Alexei Koulakov
Professor
Charles Robertson Professor of Neuroscience
Ph.D., University of Minnesota, 1998
koulakov@cshl.edu | 516-367-8470
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.
CSHL Ph.D. program: Graduating class of 2021
August 22, 2021
The CSHL School of Biological Sciences awarded Ph.D. degrees to seven students this year, who describe some of their experiences.
The doctor will sniff you now
March 1, 2021
Dogs can sniff out many diseases, likely including COVID-19. CSHL scientists are developing an AI-based “Deep Nose” to mimic that diagnostic sniff.
NeuroAI program connects AI experts with neuroscientists
November 2, 2020
The CSHL NeuroAI program is training researchers to be fluent in neuroscience and AI to expedite the development of next-generation AI.
Cold Spring Harbor Laboratory’s class of 2020
August 7, 2020
Meet the seven graduates of the Cold Spring Harbor Laboratory School of Biological Sciences. Congratulations to all.
There’s more to smell than meets the nose
July 22, 2019
Neuroscience researchers work to figure out our brains process smells, including what features are essential to identifying and separating odors.
Quantifying how the brain smells
July 22, 2019
Neuroscience researchers at CSHL are trying to figure out how the brain processes smells and what features of odors are important in that process.
What’s that smell? Neuroscientists are figuring it out
October 2, 2018
Neuroscientists Florin Albeanu and Alexei Koulakov win the NIH Director’s Transformative Research Award for their project on the olfactory system.
Portrait of a Neuroscience Powerhouse
April 27, 2018
A relatively small neuroscience group at CSHL is having an outsized impact on a dynamic and highly competitive field
Swartz Centers dedication
April 1, 2015
An official recognition of Jerome Swartz for his 25+ years of friendship and generous support of Cold Spring Harbor Laboratory neuroscience programs.
Universe to smelliverse with second-year student Daniel Kepple
October 8, 2014
Daniel Kepple hopes to figure out the chemical and neuronal rules that determine what something smells like.
Selected Publications
Neural Networks With Motivation.
11 Jan 2021 | Frontiers in Systems Neuroscience | 14:609316
Shuvaev, Sergey, Tran, Ngoc, Stephenson-Jones, Marcus, Li, Bo, Koulakov, Alexei
Mosaic representations of odors in the input and output layers of the mouse olfactory bulb
Aug 2019 | Nature Neuroscience | 22(8):1306-1317.
Chae, H, Kepple, D, Bast, W, Murthy, V, Koulakov, A, Albeanu, D
DeepNose: Using artificial neural networks to represent the space of odorants
Jun 2019 | Proceedings of the 36th International Conference on Machine Learning | 97:6305-6314
Tran, Ngoc, Kepple, Daniel, Shuvaev, Sergey, Koulakov, Alexei
Network cloning using DNA barcodes
24 Apr 2019 | Proceedings of the National Academy of Sciences of USA | 116(19):9610-9615
Shuvaev, S, Baserdem, B, Zador, A, Koulakov, A
Deconstructing Odorant Identity via Primacy in Dual Networks
14 Feb 2019 | Neural Computation | 31(4):710-737
Kepple, D, Giaffar, H, Rinberg, D, Koulakov, A
All Publications
Spatiotemporal 3D image registration for mesoscale studies of brain development
7 Mar 2022 | Scientific Reports | 12(1):3648
Shuvaev, Sergey, Lazutkin, Alexander, Kiryanov, Roman, Anokhin, Konstantin, Enikolopov, Grigori, Koulakov, Alexei
Neural stem cell spacing questions their self-renewal
9 Aug 2018 | Aging | 10(8):1793-1794
Mineyeva, O, Koulakov, A, Enikolopov, G
Computational algorithms and neural circuitry for compressed sensing in the mammalian main olfactory bulb
5 Jun 2018 | BioRxiv
Kepple, Daniel, Cazakoff, Brittany, Demmer, Heike, Eckmeier, Dennis, Shea, Stephen, Koulakov, Alexei
WM-CLICK, a new method for 3d detection, representation and analysis of dividing cells in the whole brain
1 Jun 2018 | Opera Medica et Physiologica | 4:20
Lazutkin, A, Shuvaev, S, Kiryanov, R, Anokhin, K, Koulakov, A, Enikolopov, G
A closer look at the topography of hippocampal neural stem cells indicates their limited self-renewal
1 Jun 2018 | Opera Medica et Physiologica | 4:7
Mineyeva, O, Koulakov, A, Enikolopov, G