Publications

Plaza-Alonso S, Cano-Astorga N, DeFelipe J, Alonso-Nanclares L. Volume electron microscopy reveals unique laminar synaptic characteristics in the human entorhinal cortex. Elife. 2025 Jan 30;14:e96144. https://doi.org/10.7554/eLife.96144

Gonzalez-Riano C, León-Espinosa G, Regalado-Reyes M, García A, DeFelipe J, Barbas C. Advanced lipidomics using UHPLC-ESI-QTOF-MS/MS reveals novel lipids in hibernating syrian hamsters. J Chromatogr A. 2025;1743:465692. https://doi.org/10.1016/j.chroma.2025.465692

Covelo J, Camassa A, Sanchez-Sanchez JM, Manasanch A, Porta LD, Cancino-Fuentes N, Barbero-Castillo A, Robles RM, Bosch M, Tapia-Gonzalez S, Merino-Serrais P, Carreño M, Conde-Blanco E, Arboix JR, Roldán P, DeFelipe J, Sanchez-Vives MV. Spatiotemporal network dynamics and structural correlates in the human cerebral cortex in vitro. Prog Neurobiol. 2025;246:102719. https://doi.org/10.1016/j.pneurobio.2025.102719

Merino-Serrais P, Soria JM, Arrabal CA, Ortigado-López A, Esparza MÁG, Muñoz A, Hernández F, Ávila J, DeFelipe J, León-Espinosa G. Protein tau phosphorylation in the proline rich region and its implication in the progression of Alzheimer’s disease. Exp Neurol. 2025;383:115049. https://doi.org/10.1016/j.expneurol.2024.115049

Makarova J, Toledano R, Blázquez-Llorca L, Sánchez-Herráez E, Gil-Nagel A, DeFelipe J, Herreras O. Intracranial Voltage Profiles from Untangled Human Deep Sources Reveal Multisource Composition and Source Allocation Bias. J Neurosci. 2025;45(1):e0695242024. https://doi.org/10.1523/JNEUROSCI.0695-24.2024

León-Espinosa G, Murillo AMM, Turegano-Lopez M, DeFelipe J, Holgado M. Phosphorylated Tau at T181 accumulates in the serum of hibernating Syrian hamsters and rapidly disappears after arousal. Sci Rep. 2024;14(1):20562. https://doi.org/10.1038/s41598-024-71481-5

Cano-Astorga N, Plaza-Alonso S, DeFelipe J, Alonso-Nanclares L (2024). Volume Electron Microscopy Analysis of Synapses in Primary Regions of the Human Cerebral Cortex. Cerebral Cortex 34 (8): bhae312. https://doi.org/10.1093/cercor/bhae312

Turegano-Lopez M, de Las Pozas F, Santuy A, Rodriguez JR, DeFelipe J, Merchan-Perez A (2024). Tracing nerve fibers with volume electron microscopy to quantitatively analyze brain connectivity. Commun Biol 7(1):796. https://doi.org/10.1038/s42003-024-06491-0

Benavides-Piccione R, Blazquez-Llorca L, Kastanauskaite A, Fernaud-Espinosa I, Tapia-González S, DeFelipe J (2024). Key morphological features of human pyramidal neurons. Cereb Cortex 34 (5): bhae180. https://doi.org/10.1093/cercor/bhae180

Cano-Astorga N, Plaza-Alonso S, Turegano-Lopez M, Rodrigo-Rodríguez J, Merchan-Perez A, DeFelipe J (2024). Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy. Front Neuroanat 18:1348032. https://doi.org/10.3389/fnana.2024.1348032

Mansur SS and DeFelipe J (2024). Empathy and the art of Leonardo da Vinci. Front. Psychol. 14:1260814. https://doi.org/10.3389/fpsyg.2023.1260814

Hunter D, DeFelipe J, Mehta AR, Conway BR (2024). Art, Intuition, and Identity in Ramón y Cajal. Neuroscientist. 10:10738584241234049. https://doi.org/10.1177/10738584241234049

Groden M, Moessinger HM, Schaffran B, DeFelipe J, Benavides-Piccione R, Cuntz H, Jedlicka P (2024). A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites. PLoS Comput Biol 20(2): e1011267. https://doi.org/10.1371/journal.pcbi.1011267

Masoli S, Sanchez-Ponce D, Vrieler N, Abu-Haya K, Lerner V, Shahar T, Nedelescu H, Rizza MF, Benavides-Piccione R, DeFelipe J, Yarom Y, Munoz A, D’Angelo E (2024). Human Purkinje cells outperform mouse Purkinje cells in dendritic complexity and computational capacity. Commun Biol. 2024 7(1):5. https://doi.org/10.1038/s42003-023-05689-y

Cano-Astorga N, Plaza-Alonso S, DeFelipe J, Alonso-Nanclares L (2023). 3D synaptic organization of layer III of the human anterior cingulate and temporopolar cortex. Cerebral Cortex 33: 9691–9708. https://doi.org/10.1093/cercor/bhad232

Mansur SS, DeFelipe J (2023). Empathy and the art of Leonardo da Vinci. Front. Psychol. 14:1260814. https://doi:10.3389/fpsyg.2023.1260814

Merino-Serrais P, Plaza-Alonso S, Hellal F, Valero-Freitag S, Kastanauskaite A, Plesnila N, DeFelipe J (2023). Structural changes of CA1 pyramidal neurons after stroke in the contralesional hippocampus. Brain Pathology 2023, e13222.  https://doi.org/10.1111/bpa.13222

Tapia-González S, DeFelipe J (2023). Secretagogin as a marker to distinguish between different neuron types in human frontal and temporal cortex. Front Neuroanat.17:1210502. https://doi:10.3389/fnana.2023.1210502

DeFelipe J (2023). Neuroanatomical data collection and usability. Front. Neuroanat. 17:1183883. https://doi:10.3389/fnana.2023.1183883

Insausti R, Insausti AM, Muñoz López M, Medina Lorenzo I, Arroyo-Jiménez MM, Marcos Rabal MP, de la Rosa-Prieto C, Delgado-González JC, Montón Etxeberria J, Cebada-Sánchez S, Raspeño-García JF, Iñiguez de Onzoño MM, Molina Romero FJ, Benavides-Piccione R, Tapia-González S, Wisse LEM, Ravikumar S, Wolk DA, DeFelipe J, Yushkevich P, Artacho-Pérula E (2023). Ex vivo, in situ perfusion protocol for human brain fixation compatible with microscopy, MRI techniques, and anatomical studies. Front. Neuroanat. 17:1149674. https://doi:10.3389/fnana.2023.1149674

Alonso-Nanclares L, Rodríguez JR, Merchan-Perez A, González-Soriano J, Plaza-Alonso S, Cano-Astorga N, Naumann RK, Brecht M, DeFelipe J (2023). Cortical synapses of the world’s smallest mammal: An FIB/SEM study in the Etruscan shrew. J Comp Neurol. 531:390- 414. https://doi:10.1002/cne.25432

DeFelipe J, DeFelipe-Oroquieta J, Furcila D, Muñoz-Alegre M, Maestú F, Sola RG, Blázquez-Llorca L, Armañanzas R, Kastanauskaite A, Alonso-Nanclares L, Rockland KS and Arellano JI (2022). Neuroanatomical and psychological considerations in temporal lobe epilepsy. Front. Neuroanat. 16:995286. https://doi:10.3389/fnana.2022.995286

Ostos S, Aparicio G, Fernaud-Espinosa I, DeFelipe J, Muñoz A (2022). Quantitative analysis of the GABAergic innervation of the soma and axon initial segment of pyramidal cells in the human and mouse neocortex. Cereb Cortex bhac314. https://doi:10.1093/cercor/bhac314

Bulovaite E, Qiu Z, Kratschke M, Zgraj A, Fricker DG, Tuck EJ, Gokhale R, Koniaris B, Jami SA, Merino-Serrais P, Husi E, Mendive-Tapia L, Vendrell M, O’Dell TJ, DeFelipe J, Komiyama NH, Holtmaat A, Fransén E, Grant SGN (2022). A brain atlas of synapse protein lifetime across the mouse lifespan. Neuron S0896-6273(22)00814-5. https://doi:10.1016/j.neuron.2022.09.009

DeFelipe J (2022). Manifesto of a neuroanatomist. Front. Neuroanat. 16:931547. https://www.frontiersin.org/articles/10.3389/fnana.2022.931547/full

Hunt S, Leibner Y, Mertens EJ, Barros-Zulaica N, Kanari L, Heistek TS, Karnani MM, Aardse R,Wilbers R, Heyer DB, Goriounova NA, Verhoog MB, Testa-Silva G, Obermayer J, Versluis T, Benavides-Piccione R, de Witt-Hamer P, Idema S, Noske DP, Baayen JC, Lein ES, DeFelipe J, Markram H, Mansvelder HD, Schürmann F, Segev I, de Kock CPJ (2022). Strong and reliable 33 synaptic communication between pyramidal neurons in adult human cerebral cortex. Cereb Cortex. bhac246. https://doi:10.1093/cercor/bhac246

Chindemi G, Abdellah M, Amsalem O, Benavides-Piccione R, Delattre V, Doron M, Ecker A, King J, Kumbhar P, Monney C, Perin R, Rössert C, Van Geit W, DeFelipe J, Graupner M, Segev I, Markram H, Muller E. (2022). A calcium-based plasticity model predicts long-term potentiation and depression in the neocortex. Nat Commun 13, 3038. https://doi.org/10.1038/s41467-022-30214-w

Antón-Fernández A, León-Espinosa,G, DeFelipe J, Muñoz A (2022). Pyramidal cell axon initial segment in Alzheimer´s disease. Sci Rep 12, 8722. https://doi.org/10.1038/s41598-022-12700-9

Turegano-Lopez M, Santuy A, Kastanauskaite A, Rodriguez JR, DeFelipe J, Merchan-Perez A (2022). Single-neuron labeling in fixed tissue and targeted volume electron microscopy. Front Neuroanat. 16:852057. https://doi:10.3389/fnana.2022.852057

Merino-Serrais P, Plaza-Alonso S, Hellal F, Valero-Freitag S, Kastanauskaite A, Muñoz A, Plesnila N, DeFelipe J (2022). Microanatomical study of pyramidal neurons in the contralesional somatosensory cortex after experimental ischemic stroke. Cereb Cortex bhac121. https://doi:10.1093/cercor/bhac121.

Amunts K, DeFelipe J, Pennartz C, Destexhe A, Migliore M, Ryvlin P, Furber S, Knoll A, Bitsch L, Bjaalie JG, Ioannidis Y, Lippert T, Sanchez-Vives MV, Goebel R, Jirsa V (2022). Linking brain structure, activity and cognitive function through computation. eNeuro. ENEURO.0316- 21.2022. https://doi:10.1523/ENEURO.0316-21.2022

Vidaurre-Gallart I, Fernaud-Espinosa I, Cosmin-Toader N, Talavera-Martínez L, Martin-Abadal M, Benavides-Piccione R, Gonzalez-Cid Y, Pastor L, DeFelipe J and García-Lorenzo M (2022) A deep learning-based workflow for dendritic spine segmentation. Front. Neuroanat. 16:817903. https://doi:10.3389/fnana.2022.817903

Luján R, Merchán-Pérez A, Soriano J, Martín-Belmonte A, Aguado C, Alfaro-Ruiz R, MorenoMartínez AE and DeFelipe J (2021) Neuron class and target variability in the three-dimensional localization of sk2 channels in hippocampal neurons as detected by immunogold FIB-SEM. Front. Neuroanat. 15:781314. https://doi:10.3389/fnana.2021.781314

LaTorre A, Alonso-Nanclares L, Peña JM, DeFelipe J (2021) 3D segmentation of neuronal nuclei and cell-type identification using multi-channel information. Expert Syst Appl. 183:115443. https://doi.org/10.1016/j.eswa.2021.115443

Domínguez-Álvaro M, Montero-Crespo M, Blazquez-Llorca L, Plaza-Alonso S, Cano-Astorga N, DeFelipe J, Alonso-Nanclares L (2021) 3D analysis of the synaptic organization in the entorhinal cortex in Alzheimer’s disease. eNeuro.0504-20.2021. https://doi.org/10.1523/ENEURO.0504-20

Maestú F, de Haan W, Busche MA, DeFelipe J. 2021. Neuronal excitation/inhibition imbalance: core element of a translational perspective on Alzheimer pathophysiology. Ageing Research Reviews. 69:101372. https://doi.org/10.1016/j.arr.2021.101372

Cano-Astorga N, DeFelipe J, Alonso-Nanclares L (2021) Three-dimensional synaptic organization of layer III of the human temporal neocortex. Cereb Cortex bhab120. https://doi.org/10.1093/cercor/bhab120

Benavides-Piccione R, Rojo C, Kastanauskaite A, DeFelipe J (2021) Variation in pyramidal cellmorphology across the human anterior temporal lobe. Cereb cortex 31(8):3592–3609. https://doi.org/10.1093/cercor/bhab034

Gonzalez-Riano C, Tapia-González S, Perea G, González-Arias C, DeFelipe J, Barbas C (2021) Metabolic changes in brain slices over time: a multiplatform metabolomics approach. Mol Neurobiol. 58:3224–3237. https://doi.org/10.1007/s12035-020-02264-y32

Blazquez-Llorca L, Miguéns M, Montero-Crespo M, Selvas A, Gonzalez-Soriano J, Ambrosio E, DeFelipe J (2021) 3D synaptic organization of the rat CA1 and alterations induced by cocaine self-administration. Cereb Cortex. 31(4):1927-1952. https://doi.org/10.1093/cercor/bhaa331

Loera-Valencia R, Vazquez-Juarez E, Muñoz A, Gerenu G, Gómez-Galán M, Lindskog M, DeFelipe J, Cedazo-Minguez A, Merino-Serrais P (2021) High levels of 27-hydroxycholesterol results in synaptic plasticity alterations in the hippocampus. Sci Rep. 11(1):3736. https://doi.org/10.1038/s41598-021-83008-3

Montero-Crespo M, Domínguez-Álvaro M, Alonso-Nanclares L, DeFelipe J, Blazquez-Llorca L (2021) Three-dimensional analysis of synaptic organization in the hippocampal CA1 region in Alzheimer’s disease. Brain. 144(2):553-573. https://doi.org/10.1093/brain/awaa406

DeFelipe J, De Carlos JA, Metha AR (2021) A museum for Cajal’s Legacy. The Lancet Neurology.20(1):25. https://doi.org/10.1016/S1474-4422(20)30444-0

Domínguez-Álvaro M, Montero-Crespo L Blazquez-Llorca, DeFelipe J, Alonso-Nanclares L (2021) 3D Ultrastructural study of synapses in the human entorhinal cortex. Cereb Cortex. 31:410–425. https://doi.org/10.1093/cercor/bhaa233

Regalado-Reyes M, Benavides-Piccione R, Fernaud-Espinosa I, DeFelipe J, León-Espinosa G (2020) Effect of phosphorylated tau on cortical pyramidal neuron morphology during hibernation. Cereb Cortex Communications. 1:1-25. https://doi.org/10.1093/texcom/tgaa018

Velasco I, Toharia P, Benavides-Piccione R, Fernaud-Espinosa I, Brito JP, Mata S, DeFelipe J, Pastor L, Bayona S (2020) Neuronize v2: bridging the gap between existing proprietary tools to optimize neuroscientific workflows. Front Neuroanat. 14:585793. https://doi.org/10.3389/fnana.2020.585793

Santuy A, Tomás-Roca L, Rodríguez JR, González-Soriano J, Zhu F, Qiu Z, Grant SGN, DeFelipe J, Merchan-Perez A (2020) Estimation of the number of synapses in the hippocampus and brainwide by volume electron microscopy and genetic labeling. Sci Rep. 10(1):14014. https://doi.org/10.1038/s41598-020-70859-5

Mihaljević B, Larrañaga P, Benavides-Piccione R, DeFelipe J, Bielza C (2020) Comparing basal dendrite branches in human and mouse hippocampal CA1 pyramidal neurons with Bayesian networks. Sci Rep. 10(1):18592. https://doi.org/10.1038/s41598-020-73617-9

Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, et al  (2020) A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci. 23:1456- 1468. https://dx.doi.org/10.1038%2Fs41593-020-0685-8

Rodriguez-Moreno J, Porrero C, Rollenhagen A, Rubio-Teves M, et al (2020) Area-specific synapse structure in branched posterior nucleus axons reveals a new level of complexity in thalamocortical networks. J Neurosci. 40:2663 2679. https://doi.org/10.1523/JNEUROSCI.2886-19.2020

Montero-Crespo M, Domínguez-Álvaro M, Rondón-Carrillo P, Alonso-Nanclares L, DeFelipe J, Blázquez-Llorca L (2020) Three-dimensional synaptic organization of the human hippocampal CA1 field. eLife 2020;9:e57013. https://doi.org/10.7554/eLife.57013

Kikuchi T, Gonzalez-Soriano J, Kastanauskaite A, Benavides-Piccione R, Merchan-Perez A, DeFelipe J, Blazquez-Llorca L (2020) Volume electron microscopy study of the relationship between synapses and astrocytes in the developing rat somatosensory cortex. Cereb Cortex. 30:3800–3819. https://doi.org/10.1093/cercor/bhz343

Merino-Serrais P, Tapia-González S, DeFelipe J (2020) Calbindin immunostaining in the CA1 hippocampal pyramidal cell layer of the human and mouse: A comparative study. J Chem Neuroanat. 104:101745. https://doi.org/10.1016/j.jchemneu.2020.101745

Turegano-Lopez M, Santuy A, DeFelipe J, Merchan-Perez A (2020) Size, shape, and distribution of multivesicular bodies in the juvenile rat somatosensory cortex: A 3D electron microscopy study. Cereb Cortex. 30:1887-1901. http://dx.doi.org/10.1093/cercor/bhz211

Benavides-Piccione R, Regalado-Reyes M, Fernaud-Espinosa I, Kastanauskaite A, TapiaGonzález S, León-Espinosa G, Rojo C, Insausti R, Segev I, DeFelipe J (2020) Differential structure of hippocampal CA1 pyramidal neurons in the human and mouse. Cereb Cortex 30:730- 752. https://doi.org/10.1093/cercor/bhz122

Tapia-González S, Insausti R, DeFelipe J (2019) Differential expression of secretagogin immunostaining in the hippocampal formation and the entorhinal and perirhinal cortices of humans, rats, and mice. J Comp Neurol 528:523-541. https://doi.org/10.1002/cne.24773

Mihaljević B, Benavides-Piccione R, Bielza C, Larrañaga P, DeFelipe J (2019) Classification of GABAergic interneurons by leading neuroscientists. Sci Data. 26(1):221. https://doi.org/10.1038/s41597-019-0246-8

Ortuño T, López-Madrona VJ, Makarova J, Tapia-González S, Muñoz A, DeFelipe J, Herreras O. 019. Slow-wave activity in the S1hl cortex is contributed by different layer-specific field potential sources during development. J Neurosci. 39:8900–8915. https://doi.org/10.1523/jneurosci.1212-19.2019

Furcila D, Domínguez-Álvaro M, DeFelipe J, Alonso-Nanclares L (2019) Subregional density of neurons, neurofibrillary tangles and amyloid plaques in the hippocampus of patients with Alzheimer’s disease. Front Neuroanat. 13:99. https://doi.org/10.3389/fnana.2019.00099

Domínguez-Álvaro M, Montero-Crespo M, Blázquez-Llorca L, DeFelipe J, Alonso-Nanclares L (2019) 3D electron microscopy study of synaptic organization of the normal human transentorhinal cortex and its possible alterations in Alzheimer’s disease. eNeuro. pii: ENEURO.0140-19.2019 https://doi.org/10.1523/eneuro.0140-19.2019

Regalado-Reyes M, Furcila D, Hernández F, Ávila J, DeFelipe J, León-Espinosa G (2019) Phospho-tau changes in the human CA1 during Alzheimer’s disease progression. J Alzheimers Dis, 69(1): 277–288. https://doi.org/10.3233/JAD-181263

Leguey I, Benavides-Piccione R, Rojo C, Larrañaga P, Bielza C, DeFelipe J (2019) Patterns of dendritic basal field orientation of pyramidal neurons in the rat somatosensory cortex. eNeuro, 5(6), ENEURO.0142-18.2018. https://doi.org/10.1523/eneuro.0142-18.2018

León-Espinosa G, DeFelipe J, Muñoz A (2019) The Golgi apparatus of neocortical glial cells during hibernation in the Syrian hamster. Front Neuroant.13: 92. https://doi.org/10.3389/fnana.2019.00092

Gonzalez-Riano C, Leon-Espinosa G, Regalado-Reyes M, García A, DeFelipe J, Barbas C (2019) A Metabolomic study of hibernating Syrian hamster brain: in search of neuroprotective agents J Proteome Res. 18:1175–1190 https://doi.org/10.1021/acs.jproteome.8b00816

Kwon T, Merchán-Pérez A, Rial Verde EM, Rodríguez JR, DeFelipe J, Yuste R (2019) Ultrastructural, molecular and functional mapping of GABAergic synapses on dendritic spines and shafts of neocortical pyramidal neurons. Cereb Cortex 29:2771–2781. https://doi.org/10.1093/cercor/bhy143

Aliaga Maraver JJ, Mata S, Benavides-Piccione R, DeFelipe, J, Pastor L (2018) A Method for the symbolic representation of neurons. Front Neuroanat. 12:106. https://doi.org/10.3389/fnana.2018.00106

Mihaljević B,Larrañaga, P, Benavides-Piccione R, Hill S, DeFelipe J, & Bielza C (2018) Towards a supervised classification of neocortical interneuron morphologies. BMC bioinformatics, 19(1), 511. https://doi.org/10.1186/s12859-018-2470-1

Merino-Serrais P, Loera-Valencia R, Rodriguez-Rodriguez P, Parrado-Fernandez C, Ismail MA, Maioli S, Matute E, Jimenez-Mateos EM, Björkhem I, DeFelipe J, Cedazo-Minguez A (2018) 27- Hydroxycholesterol induces aberrant morphology and synaptic dysfunction in hippocampal neurons. Cereb Cortex 29:429-446. https://doi.org/10.1093/cercor/bhy274

Rockland KS and DeFelipe J (2018) Editorial: Why Have Cortical Layers? What Is the function of layering? Do neurons in cortex integrate information across different layers? Front Neuroanat. 12:78. https://doi.org/10.3389/fnana.2018.00078

León-Espinosa G, Antón-Fernández A, Tapia-González S, DeFelipe J, Muñoz A (2018) Modifications of the axon initial segment during the hibernation of the Syrian hamster. Brain Struct Funct. 223:4307-4321. https://doi.org/10.1007/s00429-018-1753-7

Zhu F, Cizeron M, Qiu Z, Benavides-Piccione R, Kopanitsa MV, Skene NG, Koniaris B, DeFelipe J, Fransén E, Komiyama NH3, Grant SGN (2018) Architecture of the mouse brain synaptome. Neuron 99:781-799. https://doi.org/10.1016/j.neuron.2018.07.007

Santuy A, Turégano-López M1, Rodríguez JR, Alonso-Nanclares L, DeFelipe J, Merchán-Pérez A  (2018) A Quantitative study on the distribution of mitochondria in the neuropil of the juvenile rat somatosensory cortex. Cereb Cortex 28:3673–3684. http://dx.doi.org/10.1093/cercor/bhy159

Roy M, Sorokina O, McLean C, Tapia-González S, DeFelipe J, Armstrong JD, Grant SGN (2018) Regional diversity in the postsynaptic proteome of the mouse brain. Proteomes. https://doi.org/10.3390/proteomes6030031

Eyal G, Verhoog MB, Testa-Silva G, Deitcher Y, Benavides-Piccione R, DeFelipe J, de Kock CPJ, Mansvelder HD, Segev I (2018) Human cortical pyramidal neurons: from spines to spikes via models. Front Cell Neurosci. 12:181. https://doi.org/10.3389/fncel.2018.00181

Fernández-Cabrera MR, Higuera-Matas A, Fernaud-Espinosa I, DeFelipe J, Ambrosio E, Miguéns  M (2018)Selective effects of Δ9-tetrahydrocannabinol on medium spiny neurons inthe striatum. PLoS One. https://doi.org/10.1371/journal.pone.0200950

Furcila D, DeFelipe J, Alonso-Nanclares L (2018) A Study of Amyloid-β and Phosphotau in Plaques and Neurons in the Hippocampus of Alzheimer’s Disease Patients. J Alzheimers Dis. 64:417-435. https://doi.org/10.3233/jad-180173

Luengo-Sanchez S, Fernaud-Espinosa I, Bielza C, Benavides-Piccione R, Larrañaga P, DeFelipe J (2018) 3D morphology-based clustering and simulation of human pyramidal cell dendritic spines. PLoS Comput Biol. 14(6):e1006221. https://doi.org/10.1371/journal.pcbi.1006221

Varando G, Benavides-Piccione R, Muñoz A, Kastanauskaite A, Bielza C, Larrañaga P, DeFelipe J (2018) MultiMap: A tool to automatically extract and analyse spatial microscopic data from large stacks of confocal microscopy images. Front. Neuroanat. 12:37. https://doi.org/10.3389/fnana.2018.00037

Rodríguez J-R, Turégano-López M, DeFelipe J and Merchán-Pérez A (2018) Neuroanatomy from mesoscopic to nanoscopic scales: An improved method for the observation of semithin sections by high-resolution scanning electron microscopy. Front. Neuroanat. 12:14. https://doi.org/10.3389/fnana.2018.00014

Domínguez-Álvaro M,Montero-Crespo M, Blázquez-Llorca L, Insausti R, DeFelipe J, AlonsoNanclares L (2018) Three-dimensional analysis of synapses in the transentorhinal cortex of Alzheimer’s disease patients. Acta Neuropathol Commun. 6:20. https://doi.org/10.1186/s40478-018-0520-6

Santuy A, Rodríguez JR, DeFelipe J, Merchán-Pérez A (2018) Study of the size and shape of synapses in the juvenile rat somatosensory cortex with 3D Electron Microscopy. eNeuro 5(1), ENEURO.0377-17.2017. https://doi.org/10.1523/eneuro.0377-17.2017

Santuy A, Rodriguez JR, DeFelipe J, Merchan-Perez A (2018) Volume electron microscopy of the distribution of synapses in the neuropil of the juvenile rat somatosensory cortex. Brain Struct Funct. 223:77-90. https://doi.org/10.1007/s00429-017-1470-7

León-Espinosa G, Regalado-Reyes M, DeFelipe J, Muñoz A (2018) Changes in neocortical and hippocampal microglial cells during hibernation. Brain Struct Funct. 223:1881–1895. https://doi.org/10.1007/s00429-017-1596-7

Antón-Fernández A, Aparicio-Torres G, Tapia-González S, DeFelipe J, Muñoz A (2017). Morphometric alterations of Golgi apparatus in Alzheimer’s disease are related to tau hyperphosphorylation. Neurobiol Dis. 97(Pt A):11-23. https://doi.org/10.1016/j.nbd.2016.10.005

Antón-Fernández A, Merchán-Rubira J, Avila J, Hernández F, DeFelipe J, Muñoz A (2017) Phospho-Tau accumulation and structural alterations of the Golgi apparatus of cortical pyramidal neurons in the p301s tauopathy mouse model. J Alzheimers Dis. 60:651-661. https://doi.org/10.3233/jad-17033229

Rodriguez-Moreno J, Rollenhagen A, Arlandis J, Santuy A, Merchán-Pérez A, DeFelipe J, Lübke JHR, Clasca F. (2017) Quantitative 3D ultrastructure of thalamocortical synapses from the “lemniscal” ventral posteromedial nucleus in mouse barrel cortex. Cereb Cortex. 28: 3159-3175. https://doi.org/10.1093/cercor/bhx187

Blazquez-Llorca L, Valero-Freitag S, Rodrigues EF, Merchán-Pérez A, Rodríguez JR, Dorostkar MM, DeFelipe J, Herms J (2017) High plasticity of axonal pathology in Alzheimer’s disease mouse models. Acta Neuropathol Commun. 5(1):14. http://doi.org/10.1186/s40478-017-0415-y

DeFelipe J (2017) Neuroanatomy and Global Neuroscience. Neuron. 2017 Jul 5;95(1):14-18. https://doi.org/10.1016/j.neuron.2017.05.027

Anton-Sanchez L, Larrañaga P, Benavides-Piccione R, Fernaud-Espinosa I, DeFelipe J, Bielza C (2017) Three-dimensional spatial modeling of spines along dendritic networks in human cortical pyramidal neurons. PLoS One. 12(6):e0180400. https://doi.org/10.1371/journal.pone.0180400

Gonzalez-Riano C, Tapia-González S, García A, Muñoz A, DeFelipe J, Barbas C (2017) Metabolomics and neuroanatomical evaluation of post-mortem changes in the hippocampus. Brain Struct Funct. 222:2831-2853. https://doi.org/10.1007/s00429-017-1375-5

Pallas-Bazarra N, Kastanauskaite A, Avila J, DeFelipe J, Llorens-Martín M (2017) GSK-3β Overexpression Alters the Dendritic Spines of Developmentally Generated Granule Neurons in the Mouse Hippocampal Dentate Gyrus. Front Neuroanat. 11:18. https://doi.org/10.3389/fnana.2017.00018

Urrecha M, Romero I1, DeFelipe J, Merchán-Pérez A (2017) Influence of cerebral blood vessel movements on the position of perivascular synapses. PLoS One.12(2):e0172368. https://doi.org/10.1371/journal.pone.0172368

Fernandez-Gonzalez P, Benavides-Piccione R, Leguey I, Bielza C, Larrañaga P, DeFelipe J. (2017). Dendritic-branching angles of pyramidal neurons of the human cerebral cortex. Brain Struct Funct. 222:1847-1859. https://doi.org/10.1007/s00429-016-1311-0

Eyal G, Verhoog MB, Testa-Silva G, Deitcher Y, Lodder JC, Benavides-Piccione R, Morales J, DeFelipe J, de Kock CP, Mansvelder HD, Segev I (2016) Unique membrane properties and enhanced signal processing in human neocortical neurons. eLife, 5, e16553. http://doi.org/10.7554/eLife.16553.

 Bosch C, Masachs N, Exposito-Alonso D, Martínez A, Teixeira CM, Fernaud I, Pujadas L, Ulloa F, Comella JX, DeFelipe J, Merchán-Pérez A, Soriano E. (2016). Reelin regulates the maturation of dendritic spines, synaptogenesis and glial ensheathment of newborn granule cells. Cereb Cortex. 26:4282-4298. https://doi.org/10.1093/cercor/bhw216

Barth A, Burkhalter A, Callaway EM, Connors BW, Cauli B, DeFelipe J, Feldmeyer D, Freund T,Kawaguchi Y, Kisvarday Z, Kubota Y, McBain C, Oberlaender M, Rossier J, Rudy B, Staiger JF,Somogyi P, Tamas G, Yuste R (2016) Comment on “Principles of connectivity among morphologically defined cell types in adult neocortex”. Science. 2016 Sep 9;353(6304):1108. https://doi.org/10.1126/science.aaf5663

León-Espinosa G, García E, Gómez-Pinedo U, Hernández F, DeFelipe J, Ávila J (2016) Decreased adult neurogenesis in hibernating Syrian hamster. Neuroscience. 333:181-92. https://doi.org/10.1016/j.neuroscience.2016.07.016

DeFelipe J, Douglas RJ, Hill SL, Lein ES, Martin KA, Rockland KS, Segev I, Shepherd GM,Tamás G. (2016) Comments and General Discussion on “The Anatomical Problem Posed by Brain Complexity and Size: A Potential Solution”. Front Neuroanat. 10:60. https://dx.doi.org/10.3389%2Ffnana.2016.0006028

Anton-Sanchez L, Bielza C, Benavides-Piccione R, DeFelipe J, Larrañaga P (2016) Dendritic and Axonal Wiring Optimization of Cortical GABAergic Interneurons. Neuroinformatics. 14:453-64. https://doi.org/10.1007/s12021-016-9309-6

DeFelipe J (2016). Phospho-Tau and cognitive decline in alzheimer’s disease. Commentary: Tau in physiology and pathology. Front Neuroanat. 10:44. https://doi.org/10.3389/fnana.2016.00044

Broadhead MJ, Horrocks MH, Zhu F, Muresan L, Benavides-Piccione R, DeFelipe J, Fricker D, Kopanitsa MV, Duncan RR, Klenerman D, Komiyama NH, Lee SF, Grant SG (2016) PSD95 nanoclusters are postsynaptic building blocks in hippocampus circuits. Sci Rep. 6:24626. https://doi.org/10.1038/srep24626

Mellström B, Kastanauskaite A, Knafo S, Gonzalez P, Dopazo XM, Ruiz-Nuño A, Jefferys JG,Zhuo M, Bliss TV, Naranjo JR, DeFelipe J (2016). Specific cytoarchitectureal changes in hippocampal subareas in daDREAM mice. Mol Brain. 9,22. https://doi.org/10.1186/s13041-016-0204-8

Rábano A, Cuadros R, Merino-Serráis P, Rodal I, Benavides-Piccione R, Gómez E, Medina M,DeFelipe J, Avila J (2016) Protocols for monitoring the development of tau pathology in Alzheimer’s disease. Methods Mol Biol. 1303:143-60. https://doi.org/10.1007/978-1-4939-2627-5_7

Rockland KS, DeFelipe J (2016) Editorial: Neuroanatomy for the XXIst Century. Front Neuroanat.10:70. https://doi.org/10.3389/fnana.2016.00070

Leguey I, Bielza C, Larrañaga P, Kastanauskaite A, Rojo C, Benavides-Piccione R, DeFelipe J(2016) Dendritic branching angles of pyramidal cells across layers of the juvenile ratsomatosensory cortex. J Comp Neurol. 524:2567-2576. https://doi.org/10.1002/cne.23977

Toharia P, Robles OD, Fernaud-Espinosa I, Makarova J, Galindo SE, Rodriguez A, Pastor L,Herreras O, DeFelipe J, Benavides-Piccione R (2016) PyramidalExplorer: A new interactive toolto explore morpho-functional relations of human pyramidal neurons. Front Neuroanat. 9:159. https://doi.org/10.3389/fnana.2015.00159

Rojo C, Leguey I, Kastanauskaite A, Bielza C, Larrañaga P, DeFelipe J, Benavides-Piccione R(2016) Laminar differences in dendritic structure of pyramidal neurons in the juvenile rat somatosensory cortex. Cereb Cortex. 26:2811–2822 https://doi.org/10.1093/cercor/bhv316

Márquez-Neila P, Baumela L, González-Soriano J, Rodríguez JR, DeFelipe J, Merchán-Pérez A (2016) A Fast method for the segmentation of synaptic junctions and mitochondria in serial electron microscopic images of the brain. Neuroinformatics 14:235–250. https://doi.org/10.1007/s12021-015-9288-z

Antón-Fernández A, León-Espinosa G, DeFelipe J, Muñoz A (2015) Changes in the Golgiapparatus of neocortical and hippocampal neurons in the hibernating hamster. Front Neuroanat.9:157. https://doi.org/10.3389/fnana.2015.001572016

Luengo-Sanchez S, Bielza C, Benavides-Piccione R, Fernaud-Espinosa I, DeFelipe J, Larrañaga P (2015) A univocal definition of the neuronal soma morphology using Gaussian mixture models.Front Neuroanat. 9:137. https://doi.org/10.3389/fnana.2015.00137

Chamorro-López J, Miguéns M, Morgado-Bernal I, Kastanauskaite A, Selvas A, CabanéCucurella A, Aldavert-Vera L, DeFelipe J, Segura-Torres P (2015). Structural plasticity in hippocampal cells related to the facilitative effect of intracranial self-stimulation on a spatial memory task. Behav Neurosci. 129:720-730. https://doi.org/10.1037/bne0000098

Ramaswamy S, Courcol JD, Abdellah M, Adaszewski SR, Antille N, Arsever S, Atenekeng G,Bilgili A, Brukau Y, Chalimourda A, Chindemi G, Delalondre F, Dumusc R, Eilemann S, GevaertME, Gleeson P, Graham JW, Hernando JB, Kanari L, Katkov Y, Keller D, King JG, Ranjan R,Reimann MW, Rössert C, Shi Y, Shillcock JC, Telefont M, Van Geit W, Villafranca Diaz J,Walker R, Wang Y, Zaninetta SM, DeFelipe J, Hill SL, Muller J, Segev I, Schürmann F, MullerEB, Markram H (2015). The neocortical microcircuit collaboration portal: a resource for ratsomatosensory cortex. Front Neural Circuits. 9:44. https://doi.org/10.3389/fncir.2015.0004427

Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N,Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R,Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, HaenelV, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y,King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Bé JV, Magalhães BR, Merchán-Pérez A,Meystre J, Morrice BR, Muller J, Muñoz-Céspedes A, Muralidhar S, Muthurasa K, NachbaurD, Newton TH, Nolte M, Ovcharenko A, Palacios J, Pastor L, Perin R, Ranjan R, Riachi I,Rodríguez JR, Riquelme JL, Rössert C, Sfyrakis K, Shi Y, Shillcock JC, Silberberg G, Silva R,Tauheed F, Telefont M, Toledo-Rodriguez M, Tränkler T, Van Geit W, Díaz JV, Walker R,Wang Y, Zaninetta SM, DeFelipe J, Hill SL, Segev I, Schürmann F (2015) Reconstruction andSimulation of Neocortical Microcircuitry. Cell.163:456-92. https://doi.org/10.1016/j.cell.2015.09.029

DeFelipe J (2015) The anatomical problem posed by brain complexity and size: a potential solution. Front Neuroanat. 9:104. https://dx.doi.org/10.3389%2Ffnana.2015.00104

Selvas A, Coria SM, Kastanauskaite A, Fernaud-Espinosa I, DeFelipe J, Ambrosio E, Miguéns M (2015) Rat-strain dependent changes of dendritic and spine morphology in the hippocampus after cocaine self-administration. Addict Biol. 22:78-92. https://doi.org/10.1111/adb.12294

Montes J, Peña JM, DeFelipe J, Herreras O, Merchan-Perez A (2015) The influence of synaptic size on AMPA receptor activation: a Monte Carlo model. PLoS One. 10(6):e0130924. https://doi.org/10.1371/journal.pone.0130924

Bosch C, Martínez A, Masachs N, Teixeira CM, Fernaud I, Ulloa F, Pérez-Martínez E, Lois C,Comella JX, DeFelipe J, Merchán-Pérez A, Soriano E (2015) FIB/SEM technology and highthroughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons. Front Neuroanat. 9: 60. https://doi.org/10.3389/fnana.2015.00060

Íbias J, Soria-Molinillo E, Kastanauskaite A, Orgaz C, DeFelipe J, Pellón R, Miguéns M (2015) Schedule-induced polydipsia is associated with increased spine density in dorsolateral striatum neurons. Neuroscience. 300:238-245 https://doi.org/10.1016/j.neuroscience.2015.05.026

DeFelipe J (2015) The dendritic spine story: an intriguing process of discovery. Front Neuroanat.9:14. https://doi.org/10.3389/fnana.2015.00014

Mihaljevic B, Benavides-Piccione R, Guerra L, DeFelipe J, Larrañaga P, Bielza C (2015) Classifying GABAergic interneurons with semi-supervised projected model-based clustering. Artif Intell Med. 65: 49-59. https://doi.org/10.1016/j.artmed.2014.12.010

Blazquez-Llorca L, Woodruff A, Inan M, Anderson SA, Yuste R, DeFelipe J, Merchan-Perez A(2015) Spatial distribution of neurons innervated by chandelier cells. Brain Struct Funct. 220:2817-2834 https://doi.org/10.1007/s00429-014-0828-3

Mihaljević B, Benavides-Piccione R, Bielza C, DeFelipe J, Larrañaga P (2015) Bayesian network classifiers for categorizing cortical GABAergic interneurons. Neuroinformatics. 13:193-208. https://doi.org/10.1007/s12021-014-9254-126

Jimenez-Mateos EM, Engel T, Merino-Serrais P, Fernaud-Espinosa I, Rodriguez-Alvarez N,Reynolds J, Reschke CR, Conroy RM, McKiernan RC, DeFelipe J, Henshall DC (2015)Antagomirs targeting microRNA-134 increase hippocampal pyramidal neuron spine volume invivo and protect against pilocarpine-induced status epilepticus. Brain Struct Funct. 220: 2387-99. https://doi.org/10.1007/s00429-014-0798-5

Miguéns M, Kastanauskaite A, Coria SM, Selvas A, Ballesteros-Yañez I, DeFelipe J, Ambrosio E (2015) The effects of cocaine self-administration on dendritic spine density in the rat hippocampus are dependent on genetic background. Cereb Cortex. 25: 56-65. https://doi.org/10.1093/cercor/bht200

Antón-Fernández A, Rubio-Garrido P, DeFelipe J, Muñoz A (2015) Selective presence of a giant saccular organelle in the axon initial segment of a subpopulation of layer V pyramidal neurons. Brain Struct Funct. 220: 869-884. https://doi.org/10.1007/s00429-013-0689-1

Alonso-Nanclares L and DeFelipe J (2014). Alterations of the microvascular network in the sclerotic hippocampus of patients with temporal lobe epilepsy. Epilepsy Behav. 38:48-52. https://doi.org/10.1016/j.yebeh.2013.12.009

Merchán-Pérez A, Rodríguez JR, González S, Robles V, DeFelipe J, Larrañaga P, Bielza C (2014) Three-dimensional spatial distribution of synapses in the neocortex: a dual-beam electron microscopy study. Cereb Cortex 24:1579-1588. https://doi.org/10.1093/cercor/bht018

Ferreira FR, Nogueira MI, DeFelipe J (2014) The influence of James and Darwin on Cajal and his research into the neuron theory and evolution of the nervous system. Front Neuroanat. 8:1. https://doi.org/10.3389/fnana.2014.00001

Toharia P, Morales J, de Juan O, Fernaud I, Rodríguez A, DeFelipe J (2014) Musical representation of dendritic spine distribution: A new exploratory tool. Neuroinformatics. 12: 341-353. https://doi.org/10.1007/s12021-013-9195-0

Mellström B, Sahún I, Ruiz-Nuño A, Murtra P, Gomez-Villafuertes R, Savignac M, Oliveros JC, Gonzalez P, Kastanauskaite A, Knafo S, Zhuo M, Higuera-Matas A, Errington ML, Maldonado R, DeFelipe J, Jefferys JG, Bliss TV, Dierssen M, Naranjo JR (2014) DREAM controls the on/off switch of specific activity-dependent transcription pathways. Mol Cell Biol 34:877-887. https://doi.org/10.1128/mcb.00360-13

Llorens-Martín M, Blazquez-Llorca L, Benavides-Piccione R, Rabano A, Hernandez F, Avila J, DeFelipe J (2014) Selective alterations of neurons and circuits related to early memory loss in Alzheimer’s disease. Front Neuroanat. 8:38. https://doi.org/10.3389/fnana.2014.00038

Bielza C, Benavides-Piccione R, López-Cruz P, Larrañaga P, DeFelipe J (2014). Branching angles of pyramidal cell dendrites follow common geometrical design principles in different cortical areas. Sci Rep. 4:5909 https://doi.org/10.1038/srep05909

Morales J, Ruth Benavides-Piccione R, Dar M, Fernaud I, Rodríguez A, Anton-Sanchez L, Bielza C, Larrañaga P, DeFelipe J, Yuste R (2014) Random positioning of dendritic spines in the human cerebral cortex. J Neurosci. 34:10078-10084. https://doi.org/10.1523/jneurosci.1085-14.2014

Anton-Sanchez L, Bielza C, Merchán-Pérez A, Rodríguez J-R, DeFelipe J and Larrañaga P (2014) Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis. Front.Neuroanat. 8:85. https://doi.org/10.3389/fnana.2014.00085

DeFelipe J, Garrido E, Markram H (2014) The death of Cajal and the end of scientific romanticism and individualism. Trends Neurosci. 37: 525-527. https://doi.org/10.1016/j.tins.2014.08.002

Corenthy L, Garcia M, Bayona S, Santuy A, San Martin J, Benavides-Piccione R, DeFelipe J, Pastor L (2014) Haptically assisted connection procedure for the reconstruction of dendritic spines. IEEE Trans Haptics. 7: 486-498. https://doi.org/10.1109/TOH.2014.2354041

Mihaljević B, Bielza C, Benavides-Piccione R, DeFelipe J, Larrañaga P (2014) Multi-dimensional classification of GABAergic interneurons with Bayesian network-modeled label uncertainty. Front Comput Neurosci. 25; 8:150. https://doi.org/10.3389/fncom.2014.00150

Inan M, Blázquez-Llorca L, Merchán-Pérez A, Stewart A. Anderson SA, DeFelipe J, Yuste R (2013) Dense and overlapping innervation of pyramidal neurons by neocortical chandelier cells. J Neurosci 33:1907-14. https://doi.org/10.1523/jneurosci.4049-12.2013

DeFelipe J, López-Cruz PL, Benavides-Piccione R, Bielza C, Larrañaga P, Anderson S, Burkhalter A, Cauli B, Fairén A, Feldmeyer D, Fishell G, Fitzpatrick D, Freund TF, González-Burgos G, Hestrin S, Hill S, Hof PR, Huang J, Jones EG, Kawaguchi Y, Kisvárday Z, Kubota Y, Lewis DA, Marín O, Markram H, McBain CJ, Meyer HS, Monyer H, Nelson SB, Rockland K, Rossier J, Rubenstein JL, Rudy B, Scanziani M, Shepherd GM, Sherwood CC, Staiger JF, Tamás G, Thomson A, Wang Y, Yuste R, Ascoli GA (2013). New insights into the classification and nomenclature of cortical GABAergic interneurons. Nature Neurosci. 14:202-216. https://doi.org/10.1038/nrn3444

Llorens-Martín M, Fuster-Matanzo A, Teixeira CM, Jurado-Arjona J, Ulloa F, DeFelipe J, Rábano A, Hernández F, Soriano E, Avila J (2013) GSK-3β overexpression causes reversible alterations on postsynaptic densities and dendritic morphology of hippocampal granule neurons in vivo. Mol Psychiatry. 18:451-460. https://doi.org/10.1038/mp.2013.4

Blazquez-Llorca L, Merchán-Pérez A, Rodríguez R, Gascón J, DeFelipe J (2013) FIB/SEM technology and alzheimer’s disease: three-dimensional analysis of human cortical synapses. J Alzheimers Dis. 34:995-1013. https://doi.org/10.3233/jad-122038

Leon-Espinosa G, Garcia E, Garcia-Escudero V, Hernandez F DeFelipe J, Avila J (2013) Changes in tau phosphorylation in hibernating rodents. J Neurosci Res. 91:954-962. https://doi.org/10.1002/jnr.23220

Alonso-Nanclares L, Merino-Serrais P, Gonzalez S, DeFelipe J (2013) Synaptic changes in the dentate gyrus of APP/PS1 transgenic mice revealed by electron microscopy. J Neuropathol Exp Neurol. 72:386-395. https://doi.org/10.1097/nen.0b013e31828d41ec

Morales J, Rodríguez A, Rodríguez J-R, DeFelipe J, Merchán-Pérez A (2013) Characterization and extraction of the synaptic apposition surface for synaptic geometry analysis. Front. Neuroanat. 7:20. https://doi.org/10.3389/fnana.2013.00020

Armañanzas R, Alonso-Nanclares L, DeFelipe-Oroquieta J, Kastanauskaite A, de Sola RG, DeFelipe J, Bielza C, Larrañaga P (2013) Machine learning approach for the outcome prediction of temporal lobe epilepsy surgery. PLoS One. 8(4):e62819. https://doi.org/10.1371/journal.pone.0062819

Montes J, Gomez E, Merchán-Pérez A, DeFelipe J, Peña JM (2013) A machine learning method for the prediction of receptor activation in the simulation of synapses. PLoS One. 8(7):e68888. https://dx.doi.org/10.1371%2Fjournal.pone.0068888

Brito JP, Mata S, Bayona S, Pastor L, DeFelipe J, Benavides-Piccione R (2013) Neuronize: a tool for building realistic neuronal cell morphologies. Front Neuroanat. 7:15. https://doi.org/10.3389/fnana.2013.00015

Merino-Serrais P, Benavides-Piccione R, Blazquez-Llorca L, Kastanauskaite A, Rábano A, Avila J, DeFelipe J (2013) The influence of phosphotau on dendritic spines of cortical pyramidal neurons in Alzheimer’s disease patients. Brain 136:1913-1928. https://doi.org/10.1093/brain/awt088

Llorens-Martín M, Fuster-Matanzo A, Teixeira CM, Jurado-Arjona J, Ulloa F, DeFelipe J, Rábano A, Hernández F, Soriano E, Avila J (2013) Alzheimer disease-like cellular phenotype of newborn granule neurons can be reversed in GSK-3β-overexpressing mice. Mol Psychiatry. 18:395. https://doi.org/10.1038/mp.2013.27

LaTorre A, Alonso-Nanclares L, Muelas S, Peña JM, DeFelipe J (2013) Segmentation of neuronal nuclei based on clump splitting and a two-step binarization of images. Expert Systems with Applications. 40: 6521-6530. https://doi.org/10.1016/j.eswa.2013.06.010

LaTorre A, Alonso-Nanclares L, Muelas, S, Peña JM, DeFelipe J (2013) 3D Segmentations of Neuronal Nuclei from Confocal Microscope Image Stacks. Front. Neuroanat. 7:49. https://doi.org/10.3389/fnana.2013.00049

DeFelipe J (2013) Going to school to sculpt the brain. Front. Young Minds. 1:1. https://core.ac.uk/download/pdf/82842520.pdf

Knafo S, Venero C, Sánchez-Puelles C, Pereda-Peréz I, Franco A, Sandi C, Suárez LM, Solís JM, Alonso-Nanclares L, Martín ED, Merino-Serrais P, Borcel E, Li S, Chen Y, Gonzalez-Soriano J, Berezin V, Bock E, DeFelipe J, Esteban JA (2012) Facilitation of AMPA receptor synaptic delivery as a molecular mechanism for cognitive enhancement. PLoS Biol. 10(2):e1001262. https://doi.org/10.1371/journal.pbio.1001262

Martinez de Lagran M, Benavides-Piccione R, Ballesteros-Yañez I, Calvo M, Morales M, Fillat C, DeFelipe J, Ramakers GJ, Dierssen M (2012) Dyrk1a influences neuronal morphogenesis through regulation of cytoskeletal dynamics in mammalian cortical neurons. Cerebr Cortex 22:2867-2877. https://doi.org/10.1093/cercor/bhr362

León-Serrano G, DeFelipe J, Muñoz A (2012) Effects of amyloid-β Plaque proximity on the axon initial segment of pyramidal cells. J Alzheimers Dis 29:841-852. https://doi.org/10.3233/jad-2012-112036

Avila J, León-Espinosa G, García E, García-Escudero V, Hernández F, DeFelipe J (2012) Tau phosphorylation by GSK3 in different conditions. Int J Alzheimers Dis. 2012:578373. https://doi.org/10.1155/2012/578373

Morales J, Benavides-Piccione R, Rodríguez A, Pastor L, Yuste R, DeFelipe J (2012) Three-Dimensional Analysis of Spiny Dendrites Using Straightening and Unrolling Transforms. Neuroinformatics 10:391-407. https://doi.org/10.1007/s12021-012-9153-2

Benavides-Piccione R, Fernaud-Espinosa I, Robles V, Yuste R, DeFelipe J (2013) Age-based comparison of human dendritic spine structure using complete three-dimensional reconstructions. Cereb Cortex 23:1798-1810. https://doi.org/10.1093/cercor/bhs154

Rockland KS, DeFelipe J (2012) Cortical GABAergic neurons: stretching it. Front Neuroanat. 6:16. https://dx.doi.org/10.3389%2Ffnana.2012.00016

DeFelipe J, Markram H, Rockland KS (2012) The Neocortical Column. Front Neuroanat. 6:22. https://doi.org/10.3389/fnana.2012.00022

Jimenez-Mateos EM, Engel T, Merino-Serrais P, McKiernan RC, Tanaka K, Mouri G, Sano T, O’Tuathaigh C, Waddington JL, Prenter S, Delanty N, Farrell MA, O’Brien DF, Conroy RM, Stallings RL, DeFelipe J, Henshall DC (2012) Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nat Med. 18:1087-1094. https://doi.org/10.1038/nm.2834

Sánchez-Ponce D, DeFelipe J, Garrido JJ, Muñoz A (2012) Developmental expression of Kv potassium channels at the axon initial segment of cultured hippocampal neurons. Plos One 7 (10):e48557. https://doi.org/10.1371/journal.pone.0048557

López-Cruz, PL, Larrañaga, P, DeFelipe, J, Bielza, C (2013) Bayesian network modeling of the consensus between experts: An application to neuron classification. Int J Approx Reason. 55: 3-22. https://doi.org/10.1016/j.ijar.2013.03.011

Elston G, Benavides-Piccione R, Elston A, Manger P and DeFelipe J (2011) Pyramidal cells in prefrontal cortex: comparative observations reveal unparalleled specializations in neuronal structure among primate species. Front. Neuroanat. 5:2. https://doi.org/10.3389/fnana.2011.00002

Rockland KS, DeFelipe J (2011) Cortical white matter: beyond the pale. Front Neuroanat. 5:67. https://dx.doi.org/10.3389%2Ffnana.2011.00067

López-Cruz, PL, Bielza C, Larrañaga P, Benavides-Piccione R, DeFelipe J (2011) Models and simulation of 3D neuronal dendritic trees using Bayesian networks. Neuroinformatics 9:347-369. https://doi.org/10.1007/s12021-011-9103-4

Alonso-Nanclares L, Kastanauskaite A, Rodriguez JR, Gonzalez-Soriano J, DeFelipe J (2011) A stereological study of synapse number in the epileptic human hippocampus. Front. Neuroanat. 5:8. https://doi.org/10.3389/fnana.2011.00008

Morales J, Alonso-Nanclares L, Rodríguez J-R, DeFelipe J, Rodríguez A and Merchán-Pérez A (2011) ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images. Front Neuroanat. 5:18. https://doi.org/10.3389/fnana.2011.00018

DeFelipe J (2011) The evolution of the brain, the human nature of cortical circuits and intellectual creativity. Front Neuroanat. 5:29. https://dx.doi.org/10.3389%2Ffnana.2011.00029

Merino-Serrais P, Knafo S, Alonso-Nanclares L, Fernaud-Espinosa I, DeFelipe J (2011). Layer-specific alterations to CA1 dendritic spines in a mouse model of Alzheimer’s disease. Hippocampus 21:1037-1044. https://doi.org/10.1002/hipo.20861

DeFelipe J and Sotelo C (2011) Goodbye Ted (an Obituary for Edward G. Jones). Front Neuroanat. 5:44. https://doi.org/10.3389/fnana.2011.00044

Blazquez-Llorca L, Garcia-Marin V, Merino-Serrais P, Avila J, DeFelipe J (2011) Abnormal tau phosphorylation in the thorny excrescences of CA3 hippocampal neurons in patients with Alzheimer’s. J Alzheimer Disease 26: 683-698. https://doi.org/10.3233/jad-2011-110659

Sánchez-Ponce D, DeFelipe J, Garrido JJ, Muñoz A (2011) In vitro maturation of the cisternal organelle in the hippocampal neuron’s axon initial segment. Mol Cell Neurosci. 48:104-116. https://doi.org/10.1016/j.mcn.2011.06.010

Morales J, Alonso-Nanclares L, Rodriguez JR, Merchán-Pérez A, DeFelipe J, Rodriguez A (2011) Fast interactive quantification of synapses in the cerebral cortex. Int J Artif Intell T. 20:239-252. https://doi.org/10.1142/S0218213011000139

Sánchez-Ponce D, Blazquez-Llorca L, DeFelipe J, Garrido JJ, Muñoz A (2011) Co-localization of α-actinin and synaptopodin in the pyramidal cell axon initial segment. Cereb Cortex 22:1648-1661. https://doi.org/10.1093/cercor/bhr251

Markram H, Meier K, Lippert T, Grillner S, Frackowiak R, Dehaene S, Knoll A, Sompolinsky H, Verstreken K, DeFelipe J, Grant S, Changeux J-P, Saria A (2011) Introducing the Human Brain Project. Procedia Computer Science 7:39–42. https://doi.org/10.1016/j.procs.2011.12.015

Yague JG, Azcoitia I, DeFelipe J, Garcia-Segura LM, Muñoz A (2010) Aromatase expression in the normal and epileptic human hippocampus. Brain Res 1315:41-52. https://doi.org/10.1016/j.brainres.2009.09.111

Blazquez-Llorca L, Garcia-Marin V, DeFelipe J (2010) Pericellular innervation of neurons expressing abnormally hyperphosphorylated tau in the hippocampal formation of Alzheimer’s disease patients. Front Neuroanat. 4:20. https://doi.org/10.3389/fnana.2010.00020

Clancy B, Defelipe J, Espinosa A, Fairén A, Jinno S, Kanold P, Luhmann HJ, Rockland KS, Tamamaki N, Yan XX (2010). Cortical GABAergic Neurons: Stretching it Remarks, Main Conclusions and Discussion. Front Neuroanat. 4:7. https://doi.org/10.3389/neuro.05.007.2010

DeFelipe J, Fields RD, Hof PR, Höistad M, Kostovic I, Meyer G, Rockland KS (2010) Cortical white matter: beyond the pale remarks, main conclusions and discussion. Front Neuroanat. 4:4. https://dx.doi.org/10.3389%2Fneuro.05.004.2010

Ballesteros-Yáñez I, Benavides-Piccione R, Bourgeois JP, Changeux JP, DeFelipe J (2010) Alterations of cortical pyramidal neurons in mice lacking high-affinity nicotinic receptors. Proc Natl Acad Sci U S A. 107:11567-11572. https://doi.org/10.1073/pnas.1006269107

Garcia-Marin V, Blazquez-Llorca L, Rodriguez JR, Gonzalez J, DeFelipe J (2010) Differential distribution of neurons in the gyral white matter of the human cerebral cortex. J Comp Neurol 518:4740-459. https://doi.org/10.1002/cne.22485

Blazquez-Llorca L, Garcia-Marin V, DeFelipe J (2010) GABAergic complex basket formations in the human neocortex. J Comp Neurol 518:4917-4937. https://doi.org/10.1002/cne.22496

DeFelipe J (2010) From the connectome to the synaptome: an epic love history. Science 330:1198-201. https://doi.org/10.1126/science.1193378

Inda MC, DeFelipe J, Munoz A (2009) Morphology and distribution of chandelier cell axon terminals in the mouse cerebral cortex and claustroamygdaloid complex. Cereb Cortex. 19:41-54. https://doi.org/10.1093/cercor/bhn057

Knafo S, Alonso-Nanclares L, Gonzalez-Soriano J, Merino-Serrais P, Fernaud-Espinosa I, Ferrer I, DeFelipe J (2009) Widespread changes in dendritic spines in a model of Alzheimer’s disease Cereb Cortex 19:586-92. https://doi.org/10.1093/cercor/bhn111

Knafo S, Venero C, Merino-Serrais P, Fernaud-Espinosa I, Gonzalez-Soriano J, Ferrer I, Santpere G and DeFelipe J (2009) Morphological alterations to neurons of the amygdala and impaired fear conditioning in a transgenic mouse model of Alzheimer’s disease. J Pathol. 219:41-51. https://doi.org/10.1002/path.2565

Merchán-Pérez A, Rodriguez JR, Ribak CE, DeFelipe J (2009) Proximity of excitatory and inhibitory axon terminals adjacent to pyramidal cell bodies provides a putative basis for nonsynaptic interactions. Proc Natl Acad Sci USA. 106:9878-83. https://doi.org/10.1073/pnas.0900330106

Kastanauskaite A, Alonso-Nanclares L, Blazquez-Llorca L, Pastor J, Sola RG, DeFelipe J (2009) Alterations of the microvascular network in sclerotic hippocampi from patients with epilepsy. J Neuropathol Exp Neurol. 68:939-950. https://doi.org/10.1097/nen.0b013e3181b08622

Merchán-Pérez A, Rodriguez J, Alonso-Nanclares L, Schertel A and DeFelipe J (2009) Counting synapses using FIB/SEM microscopy: a true revolution for ultrastructural volume reconstruction. Front. Neuroanat. 3:18. https://doi.org/10.3389/neuro.05.018.2009

Garcia-Marin V, Blazquez-Llorca L, Rodriguez JR, Boluda S, Muntane G, Ferrer I, DeFelipe J (2009) Diminished perisomatic GABAergic terminals on cortical neurons adjacent to amyloid plaques. Front Neuroanat. 3:28. https://doi.org/10.3389/neuro.05.028.2009

2018 CBBP Scientific Publications

• Luengo-Sanchez, S., I. Fernaud-Espinosa, C. Bielza, R. Benavides-Piccione, P. Larrañaga, and J. DeFelipe, “3D morphology-based clustering and simulation of human pyramidal cell dendritic spines”, PLoS Computational Biology, vol. 14, issue 6, e1006221, 2018.
• Mihaljevic, B., P. Larrañaga, R. Benavides-Piccione, S..Hill, J. DeFelipe, and C. Bielza, “Towards a supervised classification of neocortical interneuron morphologies”, BMC Bioinformatics, vol. 19, issue 1, Article 511, 2018.
• Varando, G., R. Benavides-Piccione, A. Muñoz, A. Kastanauskaite, C. Bielza, P. Larrañaga, and J. DeFelipe, “MultiMap: A tool to automatically extract and analyze spatial microscopic data from large stacks of confocal microscopy images”, Frontiers in Neuroanatomy, vol. 12. Article 37, 2018.
• Leguey I, Benavides-Piccione R, Rojo C, Larrañaga P, Bielza C, DeFelipe J. (2019) Patterns of Dendritic Basal Field Orientation of Pyramidal Neurons in the Rat Somatosensory Cortex. eNeuro. 2019 Jan 17;5(6). pii: ENEURO.0142-18.2018
• Aliaga Maraver, J. J., Mata, S., Benavides-Piccione, R., DeFelipe, J., & Pastor, L. (2018). A Method for the Symbolic Representation of Neurons. Frontiers in neuroanatomy, 12, 106. doi:10.3389/fnana.2018.00106
• Santuy, A., Turégano-López, M., Rodríguez, J. R., Alonso-Nanclares, L., DeFelipe, J., and Merchán-Pérez, A. (2018). A Quantitative Study on the Distribution of Mitochondria in the Neuropil of the Juvenile Rat Somatosensory Cortex. Cerebral Cortex 28, 3673–3684. doi:10.1093/cercor/bhy159.
• Santuy, A., Rodriguez, J. R., DeFelipe, J., and Merchan-Perez, A. (2018). Volume electron microscopy of the distribution of synapses in the neuropil of the juvenile rat somatosensory cortex. Brain Struct Funct 223, 77–90. doi:10.1007/s00429-017-1470-7.
• Santuy, A., Rodríguez, J.-R., DeFelipe, J., and Merchán-Pérez, A. (2018). Study of the Size and Shape of Synapses in the Juvenile Rat Somatosensory Cortex with 3D Electron Microscopy. eNeuro 5. doi:10.1523/ENEURO.0377-17.2017.
• Rodríguez, J.-R., Turégano-López, M., DeFelipe, J., and Merchán-Pérez, A. (2018). Neuroanatomy from Mesoscopic to Nanoscopic Scales: An Improved Method for the Observation of Semithin Sections by High-Resolution Scanning Electron Microscopy. Front. Neuroanat. 12. doi:10.3389/fnana.2018.00014.
• León-Espinosa G, Antón-Fernández A, Tapia-González S, DeFelipe J, Muñoz A (2018) Modifications of the axon initial segment during the hibernation of the Syrian hamster. Brain Struct Funct. 223:4307-4321. doi: 10.1007/s00429-018-1753-7.
• León-Espinosa G, Regalado-Reyes M¸ DeFelipe J, and Muñoz A (2018) Changes in neocortical and hippocampal microglial cells during hibernation. Brain Structure and Function 223:1881-1895. doi: 10.1007/s00429-017-1596-7.
• Domínguez-Álvaro M; Montero-Crespo M; Blázquez-Llorca L; Insausti R; DeFelipe J; Alonso-Nanclares L (2018) Three-Dimensional Analysis of Synapses in the Transentorhinal Cortex of Alzheimer’s disease patients. Acta Neuropathologica Communications 6:20. doi.org/10.1186/s40478-018-0520-6.
• Furcila D, DeFelipe J, Alonso-Nanclares L (2018). A study of amyloid-β and phosphotau in plaques and neurons in the hippocampus of Alzheimer’s disease patients. Journal of Alzheimer Disease, 64: 417-435. Doi: 10.3233/JAD-180173
• Anton-Sanchez, L., F. Effenberger, C. Bielza, P. Larrañaga, and H. Cuntz, “A regularity index for dendrites -local statistics of a neuron’s input space”, PLoS Computational Biology, vol. 14, 11, e1006593, 2018
• Benjumeda, M., C. Bielza, and P. Larrañaga, “Learning tractable Bayesian networks in the space of elimination orders”, Artificial Intelligence, accepted, 2018
• Benjumeda, M., C. Bielza, and P. Larrañaga, “Tractability of most probable explanations in multidimensional Bayesian network classifiers”, International Journal of Approximate Reasoning, vol. 93, pp. 74-87, 2018
• Leguey, I., P. Larrañaga, C. Bielza, and S. Kato, “A circular-linear dependence measure under Johnson–Wehrly distributions and its application in Bayesian networks.”, Information Sciences, accepted, 2019.
• Mihaljevic, B., C. Bielza, and P. Larrañaga, “bnclassify: Learning Bayesian Network Classifiers”, The R Journal, accepted, 2018.
• Sujar, A., Casafranca, J. J., Serrurier, A., & Garcia, M. (2018). Real-time animation of human characters’ anatomy. Computers & Graphics. DOI: 10.1016/j.cag.2018.05.025. 2018
• Durkee CA, Covelo A, Lines J, Kofuji P, Aguilar J, Araque A (2019) Gi/o protein-coupled receptors inhibit neurons but activate astrocytes and stimulate gliotransmission. Glia (in press)
• García-Cáceres C, Balland E, Prevot V, Luquet S, Woods SC, Koch M, Horvath TL, Yi CX, Chowen JA, Verkhratsky A, Araque A, Bechmann I, Tschöp MH (2019) Role of astrocytes, microglia, and tanycytes in brain control of systemic metabolism. Nature Neuroscience 22:7-14.
• Durkee CA, Araque A (2018) Diversity and Specificity of Astrocyte-neuron Communication. Neuroscience. 396: 73-78.
• Covelo A, Araque A (2018) Stimulating Astrocytes to Remember. Cell 174: 12-13.
• Teravskis PJ, Covelo A, Miller EC, Singh B, Martell-Martínez HA, Benneyworth MA, Gallardo C, Oxnard BR, Araque A, Lee MK, Liao D (2018) A53T Mutant Alpha-Synuclein Induces Tau-Dependent Postsynaptic Impairment Independently of Neurodegenerative Changes. Journal of Neuroscience 38: 9754-9767.
• Covelo A, Araque A (2018) Neuronal activity determines distinct gliotransmitter release from a single astrocyte. eLife 7:e32237 DOI: 10.7554/eLife.32237.
• Robin LM, Oliveira da Cruz JF, Langlais VC, Martin-Fernandez M, Metna-Laurent M, Busquets-Garcia A, Bellocchio L, Soria-Gomez E, Papouin T, Varilh M, Sherwood MW, Belluomo I, Balcells G, Matias I, Bosier B, Drago F, Van Eeckhaut A, Smolders I, Georges F, Araque A, Panatier A, Oliet SHR, and Marsicano G (2018) Astroglial CB1 receptors determine synaptic D-serine availability to enable recognition memory. Neuron 98:935-944.
• Eyal G, Verhoog MB, Testa-Silva G, Deitcher Y, Benavides-Piccione R, DeFelipe J, de Kock CPJ,Mansvelder HD and Segev I (2018) Human Cortical Pyramidal Neurons: From Spines to Spikes via Models. Front. Cell. Neurosci. 12:181. doi: 10.3389/fncel.2018.00181.

2018 Scientific Publications

Data Analysis

• Atienza, D., C. Bielza, P. Larrañaga, “Efficient anomaly detection in a laser surface heat treatment process by tracking the laser spot”, submitted to IEEE Transactions on Industrial Informatics
• Benjumeda, M., S. Luengo, P. Larrañaga, C.Bielza, “Tractable learning of Bayesian networks from partially observed data”, submitted to Pattern Recognition
• Benjumeda, M., Y.-L. Tan, K.A. González-Otárula, D. Chandramohan, E.F. Chang, J.A. Hall, C. Bielza, P. Larrañaga, E. Kobayashi, R.C. Knowlton, “Multidimensional Bayesian network classifiers for individualized prediction of temporal lobe epilepsy surgical outcomes”, submitted to Journal of the American Medical Association
• Córdoba-Sanchez, I., C. Bielza, P. Larrañaga, “On Gaussian Markov models for conditional independence”, submitted to Journal of Statistical Planning and Inference
• Díaz-Rozo, J., C. Bielza, P. Larrañaga, “Gaussian mixture models-based dynamic probabilistic clustering”, submitted to Engineering Applications of Artificial Intelligence
• Fernandez-Gonzalez, P., C. Bielza, P. Larrañaga, “Random forests for regression as a weighted sum of k-potential nearest neighbors”, submitted to IEEE Access
• Gil-Begue, S., C. Bielza, and P. Larrañaga, “Multi-dimensional Bayesian network classifiers: A survey”, submitted to ACM Computing Surveys
• Leguey, I., C. Bielza, P. Larrañaga, “Circular Bayesian classifiers using wrapped Cauchy distributions”, submitted to Data & Knowledge Engineering
• Puerto-Santana, E., C. Bielza, P. Larrañaga, “Auto regressive asymmetric linear Gaussian hidden Markov models”, submitted to IEEE Pattern Analysis and Machine Intelligence
• Varando, G., C. Bielza, P. Larrañaga, E. Riccomagno, “Markov property in generative classifiers, submitted to Journal of Machine Learning Research
• Villa, C., C. Bielza, P. Larrañaga, “Feature subset selection over dynamic data: A review”, submitted to ACM Computing Surveys

Visualization (GMRV-URJC & UPM)

• Diana Furcila, Marcos García, Cosmin Toader, Juan Morales, Antonio LaTorre, Ángel Rodríguez, Luis Pastor, Javier DeFelipe, Lidia Alonso-Nanclares. InTool Explorer: an interactive exploratory analysis tool for versatile visualizations of neuroscientific data. Frontiers in Neuroanatomy. 

Physiology and Functional Modelling

• Ortuño T, López-Madrona VJ, Tapia-Gonzalez S, Muñoz A, De Felipe J, Herreras O. Developmental changes in layer-specific field potential sources in the S1HL cortex indicate intracolumnar functional reorganization. Under review (submitted to Q1 journal).

2017 CBBP Scientific Publications

• Urrecha M, Romero I1, DeFelipe J, Merchán-Pérez A. Influence of cerebral blood vessel movements on the position of perivascular synapses. PLoS One. 2017 Feb 15;12(2):e0172368. doi: 10.1371/journal.pone.0172368.
• Pallas-Bazarra N, Kastanauskaite A, Avila J, DeFelipe J, Llorens-Martín M (2017).
• GSK-3β Overexpression Alters the Dendritic Spines of Developmentally Generated Granule Neurons in the Mouse Hippocampal Dentate Gyrus. Front Neuroanat. 2017 Mar 10;11:18. doi: 10.3389/fnana.2017.00018. eCollection 2017.
• Gonzalez-Riano C, Tapia-González S, García A, Muñoz A, DeFelipe J, Barbas C. (2017) Metabolomics and neuroanatomical evaluation of post-mortem changes in the hippocampus. Brain Struct Funct. 2017 Mar 11. doi: 10.1007/s00429-017-1375-5. [Epub ahead of print]
• Anton-Sanchez L, Larrañaga P, Benavides-Piccione R, Fernaud-Espinosa I, DeFelipe J, Bielza C. Three-dimensional spatial modeling of spines along dendritic networks in human cortical pyramidal neurons. PLoS One. 2017 Jun 29;12(6):e0180400. doi: 10.1371/journal.pone.0180400. eCollection 2017.
• DeFelipe J (2017). Neuroanatomy and Global Neuroscience. Neuron. 2017 Jul 5;95(1):14-18. doi: 10.1016/j.neuron.2017.05.027.
• Santuy A, Rodriguez JR, DeFelipe J, Merchan-Perez A (2017) Volume electron microscopy of the distribution of synapses in the neuropil of the juvenile rat somatosensory cortex. Brain Struct Funct. 2017 Jul 18. doi: 10.1007/s00429-017-1470-7. [Epub ahead of print]
• P. Fernandez-Gonzalez, R. Benavides-Picione, C. Bielza, P. Larrañaga, I. Leguey, and J. DeFelipe. “Dendritic-branching angles of pyramidal neurons of the human temporal cortex”, Brain Struct Funct. 2017 May; 222(4):1847-1859. doi: 10.1007/s00429-016-1311-0. Epub 2016 Sep 30
• Gómez-Gonzalo M, Martin-Fernandez M, Martínez-Murillo R, Mederos S, Hernández-Vivanco A, Jamison S, Fernandez AP, Serrano J, Calero P, Futch HS, Corpas R, Sanfeliu C, Perea G, Araque A (2016) Neuron-astrocyte signaling is preserved in the ageing brain. Glia, 2017 Apr;65(4):569-580. doi: 10.1002/glia.23112. Epub 2017 Jan 28.
• Fernandez, A.M., Hernandez-Garzón, E., Perez-Domper, P., Perez-Alvarez, A., Mederos, S., Matsui, T., Santi, A., Trueba-Saiz, A., García-Guerra, L., Pose-Utrilla, J., Fielitz, J., Olson, E.N., Fernandez de la Rosa, R., Garcia, L.G., Pozo, M.A., Iglesias, T., Araque, A., Soya, H., Perea, G., Martin, E.D., Torres Aleman, I. (2016). Insulin Regulates Astrocytic Glucose Handling Through Cooperation With Insulin-Like Growth Factor I. Diabetes. 2017 Jan;66(1):64-74. doi: 10.2337/db16-0861. Epub 2016 Oct 10.
• Cuadrado-Tejedor M, Garcia-Barroso C, Sánchez-Arias JA, Rabal O, Pérez-González M, Mederos S, Ugarte A, Franco R, Segura V, Perea G, Oyarzabal J, Garcia-Osta A. (2016) A First-in-Class Small-Molecule that Acts as a Dual Inhibitor of HDAC and PDE5, and that Rescues Hippocampal Synaptic Impairment in Alzheimer’s Disease Mice. Neuropsychopharmacology. 2017 Jan; 42(2):524-539. doi: 10.1038/npp.2016.163. Epub 2016 Aug 23.

2016 CBBP Scientific Publications

• Anton-Sanchez, L., C. Bielza, P. Larrañaga, and J. DeFelipe, “Wiring Economy of Pyramidal Cells in the Juvenile Rat Somatosensory Cortex”, PLoS ONE, vol. 11, issue 11, 2016.
• Anton-Sanchez, L., C. Bielza, R. Benavides-Piccione, J. DeFelipe, and P. Larrañaga, “Dendritic and axonal wiring optimization of cortical GABAergic interneurons”, Neuroinformatics, vol. 14, issue 4, pp. 453-464, 2016.
• Leguey, I., C. Bielza, P. Larrañaga, A. Kastanauskaite, C. Rojo, R. Benavides-Piccione, and J. DeFelipe, “Dendritic branching angles of pyramidal cells across layers of the juvenile rat somatosensory cortex”, Journal of Comparative Neurology, vol. 524, issue 13, pp. 2567-2576, 2016.
• Rojo, C., I. Leguey, A. Kastanauskaite, C. Bielza, P. Larrañaga, J. DeFelipe, and R. Benavides-Piccione, “Laminar differences in dendritic structure of pyramidal neurons in juvenile rat somatosensory cortex”, Cerebral Cortex, vol. 26, issue 6, pp. 2811-2822, 2016.
• Márquez Neila, P. M., Baumela, L., González-Soriano, J., Rodríguez, J.-R., DeFelipe, J., and Merchán-Pérez, Á. (2016). A Fast Method for the Segmentation of Synaptic Junctions and Mitochondria in Serial Electron Microscopic Images of the Brain. Neuroinform 14, 235–250. doi:10.1007/s12021-015-9288-z.
• Toharia P, Robles OD, Fernaud-Espinosa I, Makarova J, Galindo SE, Rodriguez A, Pastor L, Herreras O, DeFelipe J, Benavides-Piccione R (2016). PyramidalExplorer: A new interactive tool to explore morpho-functional relations of human pyramidal neurons. Front Neuroanat. 9:159.
• Bosch, C., Masachs, N., Exposito-Alonso, D., Martínez, A., Teixeira, C. M., Fernaud, I., et al. (2016). Reelin Regulates the Maturation of Dendritic Spines, Synaptogenesis and Glial Ensheathment of Newborn Granule Cells. Cerebral Cortex. doi:10.1093/cercor/bhw216.
• Eyal G, Verhoog MB, Testa-Silva G, Deitcher Y, Lodder JC, Benavides-Piccione R, Morales J, DeFelipe J, de Kock CP, Mansvelder HD, Segev I. Unique membrane properties and enhanced signal processing in human neocortical neurons. Elife. 2016 Oct 6;5. pii: e16553. doi: 10.7554/eLife.16553.
• Mellström B, Kastanauskaite A, Knafo S, Gonzalez P, Dopazo XM, Ruiz-Nuño A, Jefferys JG, Zhuo M, Bliss TV, Naranjo JR, DeFelipe J (2016). Specific cytoarchitectureal changes in hippocampal subareas in daDREAM mice. Mol Brain. 2016 Feb 29;9:22. doi: 10.1186/s13041-016-0204-8.
• Broadhead MJ, Horrocks MH, Zhu F, Muresan L, Benavides-Piccione R, DeFelipe J, Fricker D, Kopanitsa MV, Duncan RR, Klenerman D, Komiyama NH, Lee SF, Grant SG (2016) PSD95 nanoclusters are postsynaptic building blocks in hippocampus circuits. Sci Rep. 2016 Apr 25;6:24626. doi: 10.1038/srep24626.
• DeFelipe J (2016). Phospho-Tau and Cognitive Decline in Alzheimer’s Disease. Commentary: Tau in physiology and pathology. Front Neuroanat. 2016 Apr 28;10:44. doi: 10.3389/fnana.2016.00044.
• DeFelipe J, Douglas RJ, Hill SL, Lein ES, Martin KA, Rockland KS, Segev I, Shepherd GM, Tamás G. (2016). Comments and General Discussion on “The Anatomical Problem Posed by Brain Complexity and Size: A Potential Solution”. Front Neuroanat. 2016 Jun 10;10:60. doi: 10.3389/fnana.2016.00060.
• León-Espinosa G, García E, Gómez-Pinedo U, Hernández F, DeFelipe J, Ávila J. (2016). Decreased adult neurogenesis in hibernating Syrian hamster. Neuroscience. 2016 Oct 1;333:181-92. doi: 10.1016/j.neuroscience.2016.07.016.
• Barth A, Burkhalter A, Callaway EM, Connors BW, Cauli B, DeFelipe J, Feldmeyer D, Freund T, Kawaguchi Y, Kisvarday Z, Kubota Y, McBain C, Oberlaender M, Rossier J, Rudy B, Staiger JF, Somogyi P, Tamas G, Yuste R. (2016). Comment on “Principles of connectivity among morphologically defined cell types in adult neocortex”. Science. 2016 Sep 9;353(6304):1108. doi: 10.1126/science.aaf5663.
• Anton-Sanchez, L., C. Bielza, and P. Larrañaga, “Network Design through Forests with Degree- and Role-constrained Minimum Spanning Trees”, in press, Journal of Heuristics
• Benjumeda, M., C. Bielza, and P. Larrañaga, “Learning Bayesian networks with low inference complexity”, Progress in Artificial Intelligence, vol. 5, issue 1, pp. 15-26, 2016.
• Borchani, H., P. Larrañaga, J. Gama, and C. Bielza, “Mining multi-dimensional concept-drifting data streams using Bayesian network classifiers”, Intelligent Data Analysis, vol. 20, no. 2, 2016.
• P. Fernandez-Gonzalez, P. Larrañaga, C. Bielza, “Univariate and bivariate truncated von Mises distributions”, Progress in Artificial Intelligence, in press (doi:10.1007/s13748-016-0109-x)
• Leitner, L., C. Bielza, S.L. Hill, and P. Larrañaga, “Data Publications Correlate with Citation Impact”, Frontiers in Neuroscience, vol. 10, issue 419, 2016.
• Rodriguez-Lujan, L., P. Larrañaga, and C. Bielza, “Frobenius norm regularization for the multivariate von Mises distribution”, International Journal of Intelligent Systems, in press (DOI: 10.1002/int.21834).
• Varando, G., C. Bielza, and P. Larrañaga, “Decision functions for chain classifiers based on Bayesian networks for multi-label classification”, International Journal of Approximate Reasoning, vol. 68, pp. 164-178, 2016.
• Galindo, S. E., Toharia, P., Robles, O. D., Pastor, L. (2016). ViSimpl: Multi-View Visual Analysis of Brain Simulation Data. Frontiers in Neuroinformatics, 10, 44. http://doi.org/10.3389/fninf.2016.00044
• Herreras O. Local Field Potentials: Myths and Misunderstandings. Front Neural Circuits. 2016 Dec 15; 10:101. doi: 10.3389/fncir.2016.00101. eCollection 2016. Review.
• Benito N, Martín-Vázquez G, Makarova J, Makarov VA, Herreras O. The right hippocampus leads the bilateral integration of gamma-parsed lateralized information. Elife. 2016 Sep 6; 5. pii: e16658. doi: 10.7554/eLife.16658.
• Dreier JP, Fabricius M, Ayata C, …, Herreras O, et al. Recording, analysis, and interpretation of spreading depolarizations in neurointensive care: Review and recommendations of the COSBID research group. J Cereb Blood Flow Metab. 2016 Jan 1:271678X16654496. doi: 10.1177/0271678X16654496.
• Martín-Vázquez G, Benito N, Makarov VA, Herreras O, Makarova J. Diversity of LFPs Activated in Different Target Regions by a Common CA3 Input. Cereb Cortex. 2016 Oct;26 (10):4082-100. doi: 10.1093/cercor/bhv211.
• Humanes-Valera D, Foffani G, Alonso-Calviño E, Fenández-López E, Aguilar J. (2016). “Dual cortical plasticity after spinal cord injury”. Cerebral Cortex Epub ahead of print. doi:10.1093/cercor/bhw142. IF: 8.66
• Alonso-Calviño E, Martínez-Camero I, Fernández-López F, Humanes-Valera D, Foffani G, Aguilar J. (2016), “Increased responses in the somatosensory thalamus immediately after spinal cord injury”. Neurobiology of Disease 87:39-49. doi:10.1016/j.nbd.2015.12.003 IF: 5.078

Cell Physiology Cajal’s Laboratory (IC-CSIC):

• Perea G, Gómez R, Mederos S, Covelo A, Ballesteros J, Schlosser L, Hernández-Vivanco A, Martín-Fernández M, Quintana R, Rayan A, Díez A, Fuenzalida M, Agarwal A, Bergles D, Bettler B, Manahan-Vaughan D, Martín ED, Kirchhoff F, Araque A (2016) Activity-dependent switch of GABAergic inhibition into glutamatergic excitation in astrocyte-neuron networks. eLife pii: e20362.
• 30. Hernandez-Garzón E, Fernandez AM, Perez-Alvarez A, Genis L, Bascuñana P, Fernandez de la Rosa R, Delgado M, Angel Pozo M, Moreno E, McCormick PJ, Santi A, Trueba-Saiz A, Garcia-Caceres C, Tschöp MH, Araque A, Martin ED, Torres Aleman I (2016) The insulin-like growth factor I receptor regulates glucose transport by astrocytes. Glia 64:1964-1971.
• Covelo A, Araque A (2015) Lateral regulation of synaptic transmission by astrocytes. Neuroscience Neuroscience. 2016 May 26;323:62-6. doi: 10.1016/j.neuroscience.2015.02.036. Epub 2015 Feb 27.

Other CBBP Publications

• DeFelipe J, Rudy B (2017) Neocortical microcircuits. Handbook of Brain Microcircuits. 2nd edition. Gordon Shepherd and Sten Grillner, eds. Oxford University Press, New York. (Submitted).
• Atienza, D., Bielza, C., Diaz, J., Larrañaga, P. (2016). “Anomaly detection with a spatio-temporal tracking of the laser spot”. Frontiers in Artificial Intelligence and Applications Series, 284, 137-142, IOS Press.
• Diaz, J., Bielza, C., Ocaña, J.L., Larrañaga, P. (2016). “Development of a cyber-physical system based on selective Gaussian naive Bayes model for a self-predict laser surface heat treatment process control”. Machine Leaning for Cyber Physical Systems, 1-8, Springer.
• Leguey, I., Bielza, C., Larrañaga, P. (2016). “Tree-structured Bayesian networks for wrapped Cauchy directional distributions”. Lecture Notes in Artificial Intelligence, 9868, 207-216. Springer.

2015 CBBP Scientific Publications

• Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N, Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R, Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, Haenel V, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y, King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Bé JV, Magalhães BR, Merchán-Pérez A, Meystre J, Morrice BR, Muller J, Muñoz-Céspedes A, Muralidhar S, Muthurasa K, Nachbaur D, Newton TH, Nolte M, Ovcharenko A, Palacios J, Pastor L, Perin R, Ranjan R, Riachi I, Rodríguez JR, Riquelme JL, Rössert C, Sfyrakis K, Shi Y, Shillcock JC, Silberberg G, Silva R, Tauheed F, Telefont M, Toledo-Rodriguez M, Tränkler T, Van Geit W, Díaz JV, Walker R, Wang Y, Zaninetta SM, DeFelipe J, Hill SL, Segev I, Schürmann F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163: 1–37.
• Ramaswamy S, Courcol JD, Abdellah M, Adaszewski SR, Antille N, Arsever S, Atenekeng G, Bilgili A, Brukau Y, Chalimourda A, Chindemi G, Delalondre F, Dumusc R, Eilemann S, Gevaert ME, Gleeson P, Graham JW, Hernando JB, Kanari L, Katkov Y, Keller D, King JG, Ranjan R, Reimann MW, Rössert C, Shi Y, Shillcock JC, Telefont M, Van Geit W, Villafranca Diaz J, Walker R, Wang Y, Zaninetta SM, DeFelipe J, Hill SL, Muller J, Segev I, Schürmann F, Muller EB, Markram H (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Front Neural Circuits. 9:44. doi: 10.3389/fncir.2015.00044
• Montes J, Peña JM, DeFelipe J, Herreras O, Merchan-Perez A. The influence of synaptic size on AMPA receptor activation: a Monte Carlo model. PLoS One. 2015 Jun 24; 10(6):e0130924. doi: 10.1371/journal.pone.0130924. eCollection 2015.
• Montes, J., LaTorre, A., Muelas, S., Merchán-Pérez, A., and Peña, J. M. (2015). Comparative Study of Metaheuristics for the Curve-Fitting Problem: Modeling Neurotransmitter Diffusion and Synaptic Receptor Activation. Abstract and Applied Analysis 2015, 16.
• Mihaljevic B, Benavides-Piccione R, Bielza C , DeFelipe J, Larrañaga P (2015) Bayesian network classifiers for categorizing cortical GABAergic interneurons. Neuroinformatics 13:193-208.
• Luengo-Sanchez S, Bielza C, Benavides-Piccione R, Fernaud-Espinosa I, DeFelipe J, Larrañaga P. (2015) A univocal definition of the neuronal soma morphology using Gaussian mixture models. Front Neuroanat. 9:137.
• Rojo, C., I. Leguey, A. Kastanauskaite, C. Bielza, P. Larrañaga, J. DeFelipe, and R. Benavides-Piccione, Laminar differences in dendritic structure of pyramidal neurons in juvenile rat somatosensory cortex, Cerebral Cortex, accepted, 2016 (doi: 10.1093/cercor/bhv316).
• Mihaljevic B, Guerra L, Benavides-Piccione R, DeFelipe J, Larrañaga P, Bielza C (2015) Classifying GABAergic interneurons with semi-supervised projected model-based clustering. Artif Intell Med. 65:49-59.
• DeFelipe J (2015) The dendritic spine story: an intriguing process of discovery. Front Neuroanat. 2015 Mar 5;9:14. doi: 10.3389/fnana.2015.00014. eCollection 2015.
• Íbias J, Soria-Molinillo E, Kastanauskaite A, Orgaz C, DeFelipe J, Pellón R, Miguéns M (2015). Schedule-induced polydipsia is associated with increased spine density in dorsolateral striatum neurons. Neuroscience. 2015 May 16;300:238-245. doi: 10.1016/j.neuroscience.2015.05.026.
• Bosch C, Martínez A, Masachs N, Teixeira CM, Fernaud I, Ulloa F, Pérez-Martínez E, Lois C, Comella JX, DeFelipe J, Merchán-Pérez A, Soriano E (2015) FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons. Front Neuroanat. 2015 May 21;9:60. doi: 10.3389/fnana.2015.00060. eCollection 2015.
• Rábano A, Cuadros R, Merino-Serráis P, Rodal I, Benavides-Piccione R, Gómez E, Medina M, DeFelipe J, Avila J. Protocols for Monitoring the Development of Tau Pathology in Alzheimer’s Disease. Methods Mol Biol. 2016, 1303:143-60. doi: 10.1007/978-1-4939-2627-5_7.
• Selvas A, Coria SM, Kastanauskaite A, Fernaud-Espinosa I, DeFelipe J, Ambrosio E, Miguéns M (2015). Rat-strain dependent changes of dendritic and spine morphology in the hippocampus after cocaine self-administration. Addict Biol. 2015 Sep 2. doi: 10.1111/adb.12294.
• DeFelipe J (2015). The anatomical problem posed by brain complexity and size: a potential solution. Front Neuroanat. 9:104. doi: 10.3389/fnana.2015.00104. eCollection 2015.
• Chamorro-López J, Miguéns M, Morgado-Bernal I, Kastanauskaite A, Selvas A, Cabané-Cucurella A, Aldavert-Vera L, DeFelipe J, Segura-Torres P (2015). Structural plasticity in hippocampal cells related to the facilitative effect of intracranial self-stimulation on a spatial memory task. Behav Neurosci. 129:720-730.
• Antón-Fernández A, León-Espinosa G, DeFelipe J, Muñoz A (2015). Changes in the Golgi Apparatus of Neocortical and Hippocampal Neurons in the Hibernating Hamster. Front Neuroanat. 9:157.
• Benjumeda, M., Larrañaga, P., Bielza, C., Learning Bayesian networks with low inference complexity, Progress in Artificial Intelligence, accepted, 2015 (DOI 10.1007/s13748-015-0070-0).
• Borchani, H., G. Varando, C. Bielza, and P. Larrañaga, Univariate and bivariate truncated regression, WIREs Data Mining and Knowledge Discovery, 5, 216-233, 2015.
• Ibañez, A., R. Armañanzas, C. Bielza, and P. Larrañaga, Genetic algorithms and Gaussian Bayesian networks to uncover the predictive core set of bibliometric indices, Journal of the American Society for Information Science and Technology, accepted, 2015 (DOI: 10.1002/asi.23467).
• Karshenas, H., C. Bielza, and P. Larrañaga, Interval-based ranking in noisy evolutionary multi-objective optimization, Computational Optimization and Applications, 61, 2, 517-555, 2015.
• Larrañaga, A., C. Bielza, P. Pongrácz, T. Faragó, P. Bálint, and P. Larrañaga, Comparing supervised learning methods for classifying sex, age, context and individual Mudi dogs from barking, Animal Cognition, 18, 2, 405-421, 2015.
• Lopez-Cruz, P. L., C. Bielza, and P. Larrañaga, Directional naive Bayes classifiers, Pattern Analysis and Applications, 18, 225-246, 2015.
• Varando, G., C. Bielza, and P. Larrañaga, Decision functions for chain classifiers based on Bayesian networks for multi-label classification, International Journal of Approximate Reasoning, 68, 164-178, 2016.
• Varando, G., C. Bielza, and P. Larrañaga, Decision boundary for discrete Bayesian network classifiers, Journal of Machine Learning Research, 16, 2015.
• Varando, G., P. L. Lopez-Cruz, T. D. Nielsen, P. Larrañaga, and C. Bielza, Conditional density approximations with mixtures of polynomials, International Journal of Intelligent Systems, 30, 3, 236–264, 2015.
• García-Grajales JA, Rucabado G, García-Dopico A, Peña J-M, Jérusalem A (2015) Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading. PLoS ONE 10(2): e0116532. doi:10.1371/journal.pone.0116532.
• Fernando Maestú, Jose-Maria Peña, Pilar Garcés, Santiago González, Ricardo Bajo, Anto Bagic, Pablo Cuesta, Michael Funke, Jyrki P. Mäkelä, Ernestina Menasalvas, Akinori Nakamura, Lauri Parkkonen, Maria E. López, Francisco del Pozo, Gustavo Sudre, Edward Zamrini, Eero Pekkonen, Richard N. Henson, James T. Becker, A multicenter study of the early detection of synaptic dysfunction in Mild Cognitive Impairment using Magnetoencephalography-derived functional connectivity, NeuroImage: Clinical, Volume 9, 2015, Pages 103-109, ISSN 2213-1582, http://dx.doi.org/10.1016/j.nicl.2015.07.011.
• Siddiqui, Zaigham Faraz and Krempl, Georg and Spiliopoulou, Myra and Pena, Jose M and Paul, Nuria and Maestu, Fernando. Predicting the post-treatment recovery of patients suffering from traumatic brain injury (TBI), Brain Informatics, Volume 2, Number 1, pages 33–44, 2015.
• Loic Corenthy, Miguel A. Otaduy, Luis Pastor, Marcos García. “Volume Haptics with Topology-Consistent Isosurfaces”. IEEE T. Haptics 8(4): 480-491 (2015)
• Ángela Mendoza Mendoza, Susana Mata, Luis Pastor: “Non-Photorealistic Rendering of Neural Cells from their Morphological Description.” J. UCS 21(7): 935-958 (2015)
• Martin R, Bajo-Grañeras R, Moratalla R, Perea G, Araque A (2015) Circuit-specific signaling in astrocyte-neuron networks in basal ganglia pathways. Science 349:730-734.
• Oliveira JF, Sardinha VM, Guerra-Gomes S, Araque A, Sousa N (2015) Do stars govern our actions? Astrocyte involvement in rodent behavior. Trends in Neurosciences 38:535-549.
• Gómez-Gonzalo M, Navarrete M, Perea G, Covelo A, Martín-Fernández M, Shigemoto R, Luján R, Araque A (2015) Endocannabinoids induce lateral long-term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex 25:3699-3712.

Other CBBP Publications

• Cajal and de Castro´s Manual for Micrographic Technique. Editors: M.A. Merchán, J. DeFelipe and F. de Castro II. Oxford University Press: New York.
• DeFelipe J (2015) Cajal y sus dibujos: cuando la ciencia era arte. Fisiología de los sueños. Cajal, Tanguy, Lorca, Dalí. Ed: Jaime Brihuega. Cultura y Política Social, Universidad de Zaragoza.
• Anton-Sanchez, L., Bielza, C., Larrañaga, P. Evolutionary computation of forests with degree- and role-constrained minimum spanning trees. Technical Report TR:UPM-ESTIINF/DIA/ 2015-2, Universidad Politécnica de Madrid, 2015.
• Fernandez-Gonzalez, P., Bielza, C., Larrañaga, P. Univariate and bivariate truncated vonMises distributions. Technical Report TR:UPM-ESTIINF/DIA/2015-1, Universidad Politécnica de Madrid, 2015.
• Mihaljević, B., Bielza, C., Larrañaga P. Neuroclassifier: An automatic classification of cortical GABAergic interneurons. 2nd Human Brain Project Education Workshop: Future Medicine – Medical Intelligence for Brain Diseases. Centre Hospitalier Universitaire Vaudois.
• Antonio LaTorre, Santiago Muelas, José-María Peña, A comprehensive comparison of large scale global optimizers, Information Sciences, Volume 316, 20 September 2015, Pages 517-549, ISSN 0020-0255, http://dx.doi.org/10.1016/j.ins.2014.09.031.
• Santiago Muelas, Antonio LaTorre, José-María Peña, A distributed VNS algorithm for optimizing dial-a-ride problems in large case scenarios. Transportation Research Part C: Emerging Technologies 54, 110-130

2014 CBBP Scientific Publications

• Bielza C, Benavides-Piccione R, López-Cruz P, Larrañaga P, DeFelipe J (2014). Branching angles of pyramidal cell dendrites follow common geometrical design principles in different cortical areas. Sci. Rep. 4, 5909; DOI: 10.1038/srep05909.
• Morales J*, Ruth Benavides-Piccione* R, Dar M, Fernaud I, Rodríguez A, Anton-Sanchez L, Bielza C, Larrañaga P, DeFelipe J, Yuste R (2014). Random Positioning of Dendritic Spines in the Human Cerebral Cortex. J Neurosci. 34:10078-10084. doi: 10.1523/JNEUROSCI.1085-14.2014. *both authors contributed equally
• Anton-Sanchez L, Bielza C, Merchán-Pérez A, Rodríguez J-R, DeFelipe J and Larrañaga P (2014). Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis. Front.Neuroanat. 8:85. doi:10.3389/fnana.2014.00085. Trends Neurosci. 2014 Oct; 37(10):525-7. doi: 10.1016/j.tins.2014.08.002.
• Mihaljević B, Bielza C, Benavides-Piccione R, DeFelipe J, Larrañaga P (2014) Multi-dimensional classification of GABAergic interneurons with Bayesian network-modeled label uncertainty. Front Comput Neurosci. 2014 Nov 25; 8:150. Doi: 10.3389/fncom.2014.00150.
• Mihaljević B, Benavides-Piccione R, Bielza C, DeFelipe J, Larrañaga P (2014) Bayesian Network Classifiers for Categorizing Cortical GABAergic Interneurons. Neuroinformatics. 2014 Nov 25. [Epub ahead of print]
• Jérusalem, A., García-Grajales, J.A., Merchán­Pérez, A., & Peña, J.M. (2014). A computational model coupling mechanics and electrophysiology in spinal cord injury. Biomechanics and Modeling in Mechanobiology (13):4 pp. 883-896
• Pablo Toharia, Juan Morales, Octavio de Juan, Isabel Fernaud-Espinosa, Angel Rodríguez, Javier DeFelipe. “Musical representation of dendritic spine distribution: a new exploratory tool” Neuroinformatics Springer Verlag. ISSN 1539-2791 DOI: 10.1007/s12021-013-9195-0 12(2): 341-353 Apr. 2014
• Loic Corenthy, Marcos García, Sofía Bayona Beriso, Andrea Santuy, Jose San Martin, Ruth Benavides-Piccione, Javier DeFelipe, Luis Pastor: A new user-adapted haptic Connection Procedure for the Reconstruction of Dendritic Spines. IEEE T. Haptics (TOH) 7(4):486-498 (2014)
• Lopez-Cruz, P.L., Larrañaga, P., J. DeFelipe, & Bielza, C. (2014). Bayesian network modeling of the consensus between experts: An application to neuron classification. International Journal of Approximate Reasoning, 55(1), 3-22.
• Merchán-Pérez, A., Rodríguez, R., González, S., Robles, V., DeFelipe, J., Larrañaga, P. & Bielza, C. (2014). Three-dimensional spatial distribution of synapses in the neocortex: A dual-beam electron microscopy study. Cerebral Cortex, 24, 1579-1588*.
• Ferreira FR, Nogueira MI, DeFelipe J (2014). The influence of James and Darwin on Cajal and his research into the neuron theory and evolution of the nervous system. Front Neuroanat. 8:1. doi: 10.3389/fnana.2014.00001.
• Mellström B, Sahún I, Ruiz-Nuño A, Murtra P, Gomez-Villafuertes R, Savignac M, Oliveros JC, Gonzalez P, Kastanauskaite A, Knafo S, Zhuo M, Higuera-Matas A, Errington ML, Maldonado R, DeFelipe J, Jefferys JG, Bliss TV, Dierssen M, Naranjo JR (2014) DREAM controls the on/off switch of specific activity-dependent transcription pathways. Mol Cell Biol 34:877-887.
• Jimenez-Mateos EM, Engel T, Merino-Serrais P, Fernaud-Espinosa I, Rodriguez-Alvarez N, Reynolds J, Reschke CR, Conroy RM, McKiernan RC, DeFelipe J, Henshall DC. Antagomirs targeting microRNA-134 increase hippocampal pyramidal neuron spine volume in vivo and protect against pilocarpine-induced status epilepticus. Brain Struct Funct. 2014 May 30. [Epub ahead of print]
• Llorens-Martín M, Blazquez-Llorca L, Benavides-Piccione R, Rabano A, Hernandez F, Avila J, DeFelipe J (2014). Selective alterations of neurons and circuits related to early memory loss in Alzheimer’s disease. Front Neuroanat. 2014 May 27;8:38. doi: 10.3389/fnana.2014.00038.
• DeFelipe J, Garrido E, Markram H (2014) The death of Cajal and the end of scientific romanticism and individualism. Trends Neurosci. 37(10): 525-527. doi: 10.1016/j.tins.2014.08.002.
• Blazquez-Llorca L, Woodruff A, Inan M, Anderson SA, Yuste R, DeFelipe J, Merchan-Perez A. (2014) Spatial distribution of neurons innervated by chandelier cells. Brain Struct Funct. 2014 Jul 24. [Epub ahead of print]
• Bielza, C. & Larrañaga, P. (2014b). Bayesian networks in neuroscience: A survey. Frontiers in Computational Neuroscience, 8, Article 131.
• Borchani, H., Bielza, C., Martínez-Martín, P. & Larrañaga, P. (2014a). Predicting EQ-5D from the Parkinson’s disease questionnaire PDQ-8 using multi-dimensional Bayesian network classifiers. Biomedical Engineering: Applications, Basis and Communications, 26(1), 1450015.
• Bielza, C. & Larrañaga, P. (2014c). Discrete Bayesian Network Classifiers: A Survey. ACM Computing Surveys, 47, 1, Article 5.
• Guerra, L., Bielza, C., V. Robles & Larrañaga, P. (2014). Semi-supervised projected model-based clustering. Data Mining and Knowledge Discovery, 28(4), 882-917.
• Ibañez, A., Bielza, C. & Larrañaga, P. (2014). Cost-sensitive selective naive Bayes classifiers for predicting the increase of the h-index for scientific journals. Neurocomputing, 135, 5, 42-52.
• Karshenas, H., Santana, R., Bielza, C. & Larrañaga, P. (2014). Multi-objective estimation of distribution algorithm based on joint modeling of objectives and variables. IEEE Transactions on Evolutionary Computation, 18(4), 519-542.
• Lopez-Cruz, P.L., Bielza, C. & Larrañaga, P. (2014). Learning mixtures of polynomials of multidimensional probability densities from data using B-spline interpolation. International Journal of Approximate Reasoning, 55(4), 989-1010.
• Read, J., Bielza, C. & Larrañaga, P. (2014). Multi-dimensional classification with super-classes. IEEE Transactions on Knowledge and Data Engineering, 26, 7, 1720-1733.
• Sucar, E., Bielza, C., Morales, E.F., Hernandez-Leal, P., Zaragoza, J.H. & Larrañaga, P. (2014). Multi-label classification with Bayesian network-based chain classifiers. Pattern Recognition Letters, 41, 14-22.
• Antonio Gracia; Santiago Gonzalez; Víctor Robles; Ernestina Menasalvas. “A methodology to compare Dimensionality Reduction algorithms in terms of quality loss”. Information Sciences, 270(0): 1-27, DOI: 10.1016/j.ins.2014.02.068 Jun. 2014.
• Antonio Gracia; Santiago González; Víctor Robles; Ernestina Menasalvas; Tatiana von Landesberger; “New insights into the suitability of the third dimension for visualizing multivariate/multidimensional data: A study based on loss of quality quantification”. Information Visualization. SAGE DOI: 10.1177/1473871614556393 Nov. 2014.
• P. Marquez-Neila, L. Baumela, L. Alvarez. A Morphological Approach to Curvature-based Evolution of Curves and Surfaces. IEEE Transactions on Pattern Analysis and Machine Intelligence, 36 (1):2-17, 2014.
• Araque A, Camignoto G, Haydon PG, Oliet SH, Robitaille R, Volterra A (2014) Gliotransmitters travel in time and space. Neuron 81:728-739.
• Perez-Alvarez A, Navarrete M, Covelo A, Martin ED, Araque A (2014) Structural and functional plasticity of astrocyte processes and dendritic spine interactions. Journal of Neuroscience 34:12738-12744.
• Perea G, Sur M, Araque A (2014) Neuron-glia networks: integral gear of brain function. Frontiers in Cellular Neuroscience 8:378.
• Jego P, Pacheco-Torres J, Araque A, Canals S (2014) Functional MRI in mice lacking IP3-dependent calcium signaling in astrocytes. Journal of Cerebral Blood Flow & Metabolism 34:1599-1603.
• Navarrete M, Díez A, Araque A (2014) Astrocytes in endocannabinoid signaling. Philosophical Transactions of the Royal Society B 369: 20130599.
• Navarrete M, Araque A (2014) The Cajal School and the physiological role of astrocytes: a way of thinking. Frontiers in Neuroanatomy 8:33.
• Laura Raya, Sofía Bayona Beriso, Luis Pastor, Marcos García: A New User-Adapted Search Haptic Algorithm to Navigate along Filiform Structures. IEEE T. Haptics (TOH) 7(3):273-284 (2014)

Other CBBP Publications

• DeFelipe J (2014) El Jardín de la Neurología: Sobre lo bello, el arte y el cerebro. Boletín Oficial del Estado y Consejo Superior de Investigaciones Científicas, Madrid.
• G. Varando, C., Bielza, P. Larrañaga (2014). Multi-output regression models with MoPs Bayesian networks. Technical Report, UPM-FI/DIA/2014-2, Technical University of Madrid.15 pages.
• Hernando, J., Duelo, C., Martin, V., Visualization of Large-Scale Neural Simulations. In: Brain-Inspired Computing. International Workshop, BrainComp 2013. Revised Selected Papers. L. Grandinetti et al. (eds.), Springer Verlag, LNCS 8603, pp. 184-197, 2014. Book chapter.
• Muelas, S., Mendiburu, A., LaTorre, A., & Peña, J. M. (2014). Distributed Estimation of Distribution Algorithms for continuous optimization: How does the exchanged information influence their behavior? Information Sciences, 268, 231-254.
• Gracia; A., Gonzalez; S., Robles; V., Menasalvas, E. (2014). A methodology to compare Dimensionality Reduction algorithms in terms of quality loss”. Information Sciences, 270(0): 1-27, DOI: 10.1016/j.ins.2014.02.068
• Peña, J. M., Viedma, J., Muelas, S., LaTorre, A., & Peña, L. (2014, August). Designer-driven 3D buildings generated using Variable Neighborhood Search. In Computational Intelligence and Games (CIG), 2014 IEEE Conference on (pp. 1-8). IEEE.
• Gracia, A., González, S., Robles, V., Menasalvas, E., & von Landesberger, T. (2014). New insights into the suitability of the third dimension for visualizing multivariate/multidimensional data: A study based on loss of quality quantification. Information Visualization, 1473871614556393.

2013 CBBP Scientific Publications

• Benavides-Piccione R, Fernaud-Espinosa I, Robles V, Yuste R, DeFelipe J. Age-Based Comparison of Human Dendritic Spine Structure Using Complete Three-Dimensional Reconstructions. Cereb Cortex. 2012 Jun 17
• Armañanzas R, Alonso-Nanclares L, DeFelipe-Oroquieta J, Kastanauskaite A, de Sola R G, DeFelipe J, Bielza C, Larrañaga P (2013). Machine learning approach for the outcome prediction of temporal lobe epilepsy surgery. PLoS ONE, 8 (4), e62819. PMID: 23646148
• Alonso-Nanclares L, Merino-Serrais P, Gonzalez S, DeFelipe J (2013). Synaptic changes in the dentate gyrus of APP/PS1 transgenic mice reveales by electron microscopy. Journal of Neuropathology and Experimental Neurology 72(5): 386-95. Doi: 10.1097/ NEN.0b013e31828d41ec. PMID: 23584198.
• LaTorre A, Alonso-Nanclares L, Muelas, S, Peña JM, DeFelipe J (2013). Segmentation of Neuronal Nuclei Based on Clump Splitting and a Two-step Binarization of Images. Expert Systems with Applications, 40 (16): 6521-30.
• Alonso-Nanclares L and DeFelipe J (2013). Alterations of the microvascular network in the sclerotic hippocampus of patients with temporal lobe epilepsy. Epilepsy and Behaviour (in press)
• LaTorre A, Alonso-Nanclares L, Muelas, S, Peña JM, DeFelipe J (2013). 3D Segmentations of Neuronal Nuclei from Confocal Microscope Image Stacks. Front. Neuroanat. 7:49. doi:10.3389/fnana.2013.00049
• Blazquez-Llorca, L., Merchán-Pérez, A., Rodríguez, J.-R., Gascón, J., and Defelipe, J. (2013). FIB/SEM Technology and Alzheimer’s Disease: Three-Dimensional Analysis of Human Cortical Synapses. J. Alzheimers Dis. 34, 995–1013.
• Inan, M., Blázquez-Llorca, L., Merchán-Pérez, A., Anderson, S. A., Defelipe, J., and Yuste, R. (2013). Dense and overlapping innervation of pyramidal neurons by chandelier cells. J. Neurosci. 33, 1907–1914.
• Merchán-Pérez, A., Rodríguez, J.-R., González, S., Robles, V., DeFelipe, J., Larrañaga, P., and Bielza, C. (2013). Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study. Cereb. Cortex, bht018.
• Montes, J., Gomez, E., Merchán-Pérez, A., DeFelipe, J., and Peña, J.-M. (2013). A Machine Learning Method for the Prediction of Receptor Activation in the Simulation of Synapses. PLoS ONE 8, e68888.
• Morales, J., Rodríguez, A., Rodríguez, J.-R., DeFelipe, J., and Merchán-Pérez, A. (2013). Characterization and extraction of the synaptic apposition surface for synaptic geometry analysis. Front. Neuroanat 7, 20.
• Benavides-Piccione R, Fernaud-Espinosa I, Robles V, Yuste R, DeFelipe J (2013) Age-Based Comparison of Human Dendritic Spine Structure Using Complete Three-Dimensional Reconstructions. Cereb Cortex 23:1798-1810.
• DeFelipe J, López-Cruz PL, Benavides-Piccione R, Bielza C, Larrañaga P, Anderson S, Burkhalter A, Cauli B, Fairén A, Feldmeyer D, Fishell G, Fitzpatrick D, Freund TF, González-Burgos G, Hestrin S, Hill S, Hof PR, Huang J, Jones EG, Kawaguchi Y, Kisvárday Z, Kubota Y, Lewis DA, Marín O, Markram H, McBain CJ, Meyer HS, Monyer H, Nelson SB, Rockland K, Rossier J, Rubenstein JL, Rudy B, Scanziani M, Shepherd GM, Sherwood CC, Staiger JF, Tamás G, Thomson A, Wang Y, Yuste R, Ascoli GA (2013). New insights into the classification and nomenclature of cortical GABAergic interneurons. Nature Neuroscience 14:202-216.
• Llorens-Martín M, Fuster-Matanzo A, Teixeira CM, Jurado-Arjona J, Ulloa F, Defelipe J, Rábano A, Hernández F, Soriano E, Avila J. GSK-3β overexpression causes reversible alterations on postsynaptic densities and dendritic morphology of hippocampal granule neurons in vivo. Mol Psychiatry. 2013 Apr; 18(4):451-60.
• Leon-Espinosa G, Garcia E, Garcia-Escudero V, Hernandez F DeFelipe J, Avila,J (2013) Changes in tau phosphorylation in hibernating rodents. J Neurosci Res. J Neurosci Res. 2013 Apr 19. doi: 10.1002/jnr.23220.
• Miguéns M, Kastanauskaite A, Coria SM, Selvas A, Ballesteros-Yañez I, Defelipe J, Ambrosio E (2013) The Effects of Cocaine Self-Administration on Dendritic Spine Density in the Rat Hippocampus Are Dependent on Genetic Background. Cereb Cortex. 2013 Aug 21. [Epub ahead of print]
• Brito JP, Mata S, Bayona S, Pastor L, Defelipe J, Benavides-Piccione R. (2013) Neuronize: a tool for building realistic neuronal cell morphologies. Front Neuroanat. 2013; 7:15. doi: 10.3389/fnana.2013.00015.
• Merino-Serrais P, Benavides-Piccione R, Blazquez-Llorca L, Kastanauskaite A, Rábano A, Avila J, DeFelipe J (2013) The influence of phosphotau on dendritic spines of cortical pyramidal neurons in Alzheimer’s disease patients. Brain 136:1913-1928.
• Llorens-Martín M, Fuster-Matanzo A, Teixeira CM, Jurado-Arjona J, Ulloa F, Defelipe J, Rábano A, Hernández F, Soriano E, Avila J. (2013) Alzheimer disease-like cellular phenotype of newborn granule neurons can be reversed in GSK-3β-overexpressing mice. Mol Psychiatry. 18(4):395. doi: 10.1038/mp.2013.27
• López-Cruz, P.L., Larrañaga, P., DeFelipe, J., Bielza, C. (2014) Bayesian network modeling of the consensus between experts: An application to neuron classification. International Journal of Approximate Reasoning 55 (1): 3-22. In Press
• Alejandro Antón-Fernández, Pablo Rubio-Garrido, Javier DeFelipe, and Alberto Muñoz (2013) Selective presence of a giant saccular organelle in the axon initial segment of a subpopulation of layer V pyramidal neurons. Brain Structure and Function. [Epub ahead of print].
• P. Toharia, J. Morales, O. de Juan, I. Fernaud-Espinosa, A. Rodríguez, J. DeFelipe, Musical representation of dendritic spine distribution: a new exploratory tool, Neuroinformatics Springer Verlag. ISSN 1539-2791 DOI: 10.1007/s12021-013-9195-0 (in, press) pp. 13
• R. Armañanzas, C. Bielza, K.R. Chaudhuri, P. Martínez-Martín, P. Larrañaga (2013). Unveiling relevant non-motor Parkinson’s disease severity symptoms using a machine learning approach. Artificial Intelligence in Medicine, 58(3), 195–202.
• H. Borchani, C. Bielza, P. Martínez-Martín, P. Larrañaga (2013). Predicting EQ-5D from the Parkinson’s disease questionnaire using multi-dimensional Bayesian network classifiers. Biomedical Engineering: Applications, Basis and Communications, in press.
• D. Morales, Y. Vives-Gilabert, B. Gómez-Ansón, E. Bengoetxea, P. Larrañaga, C. Bielza, J. Pagonabarraga, J. Kulisevsky, I. Corcuera-Solano, M. Delfino (2013). Predicting dementia development in Parkinson’s disease using Bayesian network classifiers. Psychiatry Research: NeuroImaging, 213, 92-98
• R. Santana, L. McGarry, C. Bielza, P. Larrañaga, R. Yuste (2013). Classification of neocortical interneurons using affinity propagation. Frontiers in Neural Circuits, in press.
• D. Vidaurre, C. Bielza, P. Larrañaga (2013). Classification of neural signals from sparse autoregressive features. Neurocomputing, 111, 21–26.
• C. Bielza, J.A. Fernández del Pozo, P. Larrañaga (2013). Parameter control of genetic algorithms by learning and simulation of Bayesian Networks. A case study for the optimal ordering of tables. Journal of Computer Science and Technology, 28(4), 720–731.
• H. Borchani, C. Bielza, C. Toro, P. Larrañaga (2013). Predicting human immunodeficiency virus inhibitors using multi-dimensional Bayesian network classifiers. Artificial Intelligence in Medicine, 57(3), 219–229.
• M. García-Torres, R. Armañanzas, C. Bielza, P. Larrañaga (2013). Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data. Information Sciences, 222, 229–246.
• L. Guerra, C. Bielza, V. Robles, P. Larrañaga (2013). Semi-supervised projected model-based clustering. Data Mining and Knowledge Discovery, in press.
• A. Ibáñez, C. Bielza, P. Larrañaga (2013). Análisis de la actividad científica de las universidades públicas españolas en el área de las tecnologías informáticas. Revista Española de Documentación Científica, 36(1), e002
• A. Ibáñez, C. Bielza, P. Larrañaga (2013). Cost-sensitive selective naive Bayes classifiers for predicting the increase of the h-index for scientific journals. Neurocomputing, in press.
• A. Ibáñez, P. Larrañaga, C. Bielza (2013). Cluster methods for assessing research performance: Exploring Spanish computer science. Scientometrics, in press.
• A. Ibáñez, C. Bielza, P. Larrañaga (2013). Relationship among research collaboration, number of documents and number of citations. A case study in Spanish computer science production in 2000-2009. Scientometrics, in press.
• H. Karshenas, R. Santana, C. Bielza, P. Larrañaga (2013). Multi-objective estimation of distribution algorithms based on joint modeling of objectives and variables. IEEE Transactions on Evolutionary Computation, in press.
• H. Karshenas, R. Santana, C. Bielza, P. Larrañaga (2013). Regularized continuous estimation of distribution algorithms. Applied Soft Computing, 13(5), 2412-2432.
• P. Larrañaga, H. Karshenas, C. Bielza, R. Santana (2013). A review on evolutionary algorithms in Bayesian network learning and inference tasks. Information Sciences, 233, 109–125.
• P.L. López-Cruz, C. Bielza, P. Larrañaga (2013). Directional naive Bayes classifiers. Pattern Analysis and Applications, in press.
• P.L. López-Cruz, C. Bielza, P. Larrañaga (2013). Learning mixtures of polynomials of multidimensional probability densities from data using B-spline interpolation. International Journal of Approximate Reasoning, in press.
• J. Read, C. Bielza, P. Larrañaga (2013). Multi-dimensional classification with super-classes. IEEE Transactions on Knowledge and Data Engineering, in press.
• R. Santana, R. Armañanzas, C. Bielza, P. Larrañaga (2013). Network measures for information extraction in evolutionary algorithms. International Journal of Computational Intelligence Systems, 6(6), 1163-1188.
• E. Sucar, C. Bielza,  E. F. Morales, P. Hernández-Leal,  J. H. Zaragoza,  P. Larrañaga (2013). Multi-label classification with Bayesian network-based chain classifiers. Pattern Recognition Letters, in press.
• D. Vidaurre, C. Bielza, P. Larrañaga (2013). A survey of L1 regression. International Statistical Review, in press.
• D. Vidaurre, C. Bielza, P. Larrañaga (2013). An L1-regularized naive Bayes-inspired classifier for discarding redundant predictors. International Journal on Artificial Intelligence Tools, 22(4), 1350019.
• D. Vidaurre, M. van Gerven, C. Bielza, P. Larrañaga, T. Heskes (2013). Bayesian partial least squares. Neural Computation, in press.
• D. Vidaurre, C. Bielza, P. Larrañaga (2013). Sparse regularized local regression. Computational Statistics and Data Analysis, 62, 122–135.
• Pablo Márquez-Neila, Luis Baumela, Luis Alvarez. A morphological approach to curvature-based evolution of curves and surfaces, IEEE Transactions on Pattern Analysis and Machine Intelligence. Vol. 36(1), pp. 2-17, 2014.
• A. Jérusalem, J.A. García, A. Merchán-Pérez and J.M. Peña, A computational model coupling mechanics and electrophysiology in spinal cord injury Biomechanics and Modeling in Mechanobiology, (in press)
• Araque A, Camignoto G, Haydon PG, Oliet SH, Robitaille R, Volterra A (2014) Gliotransmitters travel in time and space. Neuron (in press).
• Fields RD, Araque A, Johansen-Berg H, Lim SS, Lynch G, Nave KA, Nedergaard M, Perez R, Sejnowski T, Wake H (2013) Glial Biology in Learning and Cognition. The Neuroscientist (in press).
• Pérez-Alvarez A, Araque A, Martín ED (2013) Confocal microscopy for astrocyte in vivo imaging: Recycle and reuse in microscopy. Frontiers in Cellular Neuroscience 7:51.
• Pérez-Alvarez A, Araque A (2013) Astrocyte-neuron interaction at Tripartite Synapses. Current Drug Targets 14:1220-1224.
• Navarrete M, Perea G, Maglio L, Pastor J, de Sola RG, Araque A (2013) Astrocyte calcium signal and gliotransmission in human brain tissue. Cerebral Cortex 23: 1240-1246.

Other CBBP Publications

• Comment by Javier DeFelipe on: Stem Cells Treat Epileptic Symptoms in Mice. Alzheimer Research Forum. May 8, 2013. Available at http://www.alzforum.org/new/detail.asp?id=3483. Accessed May 17, 2013
• DeFelipe J. Análisis del cerebro: innovación tecnológica y estrategia interdisciplinar. CIC NETWORK 24-28, 2013.
• DeFelipe J. Cajal’s Butterflies of the Soul. OUPblog as it continues to be a popular title at SFN.
• DeFelipe J, Alonso-Nanclares L (2013). The Synapse: differences between men and women. In: D.W. Pfaff and Y. Christen (eds.), Multiple Origins of Sex Differences in Brain, Research and Perspectives in Endocrine Interactions. Springer-Verlag, Berlin Heidelberg (DOI 10.1007/978-3-642-33721-5_4)
• DeFelipe J (2013) Cajal and the discovery of a new artistic world: The neuronal forest. Prog Brain Res. 2013; 203:201-220. In: The Fine Arts, Neurology and Neuroscience: History and Modem Perspectives. Eds: Stanley Finger, Dahlia Zajdel, Francois Boller and Julien Bogousslavsky. Elsevier, New York
• C. Bielza, A. Salmerón, A. Alonso-Betanzos, J.I. Hidalgo, L. Martínez, A. Troncoso, E. Corchado, J.M. Corchado (Eds.) (2013). Advances in Artificial Intelligence, Lecture Notes in Artificial Intelligence, Vol 8109. Springer. 404 pages. ISBN: 978-3-642-40642-3.
• C. Bielza, A. Salmerón (Eds.) (2013). Actas de la XV Conferencia de la Asociación Española para la Inteligencia Artificial (CAEPIA 2013). 158 pages. ISBN: 978-84-695-8348-7.
• C. Bielza, P. Larrañaga (2013). More than 20 entries in Concise Encyclopaedia of Bioinformatics and Computational Biology. Wiley.
• L. Guerra, R. Benavides-Piccione, C. Bielza, V. Robles, J. DeFelipe, P. Larrañaga (2013). Semi-supervised projected clustering for classifying GABAergic interneurons. Artificial Intelligence in Medicine 2013, Lecture Notes in Artificial Intelligence 7885, pages 156-165, Springer.
• P.L. Lopez-Cruz, C. Bielza, P. Larrañaga (2013). Learning conditional linear Gaussian classifiers with probabilistic class labels. Advances in Artificial Intelligence. Lecture Notes in Computer Science 8109, pages 139-148, Springer.
• P.L. Lopez-Cruz, T.D. Nielsen, C. Bielza, P. Larrañaga (2013). Learning mixtures of polynomials of conditional densities from data. Advances in Artificial Intelligence. Lecture Notes in Computer Science 8109, pages 363-372, Springer.
• B. Mihaljevic, P. Larrañaga, C. Bielza (2013). Augmented semi-naive Bayes classifier. Advances in Artificial Intelligence. Lecture Notes in Computer Science 8109, pages159-167, Springer.
• R. Santana, C., Bielza, P. Larrañaga (2013). Changing conduction delays to maximize the number of polychronous groups with an estimation of distribution algorithm. Technical Report, UPM-FI/DIA/2013-1, Technical University of Madrid.13 pages.
• Kendrick Cetina, Pablo Márquez-Neila, Luis Baumela. Un Estudio Comparativo de Descriptores de Caracteríısticas para la Segmentación de Sinapsis y Mitocondrias. En Actas del III Workshop de Reconocimiento de Formas y Análisis de Imágenes, pp. 25-28, Septiembre 2013.
• Luis Baumela (Editor).Actas del III Workshop de Reconocimiento de Formas y Análisis de Imágenes. Madrid. 19 de septiembre de 2013. ISBN: 978-84-695-8332-6.
• Araque A, Navarrete M (2013) El ayer y hoy de los astrocitos. Mente y Cerebro 60: 86-91.

Other Publications

• P. Toharia, O. D. Robles, J. L. Bosque, Á. Rodríguez, Scalable shot boundary detection, Journal of Supercomputing. Springer Verlag. ISSN 0920-8542 DOI: 10.1007/s11227-012-0784-8 64(1): 89-99 Apr. 2013
• Validation of a Virtual Reality Knee Arthroscopy Simulator for Surgical Training. Akhtar, K; Bayona, S.; Bello, F; Gupte, CM; Cobbs, JP; Arthroscopy: The Journal of Arthroscopic & Related Surgery. Volumen: Vol 29, 10 Pág. 138 -139. Fecha: 2013/10/31, 2013. Editorial: WB Saunders, Elsevier. ISSN: 07498063. doi: 10.1016/j.arthro.2013.07.177.
• On-Board Multi-GPU Molecular Dynamics. Marcos Novalbos, Jaime Gonzalez, Miguel Angel Otaduy, Alvaro Lopez-Medrano, Alberto Sanchez: Euro-Par 2013: 862-873, August 2013
• Assessing Skills Decay on a Knee Arthroscopy Simulator. Akhtar, K; Wijendra, A; Bayona,S.; Gupte,CM; Bello,F; Standfield, N.; Cobbs, JP; Arthroscopy: The Journal of Arthroscopic & Related Surgery. Volumen: Vol 29, 10 Pág. 139-139. Fecha: 2013/10/31, 2013 WB Saunders, Elsevier, ISSN: 07498063 doi: 10.1016/j.arthro.2013.07.177
• GMonE: A complete approach to cloud monitoring. Jesús Montes, Alberto Sánchez, Bunjamin Memishi, Maria s. Pérez, Gabriel Antoniou. Future Generation Computer Systems. Volume 29, Issue 8, 2026—2040, October 2013
• Jose L. Bosque, Pablo Toharia, Oscar D. Robles, Luis Pastor. “Impact of Information Exchange Policies in Load Balancing Algorithms”. Journal of Supercomputing, under review.

2012 CBBP Scientific Publications

• Benavides-Piccione R, Fernaud-Espinosa I, Robles V, Yuste R, DeFelipe J. Age-Based Comparison of Human Dendritic Spine Structure Using Complete Three-Dimensional Reconstructions. Cereb Cortex. 2012 Jun 17
• Morales J, Benavides-Piccione R, Rodríguez A, Pastor L, Yuste R, DeFelipe J. Three-Dimensional Analysis of Spiny Dendrites Using Straightening and Unrolling Transforms. Neuroinformatics. 2012 May 27
• Knafo S, Venero C, Sánchez-Puelles C, Pereda-Peréz I, Franco A, Sandi C, Suárez LM, Solís JM, Alonso-Nanclares L, Martín ED, Merino-Serrais P, Borcel E, Li S, Chen Y, Gonzalez-Soriano J, Berezin V, Bock E, DeFelipe J, Esteban JA. Facilitation of AMPA receptor synaptic delivery as a molecular mechanism for cognitive enhancement. PLoS Biol. 2012 Feb; 10 (2):e1001262. Epub 2012 Feb 21.
• Martinez de Lagran M, Benavides-Piccione R, Ballesteros-Yañez I, Calvo M, Morales M, Fillat C, DeFelipe J, Ramakers GJ, Dierssen M. Dyrk1A Influences Neuronal Morphogenesis Through Regulation of Cytoskeletal Dynamics in Mammalian Cortical Neurons. Cereb Cortex. 2012 Jan 2.
• DeFelipe J, Markram H, Rockland KS. The neocortical column. Front Neuroanat. 2012. 6: 22. Epub 2012 Jun 26
• Avila J, León-Espinosa G, García E, García-Escudero V, Hernández F, DeFelipe J. Tau Phosphorylation by GSK3 in Different Conditions. Int J Alzheimers Dis. 2012; 2012:578373. Epub 2012 May 17.
• León-Espinosa G, DeFelipe J, Muñoz A. Effects of amyloid-β plaque proximity on the axon initial segment of pyramidal cells. J Alzheimers Dis. 2012; 29 (4):841-52.
• Rockland KS, DeFelipe J (2012) Cortical GABAergic neurons: stretching it. Front Neuroanat. 2012; 6:16. Epub 2012 May 31. Front Neuroanat. 2012; 6: 22.
• Jimenez-Mateos EM, Engel T, Merino-Serrais P, McKiernan RC, Tanaka K, Mouri G, Sano T, O’Tuathaigh C, Waddington JL, Prenter S, Delanty N, Farrell MA, O’Brien DF, Conroy RM, Stallings RL, Defelipe J, Henshall DC (2012). Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nat Med. 18:1087-1094.
• Sánchez-Ponce D, DeFelipe J, Garrido JJ, Muñoz A (2012) Developmental expression of Kv potassium channels at the axon initial segment of cultured hippocampal neurons. Plos One 7 (10):e48557. doi: 10.1371/journal.pone.0048557.
• Merchán-Pérez A, Rodríguez J-R, González S, Robles V, DeFelipe J, Larrañaga P and Bielza C. Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study. Cerebral Cortex, in press.
• Inan M, Blazquez-Llorca L, Merchan-Perez A, Anderson SA, DeFelipe J and Yuste R Dense and Overlapping Innervation of Pyramidal Neurons by Neocortical Chandelier Cells. Journal of Neuroscience, in press.
• Llorens-Martín M, Fuster-Matanzo A, Teixeira CM, Jurado-Arjona J, Ulloa F, Defelipe J, Rábano A, Hernández F, Soriano E, Avila J. GSK-3β overexpression causes reversible alterations on postsynaptic densities and dendritic morphology of hippocampal granule neurons in vivo. Mol Psychiatry. doi: 10.1038/mp.2013.4. [Epub ahead of print]
• Blazquez-Llorca L, Merchán-Pérez A, Rodríguez R, Gascón J, Defelipe J (2013) FIB/SEM Technology and Alzheimer’s Disease: Three-Dimensional Analysis of Human Cortical Synapses. J Alzheimers Dis. [Epub ahead of print]
• Leon-Espinosa G, Garcia E, Garcia-Escudero V, Hernandez F DeFelipe J, Avila,J Changes in tau phosphorylation in hibernating rodents. J Neurosci Res (in press)
• Merino-Serrais P, Benavides-Piccione R, Blazquez-Llorca L, Kastanauskaite A, Rábano A, Avila J, DeFelipe J The influence of phosphotau on dendritic spines of cortical pyramidal neurons in Alzheimer’s disease patients. Brain (in press)
• Alonso-Nanclares L, Merino-Serrais P, Gonzalez S, DeFelipe J. Synaptic changes in the dentate gyrus of app/ps1 transgenic mice revealed by electron microscopy. J Neuropathol Exp Neurol (in press)
• Pedro L. López-Cruz, Pedro Larrañaga, Javier DeFelipe, Concha Bielza. Bayesian network modeling of the consensus between experts: An application to neuron classification. International Journal of Approximate Reasoning: accepted.
• DeFelipe J, López-Cruz PL, Benavides-Piccione R, Bielza C, Larrañaga, et al. Classification and nomenclature of neocortical GABAergic interneurons. Nature Reviews Neuroscience: accepted.
• Merchán-Pérez A, Rodríguez J-R, González S, Robles V, DeFelipe J, Larrañaga P and Bielza C. Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study. Cerebral Cortex, in press.
• Larrañaga P, Concha Bielza C, DeFelipe J. Alan Turing y la neurociencia. Mente y Cerebro, 57, 49–51.
• Santana, R., Bielza, C. & Larrañaga, P. Conductance interaction identification by means of Boltzmann distribution and mutual information analysis in conductance-based neuron models. BMC Neuroscience, 13(Suppl 1), P100.
• Armañanzas, R., Larrañaga, P., Bielza, C. Ensemble transcript interaction networks: A case study on Alzheimer’s disease. Computer Methods and Programs in Biomedicine, 108(1), 442-450.
• Borchani, H., Bielza, C., Martínez-Martín, P., Larrañaga, P. Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: An application to predict the European Quality of Life-5Dimensions (EQ-5D) from the 39-item Parkinson’s Disease Questionnaire (PDQ-39). Journal of Biomedical Informatics, 45, 1175-1184.
• Morales, D., Vives-Gilabert, Y., Gómez-Ansón, B., Bengoetxea, E., Larrañaga, P., Bielza, C., Pagonabarraga, J., Kulisevsky, J., Corcuera-Solano, I., Delfino, M. Predicting dementia development in Parkinson’s disease using Bayesian network classifiers. Psychiatry Research: NeuroImaging, accepted.
• Santana, R., Bielza, C., Larrañaga, P. Regularized logistic regression and multi-objective variable selection for classifying MEG data. Biological Cybernetics, 106(6-7), 389-405.
• Vidaurre, D., Bielza, C., Larrañaga, P. Lazy lasso for local regression. Computational Statistics, 27(3), 531-550 (with application to fMRI data analysis).
• Vidaurre, D., Rodríguez, E.E., Bielza, C., Larrañaga, P., Rudomin, P. A new feature extraction method for signal classification applied to cat spinal cord signals. Journal of Neural Engineering, accepted.
• Vidaurre, D., Bielza, C., Larrañaga, P. Classification of neural signals from sparse autoregressive features. Neurocomputing: accepted.
• García-Bilbao, A., Armañanzas, R., Ispizua, Z., Calvo, B., Alonso-Varona, A., Inza, I., Larrañaga, P., López-Vivanco, G., Suárez-Merino, B., Betanzos, M. Identification of a biomarker panel for colorectal cancer diagnosis. BMC Cancer, 12(43).
• García-Torres, M., Armañanzas, R., Bielza, C. & Larrañaga, P. (2013). Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data. Information Sciences, 222, 229-246.
• Borchani, H., Bielza, C., Larrañaga, P., Toro, C. Learning multi-dimensional Bayesian network classifiers using Markov blankets: A case study in the prediction of HIV-1 reverse transcriptase and protease inhibitors. Artificial Intelligence In Medicine, accepted.
• Guerra, L., V. Robles, Bielza, C., Larrañaga, P. A comparison of clustering quality indices using outliers and noise. Intelligent Data Analysis, 16(4), 703-715.
• Ibañez, A., Bielza, C., Larrañaga, P. Relationship among research collaboration, number of documents and number of citations. A case study in Spanish computer science production in 2000-2009. Scientometrics, accepted.
• Ibañez, A., Bielza, C., Larrañaga, P. Analysis of scientific activity in Spanish public universities in the area of computer science. Revista Española de Documentación Científica, accepted.
• Larrañaga P., Bielza, C. Alan Turing and Bayesian statistics. Mathware & Soft Computing Magazine, 19, 2, 23-24.
• Larrañaga, P., Karshenas, H., Bielza, C., Santana, R. A review on probabilistic graphical models in evolutionary computation. Journal of Heuristics, 18(5), 795-819.
• P. Larrañaga, H. Karshenas, C. Bielza, R. Santana. A Review on Evolutionary Algorithms in Bayesian Network Learning and Inference Tasks. Information Sciences, accepted.
• H. Karshenas, R. Santana, C. Bielza, P. Larrañaga. Regularized Continuous Estimation of Distribution Algorithms. Applied Soft Computing, accepted.
• Morales J, Benavides-Piccione R, Rodríguez A, Pastor L, Yuste R, DeFelipe J. “Three-dimensional analysis of spiny dendrites using straightening and unrolling transforms” Neuroinformatics Springer Verlag. Vol. 10 No. 4 ISSN 1539-2791 DOI: 10.1007/s12021-012-9153-2 pp. 391-407. 2012 Indexed: JCR
• Merchán-Pérez A, Rodríguez J-R, González S, Robles V, DeFelipe J, Larrañaga P and Bielza C. Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study. Cerebral Cortex, in press.
• García JA, Peña JM,. McHugh S, Jérusalem A. A model of the spatially dependent mechanical properties of the axon during its growth. Computational Modeling in Engineering & Science (CMES), in press.
• Jérusalem A, Dao M. Continuum modeling of neuronal cell under blast loading. Acta Biomaterialia, 8 (9), 3360-3371, 2012
• Navarrete M, Perea G, Maglio L, Pastor J, de Sola RG, Araque A (2012) Astrocyte calcium signal and gliotransmission in human brain tissue. Cerebral Cortex (in press)
• Navarrete M, Perea G, Fernandez de Sevilla D, Gómez-Gonzalo M, Núñez A, Martín ED, Araque A (2012) Astrocytes mediate in vivo cholinergic-induced synaptic plasticity. Plos Biology 10: e1001259.
• Zorec R, Araque A, Carmignoto G, Haydon PG, Verkhratsky A, Parpura V (2012) Astroglial excitability and gliotransmission: An appraisal of Ca2+ as a signaling route. ASN Neuro 4: e00080.

Other CBBP Publications

• Karshenas, H., Santana, R., Bielza, C., Larrañaga, P. Continuous Estimation of Distribution Algorithms Based on Factorized Gaussian Markov Networks. In Adaptation, Learning & Optimization. Series Vol. 14 (editors), Markov Networks in Evolutionary Algorithms. Springer
• Gonzalez S. Análisis de simulación de Sinapsis. Technical report.
• Gracia A and S. Gonzalez S. MedVir aplicado a la morfología de las neuronas. Technical report.
• Alonso-Nanclares L, Merino-Serrais P, Gonzalez S, DeFelipe J. Synaptic changes in the dentate gyrus of app/ps1 transgenic mice revealed by electron microscopy. J Neuropathol Exp Neurol (in press)

Other Publications

• Peña JM. El Futuro de la Fármaco-Economía: Minería de datos y supercomputación, in “Fármaco-Economía” Monográficas de Oncología Médica, to appear 2012

2011 CBBP Scientific Publications

• From the Connectome to the Synaptome: An Epic Love Story. DeFelipe J. Science 26 November 2010: Vol. 330 no. 6008 pp. 1198-1201 DOI: 10.1126/science.1193378
• Elston G, Benavides-Piccione R, Elston A, Manger P and Defelipe J (2011). Pyramidal cells in prefrontal cortex: comparative observations reveal unparalleled specializations in neuronal structure among primate species. Front. Neuroanat. 5:2. doi: 10.3389/fnana.2011.00002
• López, PL, Bielza C, Larrañaga P, Benavides-Piccione R, DeFelipe J (2011) Models and simulation of 3D neuronal dendritic trees using Bayesian networks. Neuroinformatics (in press).
• Alonso-Nanclares L, Kastanauskaite A, Rodriguez JR, Gonzalez-Soriano J, DeFelipe J (2011) A stereological study of synapse number in the epileptic human hippocampus. Front. Neuroanat. 5:8. doi: 10.3389/fnana.2011.00008
• DeFelipe J (2011) The evolution of the brain, the human nature of cortical circuits and intellectual creativity. Front. Neuroanat. 5:29.
• Blazquez-Llorca L, Garcia-Marin V, Merino-Serrais P, Avila J and DeFelipe J (2011) Abnormal tau phosphorylation in the thorny excrescences of CA3 hippocampal neurons in patients with Alzheimer’s. J Alzheimer Disease 26: 683-698.
• Sánchez-Ponce D, Blazquez-Llorca L, DeFelipe J, Garrido JJ, Muñoz A (2011) Co-localization of α-actinin and synaptopodin in the pyramidal cell axon initial segment. Cereb Cortex (in press).
• S. Knafo, C. Venero, C. Sánchez-Puelles, I. Pereda-Peréz, A. Franco, C. Sandi, L.M. Suárez, J.M. Solís, L. Alonso-Nanclares, E.D. Martín, P. Merino-Serrais, E. Borcel, S. Li, Y. Chen, J. Gonzalez-Soriano , V. Berezin, E. Bock, J. De Felipe, J.A. Esteban. Facilitation of AMPA receptor synaptic delivery as a molecular mechanism for cognitive enhancement. PLoS Biology (in press).
• Mara et al Dyrk1A influences neuronal morphogenesis through regulation of cytoskeletal dynamics in mammalian cortical neuron. Cerebr Corteex (in press).
• Franco A, Knafo S, Banon-Rodriguez I, Merino-Serrais P, Fernaud-Espinosa I, Nieto M, Garrido JJ, Esteban JA, Wandosell F, Anton IM. (2011) WIP Is a Negative Regulator of Neuronal Maturation and Synaptic Activity. Cereb Cortex. Aug 1. [Epub ahead of print].
• Merino-Serrais P, Knafo S, Alonso-Nanclares L, Fernaud-Espinosa I, Defelipe J (2011). Layer-specific alterations to CA1 dendritic spines in a mouse model of Alzheimer’s disease. Hippocampus 21(10):1037-1044.
• Sánchez-Ponce D, Muñoz A, Garrido JJ (2011) Casein kinase 2 and microtubules control axon initial segment formation. Moll and Cell Neurosci 46: 222- 234
• Sánchez-Ponce D, DeFelipe J, Garrido JJ, AMuñoz A (2011) Maturation of the cisternal organelle in the hippocampal neuron’s axon initial segment. Moll and Cell Neurosci 48: 104-116
• Sánchez-Ponce D, Blázquez Llorca L, DeFelipe J, Garrido JJ, Alberto Muñoz (2011) Colocalization of α-actinin and synaptopodin in the pyramidal cell axon initial segment. Cerebral Cortex Epub Sep 21
• León G, DeFelipe J, Muñoz A 2011 Effects of amyloid-beta plaque proximity on the axon initial segment of pyramidal cells. Journal of Alzheimer’s Disease. In Press
• J. Morales, L. Alonso-Nanclares, J. R. Rodríguez, A. Merchán-Pérez, J. de Felipe, A. Rodríguez. “Fast interactive quantification of synapses in the cerebral cortex” International Journal of Artificial Intelligence Tools. World Scientific Publishing Co. ISSN 0218-2130 DOI: 10.1142/S0218213011000139 Vol.: 20(2) Pages: 239-252 Apr., 2011
• Navarrete M, Perea G, Fernandez de Sevilla D, Gómez-Gonzalo M, Nuñez A, Martín E and Araque A (2012) Astrocytes mediate in vivo cholinergic-induced synaptic plasticity. PLoS Biology 10: e1001259.
• Navarrete M, Perea G, Maglio L, Pastor J, García de Sola R and Araque A (2011) Astrocyte-neuron signaling in human brain tissue. Cerebral Cortex, under revision.
• Araque A, Navarrete M (2011). Electrically driven insulation in the central nervous system. Science 333: 1587-1588.
• Navarrete M, Araque A (2011) Basal synaptic transmission: astrocytes rule! Cell 146: 675-677.
• Porto-Pazos AB, Veiguela N, Mesejo P, Navarrete M, Alvarellos A, Ibáñez O, Pazos A, Araque A (2011) Artificial astrocytes improve neural network performance. PLoS One 6:e19109.
• Guerra, L., McGarry, L., Robles, V., Bielza, C., Larrañaga, P., Yuste, R. (2011). Comparison between supervised and unsupervised classification of neuronal cell types: A case study. Developmental Neurobiology, 71 (1), 71-82.
• R. Santana, C. Bielza, P. Larrañaga (2011). Optimizing brain networks topologies using multiobjective evolutionary computation. Neurinformatics, 9 (1), 3-19.
• P. López-Cruz, C. Bielza, P. Larrañaga, R. Benavides-Piccione, J. DeFelipe (2011). Models and simulation of 3D neuronal dendritic trees using Bayesian networks. Neuroinformatics, 347-369.
• D. Vidaurre, C. Bielza, P. Larrañaga (2011). On nonlinearity in neural encoding models applied to the primary visual cortex. Network: Computation in Neural Systems, 22 (1-4), 97-125.
• D. Vidaurre, C. Bielza, P. Larrañaga (2011). Lazy lasso for local regression. Computational Statistics DOI: 10.1007/s00180-011-0274-0. In Press.
• R. Armañanzas, P. Larrañaga, C. Bielza (2011). Ensemble transcript interaction networks: A case study on Alzheimer’s disease. Computer Methods and Programs in Biomedicine. In Press.
• D. Vidaurre, C. Bielza, P. Larrañaga (2011). Forward stagewise naive Bayes. Progress in Artificial Intelligence. In Press. (with application to fMRI data analysis).
• Vidaurre, D., Bielza, C. & Larrañaga, P. (2011). An L1-regularized naive Bayes-inspired classifier for discarding redundant predictors. Submitted to International Journal of Pattern Recognition and Artificial Intelligence. (with application to fMRI data analysis).
• J. Morales, L. Alonso-Nanclares, J. R. Rodríguez, A. Merchán-Pérez, J. de Felipe, A. Rodríguez. “Fast interactive quantification of synapses in the cerebral cortex” International Journal of Artificial Intelligence Tools. World Scientific Publishing Co. ISSN 0218-2130 DOI: 10.1142/S0218213011000139 Vol.: 20(2) Pages: 239-252 Apr., 2011
• J. Morales, L. Alonso-Nanclares, J. R. Rodríguez, J. de Felipe, A. Rodríguez and A. Merchán-Pérez. “ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images” Frontiers in Neuroanatomy ISSN 1662-5129 DOI: 10.3389/fnana.2011.00018 Vol.: 5(18) Pages: 1-8 Date: Mar., 2011.

Other Publications

• Higuera-Matas, A., Montoya, G.L., Coria, S.M., MIGUÉNS, M., García-Lecumberri, C., and Ambrosio, E (2011). Differential gene expression in the nucleus accumbens and frontal cortex of Lewis and Fischer 344 rats relevant to drug addiction. Current Neuropharmacology 9(1):143-150.
• Higuera-Matas A, Soto-Montenegro ML, Montoya GL, García-Vázquez V, Pascau J, MIGUÉNS M, Del Olmo N, Vaquero JJ, García-Lecumberri C, Desco M, Ambrosio E (2011). Chronic Cannabinoid Administration to Periadolescent Rats Modulates the Metabolic Response to Acute Cocaine in the Adult Brain. Mol Imaging Biol 13(3): 411-415.
• Miguens M., Coria SM., Higuera-Matas A., Fole A., Ambrosio E., Del Olmo N. (2011). Depotentiation of hippocampal long-term potentiation depends on genetic background and is modulated by cocaine self-administration. Neuroscience 187: 36-42.
• DeFelipe J and Sotelo C (2011) Goodbye Ted (an Obituary for Edward G. Jones). Front. Neuroanat. 5:44. doi: 10.3389/fnana.2011.00044
• Alejandro Higuera-Matas, Miguel Miguens, Nuria del Olmo, Carmen García-Lecumberri and Emilio Ambrosio. Neural Changes Developed during the Extinction of Cocaine Self-Administration Behavior. Pharmaceuticals 2011, 4, 1315-1327; doi: 10.3390/ph4101315.
• Armañanzas, R., Bielza, C., Larrañaga, P. & Martínez-Martín, P. (2011). Restating Parkinson’s disease severity indices by means of non-motor criteria. Technical Report, UPM-FI/DIA/2011-2.

2010 Scientific Publications

• From the Connectome to the Synaptome: An Epic Love Story. DeFelipe J. Science 26 November 2010: Vol. 330 no. 6008 pp. 1198-1201 DOI: 10.1126/science.1193378
• GABAergic complex basket formations in the human neocortex. Blazquez-Llorca L, García-Marín V, DeFelipe J. J Comp Neurol. 2010 Dec 15;518 (24):4917-37.PMID: 21031559 [PubMed – in process] Related citations
• Differential distribution of neurons in the gyral white matter of the human cerebral cortex. García-Marín V, Blazquez-Llorca L, Rodriguez JR, Gonzalez-Soriano J, DeFelipe J. J Comp Neurol. 2010 Dec 1;518(23):4740-59.PMID: 20963826 [PubMed – in process] Related citations
• Layer-specific alterations to CA1 dendritic spines in a mouse model of Alzheimer’s disease. Merino-Serrais P, Knafo S, Alonso-Nanclares L, Fernaud-Espinosa I, Defelipe J. Hippocampus. 2010 Sep 16. [Epub ahead of print]PMID: 20848609 [PubMed – as supplied by publisher]Related citations
• Pericellular innervation of neurons expressing abnormally hyperphosphorylated tau in the hippocampal formation of Alzheimer’s disease patients. Blazquez-Llorca L, Garcia-Marin V, Defelipe J. Front Neuroanat. 2010 Jun 24;4:20. PMID: 20631843 [PubMed – in process]Free PMC Article Free textRelated citations
• Alterations of cortical pyramidal neurons in mice lacking high-affinity nicotinic receptors. Ballesteros-Yáñez I, Benavides-Piccione R, Bourgeois JP, Changeux JP, DeFelipe J. Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11567-72. Epub 2010 Jun 7.PMID: 20534523 [PubMed – indexed for MEDLINE] Related citations
• Cortical white matter: beyond the pale remarks, main conclusions and discussion. Defelipe J, Fields RD, Hof PR, Höistad M, Kostovic I, Meyer G, Rockland KS.Front Neuroanat. 2010 Mar 24;4:4. No abstract available. PMID: 20428509 [PubMed – in process] Free PMC ArticleFree textRelated citations
• Cortical GABAergic Neurons: Stretching it Remarks, Main Conclusions and Discussion. Clancy B, Defelipe J, Espinosa A, Fairén A, Jinno S, Kanold P, Luhmann HJ, Rockland KS, Tamamaki N, Yan XX. Front Neuroanat. 2010 Mar 2; 4:7. No abstract available. PMID: 20224807 [PubMed – in process]Free PMC ArticleFree textRelated citations
• Aromatase expression in the normal and epileptic human hippocampus. Yague JG, Azcoitia I, DeFelipe J, Garcia-Segura LM, Muñoz A. Brain Res. 2010 Feb 22; 1315:41-52. Epub 2009 Oct 6.PMID: 19815003 [PubMed – indexed for MEDLINE] Related citations
• Dyrk1A is a major player in the dendritic abnormalities of Down syndrome patients. Martinez de Lagrán M., Benavides-Piccione R, Ballesteros-Yañez I, Calvo M, Morales M, Fillat C, DeFelipe J, Ramakers G, and Dierssen M (2010) Journal of Neuroscience (submitted).
• Pyramidal cells in prefrontal cortex of primates: marked specializations differences in neuronal structure among species Elston GN, Benavides-Piccione R, Elston A, Manger PR, DeFelipe J (2010) Frontier in Neuroscience (submitted).
• Casein kinase 2 and microtubules control axon initial segment formation. Sánchez-Ponce D, Muñoz A and Garrido JJ. Moll and Cell Neurosci 2010 (In press).
• Navarrete M, Araque A. Endocannabinoids potentiate synaptic transmission through stimulation of astrocytes. Neuron (2010) 68, 113-26.
• Araque A, Navarrete M. Glial cells in neuronal network function. Philos Trans R Soc Lond B Biol Sci. (2010) 365, 2375-81.
• Perea G, Araque A. GLIA modulates synaptic transmission. Brain Res Rev. (2010) 63, 93-102.
• Guillaume Beslon, David P. Parsons, Jose M. Peña, Christophe Rigotti, Yolanda Sanchez-Dehesa: From digital genetics to knowledge discovery: Perspectives in genetic network understanding. Intell. Data Anal. 14(2): 173-191 (2010)
• S. Lasserre, J. Hernando, S. Hill, F. Schürmann, P. de Miguel, G. Abou-Jaoudé, H. Markram, “A Neuron Membrane Mesh Representation for Visualization of Electrophysiological Simulations”, IEEE Transactions on Visualization and Computer Graphics, accepted on December 13th 2010
• L Guerra, LM McGarry, V Robles, C Bielza, P Larrañaga, R Yuste, “Comparison between supervised and unsupervised classifications of neuronal cell types: a case study”, Developmental Neurobiology, vol 71 (1), pp 71-82, 2011
• Santana, R., Bielza, C., Larrañaga, P. (2010) Optimizing Brain Networks Topologies Using Multi-objective Evolutionary Computation, Neurinformatics, in press, DOI 10.1007/s12021-010-9085-7
• López-Cruz, P., Bielza, C., Larrañaga, P., Benavides-Piccione, R., DeFelipe, J. (2010) Models and Simulation of 3D Neuronal Dendritic Trees Using Bayesian Networks, Neuroinformatics, in press.

Other CBBP Publications

• “El cerebro, la gran cepa azul”. Arte y neurociencia. Coordinador: Javier de Felipe. Noviembre 2010
• DeFelipe J, Jones EG. (2010) Neocortical Microcircuits. Handbook of Brain Microcircuits. (ed. Gordon Shepherd and Sten Grillner), Oxford University Press, New York.
• DeFelipe J, (2010) The birth of modern neuroscience. In: Portraits of the Mind: Visualizing the Brain from Antiquity to the 21st Century. Schoonover CE (ed). Abrams, New York.
• DeFelipe J (2010) Reflexiones sobre lo bello, el arte y la evolución del cerebro. En Neuroestética. Martín Araguz A (ed) Madrid. Saned, pp 51-76.
• DeFelipe J (2010) Sobre lo bello, el arte y la ciencia: Paisajes neuonales.Coordinadores Javier de Felipe y Franck González. En: El cerebro, la gran cepa azul. Arte y Neurociencia. Museo Elder. Las Palmas de Gran Canaria, pp 33-72.
• Morales, D.A. Matemáticas aplicadas en la predicción en medicina. Un paseo por la Geometría. D. Morales. Departamento de Matemáticas de la Facultad de Ciencia y Tecnología. Universidad del País Vasco. 2010. Pp 149-167

Other Publications

• Higuera-Matas, A., Montoya, G.L., Coria, S.M., Miguéns, M., García-Lecumberri, C., and Ambrosio, E (2010). Differential gene expression in the nucleus accumbens and frontal cortex of Lewis and Fischer 344 rats relevant to drug addiction. Current Neuropharmacolgy (En prensa).
• Higuera-Matas A, Soto-Montenegro ML, Montoya GL, García-Vázquez V, Pascau J, Miguens M, Del Olmo N, Vaquero JJ, García-Lecumberri C, Desco M, Ambrosio E (2010). Chronic Cannabinoid Administration to Periadolescent Rats Modulates the Metabolic Response to Acute Cocaine in the Adult Brain. Mol Imaging Biol (Epub ahead of print).
• Higuera-Matas A, Botreau F, Del Olmo N, Miguéns M, Olías O, Montoya GL, García-Lecumberri C, Ambrosio E (2010). Periadolescent exposure to cannabinoids alters the striatal and hippocampal dopaminergic system in the adult rat brain. Eur Neuropsychopharmacol. Dec; 20(12):895-906.
• García-Lecumberri, C., Torres, I., Martín, S., Crespo, J.A., Miguéns, M., Higuera-Matas, A., Nicanor, C. Ambrosio, E (2010). Strain differences in the dose-response relationship for morphine self-administration and impulsive choice between lewis and fischer 344 rats. J. Psychopharmacology (Epub ahead of print).
• Guillaume Beslon, David P. Parsons, Yolanda Sanchez-Dehesa, José M. Peña, Carole Knibbe: Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness? Biosystems 102(1): 32-40 (2010)
• Santiago González, Luis Guerra, Víctor Robles, José M. Peña, Fazel Famili: CliDaPa: A new approach to combining clinical data with DNA microarrays. Intell. Data Anal. 14(2): 207-223 (2010)
• Antonio LaTorre, José María Peña, Santiago Muelas, Alex A. Freitas: Learning hybridization strategies in evolutionary algorithms. Intell. Data Anal. 14(3): 333-354 (2010)
• S. Muelas, J.M. Peña, A. LaTorre, and V. Robles, “A new initialization procedure for the distributed estimation of distribution algorithms” Soft Computing – A Fusion of Foundations, Methodologies and Applications, 2010.
• S. Muelas, A. LaTorre, and J.M. Peña, “A New Methodology for the Automatic Creation of Adaptive Hybrid Algorithms” Intelligent Data Analysis Journal (accepted, to be published in 2011)
• LaTorre, A.; Muelas, S. & Peña, J.M. A MOS-based Dynamic Memetic Differential Evolution Algorithm for Continuous Optimization: A Scalability Test (accessible on-line: DOI: 10.1007/s00500-010-0646-3) Soft Computing – A Fusion of Foundations, Methodologies and Applications, 2010, 1-13
• Vidaurre, D., Bielza, C., Larrañaga, P. (2010) Learning an L1-regularized Gaussian Bayesian Network in the Equivalence Class Space, IEEE Transactions on Systems, Man and Cybernetics, Part B, 40, 5, 1231–1242
• Jorge Muruzábal · Diego Vidaurre · Julián Sánchez “SOMwise Regression: a new clusterwise regression method”, Neural Computing and Applications, (Submmitted in September 2010), 2011. In press.
• Santana, R., Bielza, C., Larrañaga, P., Lozano, J.A., Echegoyen, C., Mendiburu, A., Armañanzas, A., Shakya, S. (2010) Mateda-2.0: Estimation of Distribution Algorithms in MATLAB, Journal of Statistical Software, 35, 7, 1-30
• Cuesta, I., Bielza, C., Cuenca-Estrella, M., Larrañaga, P., Rodríguez-Tudela, J.L. (2010) Evaluation by data mining techniques of fluconazole breakpoints established by the clinical and laboratory standards institute (CLSI) and comparison with those of the European committee on antimicrobial susceptibility testing (EUCAST). Antimicrobial Agents and Chemotherapy, 54, 4, 1541-1546
• Bielza, C., Gómez, M., Shenoy, P.P. (2010) Modelling Challenges with Influence Diagrams: Constructing Probability and Utility Models, Decision Support Systems, 49, 354–364
• Bielza, C., Gómez, M., Shenoy, P.P. (2010) A Review of Representation Issues and Modelling Challenges with Influence Diagrams, Omega, 39, 227–241
• C. Bielza, J. A. Fernández del Pozo, P. Larrañaga, E. Bengoetxea (2010) Multidimensional statistical analysis of the parameterization of a genetic algorithm for the optimal ordering of tables. Expert Systems with Applications (37), 804-815
• R. Santana, P. Larrañaga, J. A. Lozano (2010) Learning factorizations in estimation of distribution algorithms using afinity propagation. Evolutionary Computation 18, 4, 515-546
• Armañanzas, R., Saeys, Y., Inza, I., García-Torres, M., Bielza, C., van de Peer, Y., Larrañaga, P. (2011) Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.18 Borchani, H., Larrañaga, P., Bielza, C. (2010) Classifying Evolving Data Streams with Partially Labelled Data, Intelligent Data Analysis, in press
• P. Larrañaga, S. Moral (2011) Probabilistic graphical models in artificial intelligence. Applied Soft Computing (in press)
• Bielza, C., Li, G., Larrañaga, P. (2011). Multi-Dimensional Classfication with Bayesian Networks. International Journal of Approximate Reasoning (in press)
• Bielza, C., Robles, V., Larrañaga, P. (2010) Regularized Logistic Regression without a Penalty Term: An Application to Cancer Classification with Microarray Data, Expert Systems with Applications, in press (doi: 10.1016/j.eswa.2010.09.140)
• Fernández del Pozo, J.A., Bielza, C. (2011) Dealing with Complex Queries in Decision Support Systems, Data & Knowledge Engineering, 70, 167-181
• D.A. Morales, E. Bengoetxea, P. Larranaga. Automatic characterization of human embryos for improved selection on in-vitro fertilization using Bayesian classifiers. Artificial Intelligence in Medicine. Submitted response for reviewers.R. Santana, A. Mendiburu, N. Zaitlen, E. Eskin and J. A. Lozano (2010). Multi-marker tagging SNP selection using estimation of distribution algorithms. Artificial Intelligence in Medicine. Vol. 50 No. 3. Pp. 193:201.
• M. García-Torres, R. Armañanzas, C. Bielza, P. Larrañaga (2010). Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data. Information Sciences, accepted for publication.
• A high performance suite of data services for grids. Alberto Sánchez, María S. Pérez, Jesús Montes, Toni Cortés. Future Generation Computer Systems, Elsevier Science Publishers ISSN:0167-739X , Volume 26, Number 4, page 622–632 – 2010
• Finding order in chaos: a behavior model of the whole grid. Jesús Montes, Alberto Sánchez, Julio J. Valdés, María S. Pérez, Pilar Herrero. Concurrency and Computation: Practice and Experience. John Wiley & Sons, Volume 22, page 1386–1415 – 2010.
• GCViR: Grid Content-Based Video Retrieval with Work Allocation Brokering. Pablo Toharia, Alberto Sánchez, José L. Bosque, Óscar D. Robles. Concurrency and Computation, Practice and Experience. John Wiley & Sons, Volume 22, page 1450–1475 – 2010
• Toharia Pablo, Sánchez Campos Alberto, Bosque José L., Robles Sánchez Óscar D. “GCViR: Grid Content-Based Video Retrieval with Work Allocation Brokering”. Concurrency and Computation, Practice and Experience. John Wiley & Sons, Volume 22, page 1450–1475 – 2010
• García Lorenzo Marcos, Otaduy Miguel Ángel, O ‘Sullivan  Carol.  Perceptually validated global/local deformations.   Computer Animation and Virtual Worlds.  Volume 21, Issue 3-4, pages 245–254, May 2010.
• C. Pedraza, E. Castillo, J. Castillo, J. L. Bosque, J. I. Martínez, O. D. Robles, J. Cano, P. Huerta. Content-based image retrieval algorithm acceleration in a low-cost reconfigurable FPGA cluster. Vol: 56 (1), pp: 633-640, 2010, ISSN:1383-7621 DOI: 10.1016/j.sysarc.2010.07.017, Elsevier – Academic Press. Journal of Systems Architecture.
• Bengoetxea, E., Larrañaga, P., Bielza, C., Fernández del Pozo, J.A. (2010) Optimal Row and Column Ordering to Improve Table Interpretation Using Estimation of Distribution Algorithms, Journal of Heuristics, DOI 10.1007/s10732-010-9145-z
• C. Echegoyen, A. Mendiburu, R. Santana and J. A. Lozano. Towards understanding EDAs based on Bayesian networks through a quantitative analysis. IEEE Transactions on Evolutionary Computation. Accepted for publication.
• C. Echegoyen, A. Mendiburu, R. Santana, and J. A. Lozano. Analyzing the k Most Probable Solutions in EDAs based on Bayesian Networks. In Exploitation of linkage learning in evolutionary algorithms. Evolutionary Learning and Optimization. Springer. Y.-P. Chen editor. 2010.

2009 CBBP Scientific Publications

• Merchán-Pérez A, Rodriguez JR, Ribak CE, DeFelipe J (2009) Proximity of excitatory and inhibitory axon terminals adjacent to pyramidal cell bodies provides a putative basis for nonsynaptic interactions. Proc Natl Acad Sci USA. 106(24):9878-83.
• Merchan-Pérez A, Rodriguez J, Alonso-Nanclares L, Schertel A and DeFelipe J (2009) Counting synapses using FIB/SEM microscopy: a true revolution for ultrastructural volume reconstruction. Front. Neuroanat. 3:18. doi:10.3389/neuro.05.018.2009.
• Inda MC, DeFelipe J, Munoz A. (2009) Morphology and Distribution of Chandelier Cell Axon Terminals in the Mouse Cerebral Cortex and Claustroamygdaloid Complex. Cereb Cortex. 19(1):41-54.
• Knafo S, Alonso-Nanclares L, J. Gonzalez-Soriano J, Merino-Serrais P, I. Fernaud-Espinosa1 I, Ferrer I, DeFelipe J (2009) Widespread changes in dendritic spines in a model of Alzheimer’s disease. Cereb Cortex 19(3):586-92.
• Knafo S, Venero C, Merino-Serrais P, Fernaud-Espinosa I, Gonzalez-Soriano J, Ferrer I, Santpere G and DeFelipe J (2009) Morphological alterations to neurons of the amygdala and impaired fear conditioning in a transgenic mouse model of Alzheimer’s disease. J. Pathol. 219:41-51.
• Kastanauskaite A, Alonso-Nanclares L, Blazquez-Llorca L, Pastor J, Sola RG, DeFelipe J (2009) Alterations of the microvascular network in sclerotic hippocampi from patients with epilepsy. J Neuropathol Exp Neurol. 68:939-950.
• Yague JG, Azcoitia I, DeFelipe J, Garcia-Segura LM, Muñoz A (2009) Aromatase expression in the normal and epileptic human hippocampus. Brain Res. 2009 Oct 6. [Epub ahead of print].
• Garcia-Marin V, Blazquez-Llorca L, Rodriguez JR, Boluda S, Muntane G, Ferrer I, DeFelipe J (2009) Diminished perisomatic GABAergic terminals on cortical neurons adjacent to amyloid plaques. Front Neuroanat. 3:28. Epub 2009 Nov 20.
• Perea G, Araque A (2009) Glia modulates synaptic transmission. Brain Research Reviews (in press).
• Araque A, Navarrete M (2009) Glial cells in neuronal network function. Philosophical Transactions of the Royal Society B (in press).
• Perea G, Navarrete M, Araque A (2009) Tripartite synapses: astrocytes process and control synaptic information. Trends in Neurosciences 32: 421-431.
• A. LaTorre, JM Peña, S. Muelas, AA. Freitas. Learning Hybridization Strategies in Evolutionary Algorithms. Intelligent Data Analysis 14 (3), 2010
• S. Muelas, JM Peña, A. LaTorre. A New Initialization Procedure for the Estimation of Distribution Algorithms. Softcomputing (Accepted for publication)
• G. Beslon, D. Parsons, JM Peña, C Rigotti, Y. Sanchez-Dehesa. From Digital Genetics to Knowledge Discovery: Perspectives in Genetic Network Understanding Intelligent Data Analysis (Accepted for Publication)
• MS. Pérez, A. Sánchez, JH. Abawajy, V. Robles JM. Peña An agent architecture for managing data resources in a grid environment Future Generation Computer Systems 25, (7), 2009, 747-755
• Y. Sanchez-Dehesa, D. Parsons, JM. Peña, G. Beslon. Modelling Evolution of Regulatory Networks in Artificial Bacteria. Mathematical Modelling of Natural Phenomena 3(2), 2008 :27-66
• S. Gonzalez, L. Guerra, V. Robles, JM. Peña, F. Famili. CliDaPa: A New Approach to Combining Clinical Data with DNA Microarrays Intelligent Data Analysis (Accepted for Publication)
• G. Beslon, D. Parsons, Y. Sanchez-Dehesa, JM Peña, C. Knibbe. Scaling Laws in Bacterial Genomes : A Side-Effect of Selection of Mutational Robustness?. Biosystems (Accepted for Publication).
• M-L. Zhang, JM Peña, V Robles. Feature selection for multi-label naive Bayes classification. Information Science 179 (19), 2009: 3218-3229
• R. Santana, C. Bielza, P. Larrañaga, J. A. Lozano, C. Echegoyen, A. Mendiburu, R. Armañanzas, S. Shakya. MATEDA: A Matlab package for the implementation and analysis of estimation of distribution algorithms. Journal of Statistical Software. Accepted for publication.
• D. Otaegui, S. Baranzini, R. Armañanzas, B. Calvo, M. Muñoz-Culla, P. Khankhanian, I. Inza, J. A. Lozano, A. Asensio, T. Castillo-Triviño, J. Olsacoaga, A. López de Munain. Differential micro RNA expression in PBMC from multiple sclerosis patients. PLoS ONE, vol 4(7), e6309.
• Inza, B. Calvo, R. Armañanzas, E. Bengoetxea, P. Larrañaga, J. A. Lozano. Machine learning: An indispensable tool in bioinformatics. In R. Matthiesen, editor, Bioinformatics Methods in Clinical Research. Humana Press

Other CBBP Publications

• DeFelipe J, Jones EG. (2009) Neocortical Microcircuits. Handbook of Brain Microcircuits. (ed. Gordon Shepherd and Sten Grillner), Oxford University Press, New York (en prensa).
• DeFelipe J (2009) Cajal y las mariposas del alma: plasticidad cerebral y procesos mentales. Ateneo (Madrid).
• LaTorre, JM. Peña, V. Robles, S. Muelas, P. deMiguel. Supercomputer Scheduling with Combined Evolutionary Techniques. In the book Meta-heuristics for Scheduling: Distributed Computing Environments. Springer-Verlag ISBN 978-3-540-69260-7