Alexei Koulakov
Professor
Charles Robertson Professor of Neuroscience
Ph.D., University of Minnesota, 1998
koulakov@cshl.edu | 516-367-8470
Faculty ProfileThe 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.
President’s essay: Bringing bold visions to life
May 26, 2023
CSHL President & CEO Bruce Stillman sees the Laboratory as a global hub for scientific expertise and a powerful launchpad for early-career scientists.
Follow your nose: Tracking the brain’s smell circuits
February 27, 2023
Take this 8-bit trip along the brain’s olfactory circuits to see what happens up there when you smell something.
Can you outsmart this AI quiz?
February 6, 2023
Think you’re plugged into the latest artificial intelligence advancements? Test your tech knowledge with this quiz on AI and computational biology.
Mapping the path from smell to perception
October 27, 2022
Smell remains the most mysterious of our five senses, but CSHL neuroscientists are now closer than ever to understanding it.
Building better AI with the power of neuroscience
June 8, 2022
Artificial Intelligence (AI) experts at CSHL are creating better AI by deciphering brain circuits.
President’s essay: Foundations for the future
May 25, 2022
Strategically designed to spark scientific exchange and inspiration, CSHL is a unique research and education environment for advancing science.
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.
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
Network cloning using DNA barcodes
24 Apr 2019 | Proceedings of the National Academy of Sciences of the United States of America | 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
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
All Publications
Catalyzing next-generation Artificial Intelligence through NeuroAI
22 Mar 2023 | Nature Communications | 14(1):1597
Zador, Anthony, Escola, Sean, Richards, Blake, Ölveczky, Bence, Bengio, Yoshua, Boahen, Kwabena, Botvinick, Matthew, Chklovskii, Dmitri, Churchland, Anne, Clopath, Claudia, DiCarlo, James, Ganguli, Surya, Hawkins, Jeff, Körding, Konrad, Koulakov, Alexei, LeCun, Yann, Lillicrap, Timothy, Marblestone, Adam, Olshausen, Bruno, Pouget, Alexandre, Savin, Cristina, Sejnowski, Terrence, Simoncelli, Eero, Solla, Sara, Sussillo, David, Tolias, Andreas, Tsao, Doris
A normative theory of social conflict
7 Mar 2023
Shuvaev, Sergey, Amelchenko, Evgeny, Smagin, Dmitry, Kudryavtseva, Natalia, Enikolopov, Grigori, Koulakov, Alexei
High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex
27 Oct 2022 | Cell | 185(22):4117-4134.e28
Chen, Yushu, Chen, Xiaoyin, Baserdem, Batuhan, Zhan, Huiqing, Li, Yan, Davis, Martin, Kebschull, Justus, Zador, Anthony, Koulakov, Alexei, Albeanu, Dinu
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
Wiring logic of the early rodent olfactory system revealed by high-throughput sequencing of single neuron projections
2021 | bioRxiv
Chen, Yushu, Chen, Xiaoyin, Baserdem, Batuhan, Zhan, Huiqing, Li, Yan, Davis, Martin, Kebschull, Justus, Zador, Anthony, Koulakov, Alexei, Albeanu, Dinu