lima D and Aguiar P*, "The pronociceptive dorsal reticular nucleus contains mostly tonic neurons and frequently shows spontaneous activity without ascending input from the spinal cord", (2014) J Neurophysiology, 111 (7), pp 1507-1518.

[21] Afonso O, Matos I, Pereira A, Aguiar P, Lampson A, Maiato H, "Feedback control of chromosome separation by a midzone Aurora B gradient", (2014) Science, 345 (6194), pp 332-336.

[20] Neto E, Alves C, Sousa D, Alencastre I, Lourenço A, Leitão L, Ryu H, Jeon N, Aguiar P, Almeida R, Lamghari M, "Bone cells and sensory neurons: close partners in a microfluidic platform", (2014) Integrative Biology (Camb), 6(6):586-95.

[19] Horta R, Aguiar P, Monteiro D, Silva A, Amarante JM, "A facegram for spatial-temporal analysis of facial excursion: Applicability in the microsurgical reanimation of long-standing paralysis and pretransplantation", (2014) Journal of Cranio-Maxillofacial Surgery, 42(7):1250-9

[18] Sousa M, Aguiar P*, "Building, simulating and visualizing large spiking neural networks with NeuralSyns", (2014) Neurocomputing, 123, pp. 372-380

[17] Castro L, Aguiar P*, "A feedforward model for the formation of a grid field where spatial information is provided solely from place cells", (2014) Biological Cybernetics, 108 (2), pp. 133-143

[16] Horta R, Aguiar P, Silva P, Monteiro D, Amarante JM, "Facial disfigurement: Restoration of facial dynamics in a patient with concomitant facial paralysis and blindness", (2014) Journal of Reconstructive Microsurgery, 30 (3), pp. 207-210

[15] Aguiar P*, Sousa M, Szucs P, "Versatile morphometric analysis and visualization of the three-dimensional structure of neurons", (2013) Neuroinformatics, 11 (4), pp. 393-403

[14] Moutinho-Pereira S, Stuurman N, Afonso O, Hornsveld M, Aguiar P, Goshima G, Vale RD, Maiato H, "Genes involved in centrosome-independent mitotic spindle assembly in Drosophila S2 cells", (2013) PNAS - Proceedings of the National Academy of Sciences of the United States of America, 110 (49), pp. 19808-19813

[13] Guimaraes J, Moura E, Silva E, Aguiar P, Garrett C, Vieira-Coelho MA, "Locus coeruleus is involved in weight loss in a rat model of Parkinson's disease: An effect reversed by deep brain stimulation", (2013) Brain Stimulation, 6 (6), pp. 845-855

[12] Conde-Sousa E, Aguiar P*, "A working memory model for serial order that stores information in the intrinsic excitability properties of neurons", (2013) Journal of Computational Neuroscience, 35 (2), pp. 187-199

[11] Horta R, Monteiro D, Silva A, Amarante JM, Aguiar P*, "Evaluation of a facial transplant candidate with a facegram: A baseline analysis", (Plastic and Reconstructive Surgery (2013) 132 (479e-480)), (2013) Plastic and Reconstructive Surgery, 132 (4), pp. 1040-1041

[10] Silva P, Garganta J, Araújo D, Davids K, Aguiar P, "Shared knowledge or shared affordances? Insights from an ecological dynamics approach to team coordination in sports", (2013) Sports Medicine, 43 (9), pp. 765-772

[9] Szucs P, Luz LL, Pinho R, Aguiar P, Antal Z, Tiong SYX, Todd AJ, Safronov BV, "Axon diversity of lamina I local-circuit neurons in the lumbar spinal cord", (2013) Journal of Comparative Neurology, 521 (12), pp. 2719-2741

[8] Carneiro J, Duarte-Pereira S, Azevedo L, Castro LFC, Aguiar P, Moreira IS, Amorim A, Silva RM, "The Evolutionary Portrait of Metazoan NAD Salvage", (2013) PLoS ONE, 8 (5), art. no. e64674

[7] Pinto S, Krishna R, Dias C, Pimentel G, Oliveira GNP, Teixeira JM, Aguiar P, Titus E, Gracio J, Ventura J, Araujo JP, "Resistive switching and activity-dependent modifications in Ni-doped graphene oxide thin films", (2012) Applied Physics Letters, 101 (6), art. no. 063104

[6] Castro L, Aguiar P*, "Phase precession through acceleration of local theta rhythm: A biophysical model for the interaction between place cells and local inhibitory neurons", (2012) Journal of Computational Neuroscience, 33 (1), pp. 141-150

[5] Pais-Vieira M, Aguiar P, Lima D, Galhardo V, "Inflammatory pain disrupts the orbitofrontal neuronal activity and risk-assessment performance in a rodent decision-making task", (2012) Pain, 153 (8), pp. 1625-1635

[4] Aguiar P*, Sousa M, Lima D, "NMDA channels together with L-type calcium currents and calcium-activated nonspecific cationic currents are sufficient to generate windup in WDR neurons", (2010) Journal of Neurophysiology, 104 (2), pp. 1155-1166

[3] Aguiar P*, Mendonça L, Galhardo V, "OpenControl: A free opensource software for video tracking and automated control of behavioral mazes", (2007) Journal of Neuroscience Methods, 166 (1), pp. 66-72

[2] Vourvouhaki E, Carvalho C, Aguiar P, "Model for Osteosarcoma-9 as a potent factor in cell survival and resistance to apoptosis", (2007) Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 76 (1), art. no. 011926

[1] Aguiar P, Willshaw D, "Hippocampal mossy fibre boutons as dynamical synapses", (2004) Neurocomputing, 58-60, pp. 699-703

Peer reviewed conferences [not updated]

[23] Monteiro J, Oliveira H, Aguiar P, Cardoso J, "A Depth-Map Approach for Automatic Mice Behavior Recognition", IEEE International Conference on Image Processing 2014 [accepted]

[22] Castro L and Aguiar P*, "A model for grid cells where spatially correlated place cells compete for the grid map nodes", CNS 2013, BMC Neuroscience 2013, 14(Suppl 1):P2; doi:10.1186/1471-2202-14-S1-P2

[21] Conde-Sousa E and Aguiar P*, "Conversion from spatial patterns of activity to sequences of neuronal activations using gate interneurons", CNS 2013, BMC Neuroscience 2013, 14(Suppl 1):P3; doi:10.1186/1471-2202-14-S1-P3

[20] Sousa M, Szucs P and Aguiar P*, "Reduction in inhibitory control is sufficient to generate hyperalgesia in a spiking model of nociceptive integration in the superficial dorsal horn", CNS 2013, BMC Neuroscience 2013, 14(Suppl 1):P1; doi:10.1186/1471-2202-14-S1-P1

[19] Neto E, Aguiar P, Almeida R and Lamghari M, "Quantitative method for assessing axonal outgrowth on microfluidic devices", Bioimaging 2012

[18] Conde-Sousa E and Aguiar P*, "A working memory model capable of storing sequences of patterns without using synaptic plasticity", Champalimaud Neuroscience Symposium 2012

[17] Castro L and Aguiar P*, "Inhibitory synaptic plasticity, allied with place fields competition and compactness, can give rise to grid-like firing pattern", Champalimaud Neurosci. Symposium 2012

[16] Castro L and Aguiar P*, "Phase precession through acceleration of local theta rhythm: a biophysical model for the interaction between complex spike cells and theta cells", CNS 2011, BMC Neuroscience 2011, 12(Suppl 1):P2 (18 July 2011) doi:10.1186/1471-2202-12-S1-P2

[15] Aguiar P* and Szucs P, "Detailed visualization and morphometric analysis of reconstructed neurons using Blender and Python", CNS 2011, BMC Neuroscience 2011, 12(Suppl 1):P323 (18 July 2011) doi:10.1186/1471-2202-12-S1-P323

[14] Luz LL, Pinho R, Aguiar P, Antal Zs, Todd A, Safronov BV and Szucs P, "Morphological analysis of lamina I local-circuit neurons in the lumbar spinal cord of the rat", Champalimaud Neuroscience Symposium 2011

[13] Sousa M, Aguiar P and Szucs P, "Towards biophysically realistic models of the neuronal dynamics in the reticular nucleus of medulla oblongata", Champalimaud Neuroscience Symposium 2011

[12] Conde-Sousa E and Aguiar P*, "Storing information in membrane conductances dynamics - working memory without synaptic plasticity", Champalimaud Neuroscience Symposium 2011

[11] Aguiar P*, Sousa M and Lima D, "Analysis of the mechanisms underlying windup using a detailed biophysical model of WDR neurons", CNS 2010, BMC Neuroscience 2010, 11(Suppl 1):O14, doi:10.1186/1471-2202-11-S1-O14

[10] Aguiar P*, Rodrigues M, "Neuronal connectivity inference from spike trains using an empirical probabilistic causality measure", CNS 2010, BMC Neuroscience 2009, 10(Suppl 1):P169, doi:10.1186/1471-2202-10-S1-P169

[9] Sousa M and Aguiar P*, "NetBuilder: a tool for constructing large and complex neural networks", Portuguese Society for Neurosciences Meeting 2009, doi: 10.3389/conf.neuro.01.2009.11.068

[8] Aguiar P*, "NeuralSyns: A Novel Tool For Simulating Large Neuronal Networks With Complex Architectures", Portuguese Society for Neurosciences Meeting 2009, doi: 10.3389/conf.neuro.01.2009.11.045

[7] Aguiar P*,"Functional model for nociceptive allodynia and hyperalgesia", COSYNE 2008

[6] Aguiar P* and Willshaw D, "Simulating large and heterogeneous networks of spiking neurons with SpiNet", CNS 2007, BMC Neuroscience 2007, 8(Suppl 2):P9, doi:10.1186/1471-2202-8-S2-P9

[5] Aguiar P*, "Hippocampal place cells and coding through constellations of active neurons", CNS 2006

[4] Aguiar P* and Willshaw D, "Hippocampal mossy fibres", CNS 2003

[3] Mourao A, Aguiar P, Cruz M and Lopes A, "Nearby Type Ia supernova searches: the Portuguese experience and plans for the future.", in Astronomy and Astrophysics: Recent developments, Proceedings of the 10th Portuguese Meeting in Astronomy and Astrophysics 2011, World Scientific 2001

[2] Cruz MJ, Aguiar P, Lopes AM and Mourao AM, "Type Ia Supernova", in "Simililarities and universality in relativistic flows", PhD Euroconference 2001, Logos Verlag Berlin, 2001.

[1] Aguiar P, Paulo S, David A and Rosa A, "EEGSolver - Brain Activity and Genetic Algorithms", ACM - Symposium on Applied Computing Proceedings 2000, Italy 2000;

Other Conferences [not updated]

[7] Sousa M, Antal Z, Conde-Sousa E, Aguiar P and Szucs P, "Distinct Patterns of Synaptic Integration in the Dendrites of Tonic Spinal Lamina I and Lateral Spinal Nucleus Neurons", IBRO Workshop 2014. January 16-17. Debrecen, Hungary.

[6] Sousa M, Szucs P and Aguiar P*, "Parameterization of ionic currents dynamics in tonic firing neurons of the dorsal reticular nucleus (DRt)", FENS 2012

[5] Szucs P, Luz L, Pinho R, Aguiar P, Antal Z, Tiong S, Todd A and Safronov B, "Morphological analysis of lamina I local-circuit neurons of the lumbar spinal cord", FENS 2012

[4] Sousa M and Aguiar P*, "Building complex neuronal network architectures with NetBuilder", FENS Abstr., vol.5, 207.7, FENS 2010

[3] Aguiar P*, Sousa M and Galhardo V, "Dependence of windup with substance P release dynamics: a detailed biophysical model approach", FENS Abstr., vol.4, 124.1, FENS 2008

[2] Aguiar P* and Galhardo V, "Computational model of nociceptive integration in laminae I and II", FENS Abstr., vol.3, A144.2, FENS 2006

[1] Aguiar P* and Willshaw D. "A General Model for Spatial Memory and Pattern Recognition", FENS 2004

Scientific Software

A more extensive list is presented under the tab Software

[4] Py3DN: morphometric analysis and visualization of the 3D structure of neurons, http://sourceforge.net/projects/py3dn/

[3] AxoFluidic: quantification of axonal plexus spatial coverage in microfluidic devices, http://tinyurl.com/AxoFluidic

[2] NeuralSyns: simulation environment for large and heterogeneous spiking networks, http://sourceforge.net/projects/neuralsyns/

[1] OpenControl: automation for behavioral neuroscience with video tracking and other tools, http://sourceforge.net/projects/opencontrol/

PhD Thesis

A General Hippocampal Computational Model: Combining Episodic and Spatial Memory in a Spiking Model - link

My complete CV is here.

ORCID: 0000-0003-4164-5713