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Alexei Koulakov, PhD

Cold Spring Harbor Laboratory


The complexity of the mammalian brain challenges our ability to explain it. My group applies methods from mathematics and theoretical physics to understand the brain. We are generating novel ideas about neural computation and brain development, including how neurons process information, how brain networks assemble during development, and how brain architecture evolved to facilitate its function.

Alexei Koulakov and colleagues are trying to determine the mathematical rules by which the brain assembles itself, with particular focus on the formation of sensory circuits such as those involved in visual perception and olfaction. The visual system of the mouse was chosen for study in part because its components, in neuroanatomical terms, are well understood. What is not known is how projections are generated that lead from the eye through the thalamus and into the visual cortex, how an individual’s experience influences the configuration of the network, and what parameters for the process are set by genetic factors. Even less is known about the assembly of the neural net within the mouse olfactory system, which, in the end, enables the individual to distinguish one smell from another with astonishing specificity and to remember such distinctions over time. These are among the challenges that engage Koulakov and his team.

The Lab

Khristina Samoilova.jpg

Khristina Samoilova

Graduate Student


Farhad Pashakhanloo

Swartz Fellow in Theoretical Neuroscience

Cyrille Mascart.jpg

Cyrille Mascart

Graduate Student

Batuhan Baserdem.jpg

Batuhan Başerdem

Post Grad Student

Sergey Shuvaev.jpg

Sergey Shuvaev

Postdoctoral fellow

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Khue Hoai Tran

Graduate Student

Selected Publications


Giaffar H, Shuvaev S, Rinberg D, Koulakov A (2023).

The primacy model and the structure of olfactory space, Biorxiv.

Chae H, Kepple D, Bast W, Murthy V, Koulakov A, Albeanu D (2019)
Mosaic representations of odors in the input and output layers of the mouse olfactory bulb. Nat Neurosci.


Tran, Ngoc and Kepple, Daniel and Shuvaev, Sergey A. and Koulakov, A.
DeepNose: Using artificial neural networks to represent the space of odorants, PLMR.


Shuvaev, S. A. and Baserdem, B. and Zador, A. M. and Koulakov, A. A. (2019)
Network cloning using DNA barcodesPNAS. [pdf]


Kepple D R, Giaffar H, Rinberg D. and Koulakov A (2019)
Deconstructing Odorant Identity via Primacy in Dual Networks. Neural Computation, [link]


Kepple, D. R. and Giaffar, H. and Rinberg, D. and Koulakov, A. A. (2018)
Primacy coding in dual olfactory networks.51st Asilomar Conference on Signals, Systems, and Computers, 2017-O pp. 587-592. Institute of Electrical and Electronics Engineers Inc. [link]

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