CmpE 59I Sp.Tp. Brain Dynamics 2016 Spring


Course Schedule: 

WWW 567

Course Program: 

Weekly Program (Tentative)

# date



by Haluk Bingol, Computer Engineering, Bogazici U
  • Rubinov2010-Complex network measures of brain connectivity: Uses and interpretations -- Nouroimage

Further readings:

2 17.02.2016 Human Brain (Distribute vs Local, Development, Evolution)
by Berrin Aktekin, Neurology, Yeditepe U.
3 24.02.2016 Neural Conductance
by Hale Saybasili, Biomedical Engineering, Bogazici U.
  • Purves Ch 2 Electrical signals of nerve cells
  • Purves Ch 3 Voltage dependent membrane permeability
  • Purves Ch 4 Channels and transporters

Further readings:

4 02.03.2016 Functional neuroimaging (EEG, MEG, fMRI, PET, fNIRS, DWI, DTI, ERP)
by Ata Akin, Genetics and Bioengineering, Acıbadem U.
  • Friston2009-Modalities modes and models in functional neuroimaging -- science
  • Savoy2001-History and future directions of human brain mapping and functional neuroimaging -- Acta Psychologica
  • Shibasaki2008-Human brain mapping- hemodynamic response and electrophysiology -- Clinical Neurophysiology
  • Akin2012-Functional neuroimaging lecture notes.pdf
  • Villringer1997-Non-invasive optical spectroscopy and imaging of human brain function -- Trends in neurosciences
5 09.03.2016

Electrical source imaging and Multi model image fusion
by A. Deniz Duru, Biomedical Engineering, Bogazici U.

  • Hallez-2007-Review on solving the forward problem in eeg source analysis -- journal of neuroengineering and rehabilitation
  • Michel2004-EEG source imaging -- Clinical neurophysiology
6 16.03.2016

by Esin Ozturk, Biomedical Engineering, Bogazici U.

7 23.03.2016 Brain pathways and functions
by Zeynep Firat, Yeditepe U.
  • Kovanlikaya2011-Assessment of the corticospinal tract alterations before and after resection of brainstem lesions using Diffusion Tensor Imaging (DTI) and tractography at 3T --European journal of radiology
  • Melhem2002-Diffusion tensor MR imaging of the brain and white matter tractography -- American Journal of Roentgenology
8 30.03.2016 Physiology and psychophysics of the sense of touch
by Burak Guclu, Biomedical Engineering, Bogazici U.
  • Kandel5e Chapter 21
  • Kandel5e Chapter 22
  • Kandel5e Chapter 23
  • Tabot et al., Restoring the sense of touch with a prosthetic hand through a brain interface --PNAS ​doi:10.1073/pnas.1221113110
6 06.04.2016 Hemispheric asymmetries
by Resit Canbeyli, Psychology, Bogazici U.
  • Hopkins, Cantalupo - 2008 - Theoretical Speculations on the Evolutionary Origins of Hemispheric Specialization - Current Directions in Psychological Science
  • Toga2003-Mapping brain asymmetry  -- Nature neuroscience
  • Vallortigara - 2006 - The evolutionary psychology of left and right costs and benefits of lateralization - Developmental psychobiology
  • Hutsler2003-Hemispheric asymmetries in cerebral cortical networks -- trends in neurosciences
10 13.04.2016 Social Neuroscience
by Adil Saribay, Psychology, Bogazici U.
  • Harris, L. T., & Fiske, S. T. (2006). Dehumanizing the lowest of the low neuroimaging responses to extreme out-groups. Psychological Science, 17(10), 847-853.
  • Kelley, W. M., Macrae, C. N., Wyland, C. L., Caglar, S., Inati, S., & Heatherton, T. F. (2002). Finding the self? An event-related fMRI study. Journal of Cognitive Neuroscience, 14(5), 785-794.

Further readings:

  • Ochsner, K. N., & Lieberman, M. D. (2001). The emergence of social cognitive neuroscience. American Psychologist, 56, 717-734.
  • Klein, S. B., & Kihlstrom, J. F. (1998). On bridging the gap between social-personality psychology and neuropsychology. Personality and Social Psychology Review, 2, 228-242.
- 20.04.2016 == spring break ==
11 27.04.2016 Vision and Temporal Dynamics
by Inci Ayhan, Psychology, Bogazici U.
  • Zeki - 1992 - The Visual Image in Mind and Brain -- Scientific American
  • Eagleman - 2008 - Human time perception and its illusions. -- Current opinion in neurobiology

Further readings:

  • Mauk, Buonomano - 2004 - The neural basis of temporal processing. -- Annual review of neuroscience
  • Nassi, Callaway - 2009 - Parallel processing strategies of the primate visual system. -- Nature reviews. Neuroscience

Further videos:

12 04.05.2016 Gene-Environment Interactions and Epigenetics
by Elif Duman, Psychology, Bogazici U.
  • Meaney, M. J., & Ferguson-Smith, A. C. (2010). Epigenetic regulation of the neural transcriptome: the meaning of the marks -- Nature neuroscience, 13(11), 1313-1318.
  • Caspi, A., & Moffitt, T. E. (2006). Gene–environment interactions in psychiatry: joining forces with neuroscience -- Nature Reviews Neuroscience, 7(7), 583-590.

Further videos:
The first four chapters of Human Genetics for the Social Sciences

13 11.05.2016 Brain computer interface
by Albert Ali Salah, Computer Engineering, Bogazici U.
  • Gurkok2012-Brain–Computer Interfaces for Multimodal Interaction: A Survey and Principles -- int. J. Human Computer Interaction

Reading materials:

  • Kandel5e
    Principles of Neural Science, 5e,
    Kandel, Schwartz, Jessell,
    McGraw-Hill, 2013. [QP355.2 .P76 2013] in reserve.
  • Purves
    Purves, G.Augustine, Fitzpatrick, Hall, Lamantia, McNamara, Williams,
    1997. [QP355.2 .N487 1997] in reserve.

Weekly Questions

Each week 3 questions about the reading material should be prepared and submitted to moodle by Monday 09:00. Please zip both .tex and .pdf files into one zip file and submit the zip file. Please use LaTeX for your questions. Please use the LaTeX template for weekly questions in my LaTeX site.


For extra information on projects see Projects.

  • Project groups are decided.
  • Please use project proposal template for your proposals.

Homeworks (HW)

No homework this time.


14.03.2016 Project proposals
xx.06.2016 Project presentations


 Any kind of submission, including homeworks, weekly questions, midterms, should be done by Moodle.


We will use LaTeX for material that you produce. You can find further info about LaTeX on the web. See also my LaTeX site. You can use


Course cmpe59i Brain Dynamics
Semester 2016 Spring
Instructor Haluk Bingol
TA none
Web Site
Time/Room Lectures: WWW 567 @ BM B3
First Meeting 10.02.2016
Text Book none
Reference Books
  • Principles of Neural Science, 4e, Kandel, Schwartz, Jessell, McGraw-Hill, 2002. [QP355.2 .P76 2000]
  • The cognitive neurosciences, 4e, Gazzaniga (ed.), MIT Press, 2009. [QP360.5 .N4986 2009]
  • Neuroscience: Exploring the Brain, 4e, Bear, Connors, Paradio, LWW, 2007. [ QP355.2 .B42 2007]
  • 30% Midterm
  • 50% Project
  • 20% Contribution to Discussions & Homeworks & Attendance
Catalog Data Single neuron to human brain: Cell types, cellular transmission mechanisms. Brain anatomy, development, evolution. Brain disorders. Measurable quantities, processing and their interpretations. Mechanisms, approaches, and models.
Prerequisites none



Contact us

Department of Computer Engineering, Boğaziçi University,
34342 Bebek, Istanbul, Turkey

  • Phone: +90 212 359 45 23/24
  • Fax: +90 212 2872461

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