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Peer-reviewed articles of Theoretical Neuroanatomy

  • Timonidis N., Bakker R., Tiesinga P. (2020) Prediction of a Cell-Class-Specific Mouse Mesoconnectome Using Gene Expression Data. Neuroinformatics 18(4):611-626 DOI:10.1007/s12021-020-09471-x
  • Gleeson P., Cantarelli M., Marin B., ... van Albada SJ., van Geit W., R Silver RA. (2019) Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits Neuron 103, 3, 395-411.e5 DOI:10.1016/j.neuron.2019.05.019
  • Hilgetag CC., Beul SF., van Albada SJ., Goulas A. (2019) An architectonic type principle integrates macroscopic cortico-cortical connections with intrinsic cortical circuits of the primate brain Network Neuroscience DOI:10.1162/netn_a_00100
  • Zajzon B., Morales-Gregorio A. (2019) Trans-thalamic Pathways: Strong Candidates for Supporting Communication between Functionally Distinct Cortical Areas Journal of Neuroscience 4 September 2019, 39 (36) 7034-7036 DOI:10.1523/JNEUROSCI.0656-19.2019
  • Maksimov A., Diesmann M., van Albada SJ. (2018) Criteria on balance, stability and excitability in cortical networks for constraining computational models Front Comput Neurosci. 12:44 DOI:10.3389/fncom.2018.00044
  • Schmidt M., Bakker R., Hilgetag CC., Diesmann M., van Albada SJ. (2018). Multi-scale account of the network structure of macaque visual cortex. Brain Structure and Function 223(3):1409-1435. DOI:10.1007/s00429-017-1554-4.
  • Schmidt M., Bakker R., Shen K., Bezgin G., Diesmann M., van Albada SJ. (2018) A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas. PLOS Comp Biol 14(10):e1006359 DOI:10.1371/journal.pcbi.1006359
  • van Albada SJ., Rowley AG., Senk J., Hopkins M., Schmidt M., Stokes AB., Lester DR., Diesmann M., Furber SB. (2018) Performance comparison of the digital neuromorphic hardware SpiNNaker and the neural network simulation software NEST for a full-scale cortical microcircuit model. Frontiers in Neuroscience 12:291 DOI:10.3389/fnins.2018.00291
  • Bezgin G., Solodkin A., Bakker R., Ritter P., McIntosh AR. (2017). Mapping complementary features of cross-species structural connectivity to construct realistic “virtual brains”: multimodal structural connectivity for realistic virtual brains. Human Brain Mapping 38:2080–2093. DOI: 10.1002/hbm.23506.
  • Hinne M., Meijers A., Bakker R., Tiesinga PHE., Mørup M., van Gerven MAJ. (2017). The missing link: predicting connectomes from noisy and partially observed tract tracing data. PLOS Computational Biology 13:e1005374. DOI: 10.1371/journal.pcbi.1005374.
  • Müller EJ., van Albada SJ., Kim JW., Robinson PA. (2017). Unified neural field theory of brain dynamics underlying oscillations in parkinson’s disease and generalized epilepsies. Journal of Theoretical Biology 428:132–146. DOI: 10.1016/j.jtbi.2017.06.016.
  • Schuecker J., Schmidt M., van Albada SJ., Diesmann M., Helias M. (2017). Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome. PLOS Computational Biology 13:e1005179. DOI: 10.1371/journal.pcbi.1005179.
  • Hagen E., Dahmen D., Stavrinou ML., Lindén H., Tetzlaff T., van Albada SJ., Grün S., Diesmann M., Einevoll GT. (2016). Hybrid scheme for modeling local field potentials from point-neuron networks. Cerebral Cortex 26:4461–4496. DOI: 10.1093/cercor/bhw237.
  • Maksimov A, van Albada SJ, Diesmann M, (2016) [Re] Cellular and Network Mechanisms of Slow Oscillatory Activity (<1 Hz) and Wave Propagations in a Cortical Network Model. Rescience. DOI:10.5281/zenodo.161526
  • van Albada SJ., Helias M., Diesmann M. (2015). Scalability of asynchronous networks is limited by one-to-one mapping between effective connectivity and correlations. PLOS Computational Biology 11:e1004490. DOI: 10.1371/journal.pcbi.1004490.
  • Bakker R., Tiesinga P., Kötter R. (2015). The scalable brain atlas: instant web-based access to public brain atlases and related content. Neuroinformatics 13:353–366. DOI: 10.1007/s12021-014-9258-x.
  • Sergejeva M., Papp EA., Bakker R., Gaudnek MA., Okamura-Oho Y., Boline J., Bjaalie JG., Hess A. (2015). Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates. Journal of Neuroscience Methods 240:161–169. DOI: 10.1016/j.jneumeth.2014.11.005.
  • Tiesinga P., Bakker R., Hill S., Bjaalie JG. (2015). Feeding the human brain model. Current Opinion in Neurobiology 32:107–114. DOI: 10.1016/j.conb.2015.02.003.
  • Bezgin G., Rybacki K., van Opstal AJ., Bakker R., Shen K., Vakorin VA., McIntosh AR., Kötter R. (2014). Auditory–prefrontal axonal connectivity in the macaque cortex: quantitative assessment of processing streams. Brain and Language 135:73–84. DOI: 10.1016/j.bandl.2014.05.006.
  • Kerr CC., van Albada SJ., Neymotin SA., Chadderdon GL., Robinson PA., Lytton WW. (2013). Cortical information flow in parkinson’s disease: a composite network/field model. Frontiers in Computational Neuroscience 7:39. DOI: 10.3389/fncom.2013.00039.
  • Nowke C, Hentschel B, Kuhlen T, Schmidt M, van Albada SJ, Eppler JM, Bakker R, Diesmann M (2013) VisNEST – interactive analysis of neural activity data IEEE BioVis 65-72
  • van Albada SJ., Robinson PA. (2013). Relationships between electroencephalographic spectral peaks across frequency bands. Frontiers in Human Neuroscience 7:56. DOI: 10.3389/fnhum.2013.00056.
  • Bakker R., Wachtler T., Diesmann M. (2012). CoCoMac 2.0 and the future of tract-tracing databases. Frontiers in Neuroinformatics 6:30. DOI: 10.3389/fninf.2012.00030.
  • Bezgin G., Vakorin VA., van Opstal AJ., McIntosh AR., Bakker R. (2012). Hundreds of brain maps in one atlas: registering coordinate-independent primate neuro-anatomical data to a standard brain. NeuroImage 62:67–76. DOI: 10.1016/j.neuroimage.2012.04.013.
  • Crook SM., Bednar JA., Berger S., Cannon R., Davison AP., Djurfeldt M., Eppler J., Kriener B., Furber S., Graham B., Plesser HE., Schwabe L., Smith L., Steuber V., Albada S van. (2012). Creating, documenting and sharing network models. Network: Computation in Neural Systems 23:131–149. DOI: 10.3109/0954898X.2012.722743.
  • Chiang AKI., Rennie CJ., Robinson PA., van Albada SJ., Kerr CC. (2011). Age trends and sex differences of alpha rhythms including split alpha peaks. Clinical Neurophysiology 122:1505–1517. DOI: 10.1016/j.clinph.2011.01.040.

Book Chapters of Theoretical Neuroanatomy

  • van Albada S., Pronold J., van Meegen A., Diesmann M. (2021) Usage and scaling of an open-source spiking multi-area model of monkey cortex. In: Amunts K., Grandinetti L., Lippert Th., Petkov N. eds. Brain-Inspired Computing. Cham : Springer, Lecture Notes in Computer Science 12339, 47-59. DOI: 10.1007/978-3-030-82427-3
  • Schmidt M., Diesmann M., van Albada SJ. (2018) Necessity and feasibility of large-scale neuronal network simulations. In: Lecture Notes of the 49th IFF Spring School “Physics of Life"
  • Senk J., Yegenoglu A., Amblet O., Brukau Y., Davison A., Lester DR., Lührs A., Quaglio P., Rostami V., Rowley A., Schuller B., Stokes AB., van Albada SJ., Zielasko D., Diesmann M., Weyers B., Denker M., Grün S. (2017). A collaborative simulation-analysis workflow for computational neuroscience using hpc. In: Di Napoli E, Hermanns M-A, Iliev H, Lintermann A, Peyser A eds. High-Performance Scientific Computing. Cham: Springer International Publishing, 243–256. DOI: 10.1007/978-3-319-53862-4_21.
  • van Albada SJ., Kunkel S., Morrison A., Diesmann M. (2014). Integrating brain structure and dynamics on supercomputers. In: Grandinetti L, Lippert T, Petkov N eds. Brain-Inspired Computing: International Workshop, BrainComp 2013, Cetraro, Italy, July 8-11, 2013, Revised Selected Papers. Cham: Springer International Publishing, 22–32. DOI: 10.1007/978-3-319-12084-3_3.