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Institute of Neuroscience and Medicine
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Publications of Rembrandt Bakker

Articles in peer reviewed journals

2018
  • 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
2017
  • 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.
  • Schmidt M., Bakker R., Hilgetag CC., Diesmann M., van Albada SJ. (2017). Multi-scale account of the network structure of macaque visual cortex. Brain Structure and Function pp. 1-27. DOI:10.1007/s00429-017-1554-4.
2015
  • 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.
2014
  • 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.
2012
  • 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.
2009
  • Bakker R., Schubert D., Levels K., Bezgin G., Bojak I., Kötter R. (2009) Classification of cortical microcircuits based on micro-electrode-array data from slices of rat barrel cortex. Neural Netw. 22(8):1159-68. DOI: 10.1016/j.neunet.2009.07.014.

PhD Thesis

  • Bakker R. (2007) Learning to simulate and predict chaotic dynamical systems Online version

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