
Bio:
Anton Arkhipov joined the Allen Institute in 2013 as an Assistant Investigator in the Modeling, Analysis, and Theory group. He is leading efforts to carry out biophysically detailed simulations of individual neurons as well as large-scale neuronal circuits from the mouse visual system. The main focus of his research is on integration of experimental anatomical and physiological data to build sophisticated, highly realistic computational models of cortical circuitry, with the aim of elucidating mechanisms underlying processing of visual information in the cortex. Before joining the Allen Institute he was a Postdoctoral Fellow at D. E. Shaw Research in New York City, where he used a specialized supercomputing architecture to perform computational studies of structure-function relationships in proteins, with the emphasis on cancer-associated cell-surface receptors. Arkhipov received his B.S. and M.S. in Physics from Moscow Institute of Physics and Technology and a Ph.D. in Physics from the University of Illinois at Urbana-Champaign.
Research Focus:
Anton Arkhipov applies high-performance computing to simulate neuronal activity in the mouse visual system. Using experimentally observed neuronal morphologies, connectivity patterns, and electrophysiological properties, he constructs highly detailed, biophysically accurate models of neuronal circuits. The main aim is to build powerful models that, on the one hand, reproduce major features of in vivo experimental recordings from anesthetized and awake mice and, on the other, allow for testable predictions about mechanisms involved in processing of the visual information in the cortex.News & Events
Mapping the whole human brain: Allen Institute to lead global collaboration
2025 Allen Institute Modeling Software Workshop
Mapping the whole human brain: Allen Institute to lead global collaboration
2025 Allen Institute Modeling Software Workshop
Mapping the whole human brain: Allen Institute to lead global collaboration
Publications
PLoS computational biology
Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations
Mar 01, 2024
J. Galván Fraile, Franz Scherr, José J. Ramasco, Anton Arkhipov, Wolfgang Maass, Claudio R. Mirasso
Read MoreNeuron
Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex
Feb 29, 2024
Alex Piet, Nick Ponvert, Douglas Ollerenshaw, Marina Garrett, Peter A. Groblewski, Shawn Olsen, Christof Koch, Anton Arkhipov
Read MoreeLife
Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex
Jul 24, 2023
Atle E. Rimehaug, Alexander J. Stasik, Espen Hagen, Yazan N. Billeh, Josh H. Siegle, Kael Dai, Shawn R. Olsen, Christof Koch, Gaute T. Einevoll, Anton Arkhipov
Read MoreNeuron
Influence of claustrum on cortex varies by area, layer, and cell type
Jan 18, 2023
Ethan G. McBride, Saurabh R. Gandhi, Jacqulyn R. Kuyat, Douglas R. Ollerenshaw, Anton Arkhipov, Christof Koch, Shawn R. Olsen
Read MoreFrontiers in Computational Neuroscience
A survey of neurophysiological differentiation across mouse visual brain areas and timescales
Jan 01, 2023
Saurabh R. Gandhi, William G. P. Mayner, William Marshall, Yazan N. Billeh, Corbett Bennett, Samuel D. Gale, Chris Mochizuki, Joshua H. Siegle, Shawn Olsen, Giulio Tononi, Christof Koch, Anton Arkhipov
Read MoreThe Journal of Physiology
Simulations of cortical networks using spatially extended conductance-based neuronal models
Dec 25, 2022
Darrell Haufler, Shinya Ito, Christof Koch, Anton Arkhipov
Read MoreEntropy (Basel, Switzerland)
Non-Separability of Physical Systems as a Foundation of Consciousness
Oct 26, 2022
Anton Arkhipov
Read MoreScience (New York, N.Y.)
Local connectivity and synaptic dynamics in mouse and human neocortex
Mar 11, 2022
Luke Campagnola, Stephanie C. Seeman, Thomas Chartrand, Lisa Kim, Alex Hoggarth, Clare Gamlin, Shinya Ito, Jessica Trinh, Pasha Davoudian, Cristina Radaelli, Mean-Hwan Kim, Travis Hage, Thomas Braun, Lauren Alfiler, Julia Andrade, Phillip Bohn, Rachel Dalley, Alex Henry, Sara Kebede, Mukora Alice, David Sandman, Grace Williams, Rachael Larsen, Corinne Teeter, Tanya L. Daigle, Kyla Berry, Nadia Dotson, Rachel Enstrom, Melissa Gorham, Madie Hupp, Samuel Dingman Lee, Kiet Ngo, Philip R. Nicovich, Lydia Potekhina, Shea Ransford, Amanda Gary, Jeff Goldy, Delissa McMillen, Trangthanh Pham, Michael Tieu, La'Akea Siverts, Miranda Walker, Colin Farrell, Martin Schroedter, Cliff Slaughterbeck, Charles Cobb, Richard Ellenbogen, Ryder P. Gwinn, C. Dirk Keene, Andrew L. Ko, Jeffrey G. Ojemann, Daniel L. Silbergeld, Daniel Carey, Tamara Casper, Kirsten Crichton, Michael Clark, Nick Dee, Lauren Ellingwood, Jessica Gloe, Matthew Kroll, Josef Sulc, Herman Tung, Katherine Wadhwani, Krissy Brouner, Tom Egdorf, Michelle Maxwell, Medea McGraw, Christina Alice Pom, Augustin Ruiz, Jasmine Bomben, David Feng, Nika Hejazinia, Shu Shi, Aaron Szafer, Wayne Wakeman, John Phillips, Amy Bernard, Luke Esposito, Florence D. D'Orazi, Susan Sunkin, Kimberly Smith, Bosiljka Tasic, Anton Arkhipov, Staci Sorensen, Ed Lein, Christof Koch, Gabe Murphy, Hongkui Zeng, Tim Jarsky
Read MoreeNeuro
Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex
Feb 01, 2022
William G. P. Mayner, William Marshall, Yazan N. Billeh, Saurabh R. Gandhi, Shiella Caldejon, Andrew Cho, Fiona Griffin, Nicole Hancock, Sophie Lambert, Eric K. Lee, Jennifer A. Luviano, Kyla Mace, Chelsea Nayan, Thuyanh V. Nguyen, Kat North, Sam Seid, Ali Williford, Chiara Cirelli, Peter A. Groblewski, Jerome Lecoq, Giulio Tononi, Christof Koch, Anton Arkhipov
Read MoreNature
Human neocortical expansion involves glutamatergic neuron diversification
Oct 01, 2021
Jim Berg, Staci A. Sorensen, Jonathan T. Ting, Jeremy A. Miller, Thomas Chartrand, Anatoly Buchin, Trygve E. Bakken, Agata Budzillo, Nick Dee, Song-Lin Ding, Nathan W. Gouwens, Rebecca D. Hodge, Brian Kalmbach, Changkyu Lee, Brian R. Lee, Lauren Alfiler, Katherine Baker, Eliza Barkan, Allison Beller, Kyla Berry, Darren Bertagnolli, Kris Bickley, Jasmine Bomben, Thomas Braun, Krissy Brouner, Tamara Casper, Peter Chong, Kirsten Crichton, Rachel Dalley, Rebecca de Frates, Tsega Desta, Samuel Dingman Lee, Florence D'Orazi, Nadezhda Dotson, Tom Egdorf, Rachel Enstrom, Colin Farrell, David Feng, Olivia Fong, Szabina Furdan, Anna A. Galakhova, Clare Gamlin, Amanda Gary, Alexandra Glandon, Jeff Goldy, Melissa Gorham, Natalia A. Goriounova, Sergey Gratiy, Lucas Graybuck, Hong Gu, Kristen Hadley, Nathan Hansen, Tim S. Heistek, Alex M. Henry, Djai B. Heyer, DiJon Hill, Chris Hill, Madie Hupp, Tim Jarsky, Sara Kebede, Lisa Keene, Lisa Kim, Mean-Hwan Kim, Matthew Kroll, Caitlin Latimer, Boaz P. Levi, Katherine E. Link, Matthew Mallory, Rusty Mann, Desiree Marshall, Michelle Maxwell, Medea McGraw, Delissa McMillen, Erica Melief, Eline J. Mertens, Leona Mezei, Norbert Mihut, Stephanie Mok, Gabor Molnar, Alice Mukora, Lindsay Ng, Kiet Ngo, Philip R. Nicovich, Julie Nyhus, Gaspar Olah, Aaron Oldre, Victoria Omstead, Attila Ozsvar, Daniel Park, Hanchuan Peng, Trangthanh Pham, Christina A. Pom, Lydia Potekhina, Ramkumar Rajanbabu, Shea Ransford, David Reid, Christine Rimorin, Augustin Ruiz, David Sandman, Josef Sulc, Susan M. Sunkin, Aaron Szafer, Viktor Szemenyei, Elliot R. Thomsen, Michael Tieu, Amy Torkelson, Jessica Trinh, Herman Tung, Wayne Wakeman, Femke Waleboer, Katelyn Ward, René Wilbers, Grace Williams, Zizhen Yao, Jae-Geun Yoon, Costas Anastassiou, Anton Arkhipov, Pal Barzo, Amy Bernard, Charles Cobbs, Philip C. de Witt Hamer, Richard G. Ellenbogen, Luke Esposito, Manuel Ferreira, Ryder P. Gwinn, Michael J. Hawrylycz, Patrick R. Hof, Sander Idema, Allan R. Jones, C. Dirk Keene, Andrew L. Ko, Gabe J. Murphy, Lydia Ng, Jeffrey G. Ojemann, Anoop P. Patel, John W. Phillips, Daniel L. Silbergeld, Kimberly Smith, Bosiljka Tasic, Rafael Yuste, Idan Segev, Christiaan P. J. de Kock, Huibert D. Mansvelder, Gabor Tamas, Hongkui Zeng, Christof Koch, Ed S. Lein
Read MoreNature
Survey of spiking in the mouse visual system reveals functional hierarchy
Apr 01, 2021
Joshua H. Siegle, Xiaoxuan Jia, Séverine Durand, Sam Gale, Corbett Bennett, Nile Graddis, Greggory Heller, Tamina K. Ramirez, Hannah Choi, Jennifer A. Luviano, Peter A. Groblewski, Ruweida Ahmed, Anton Arkhipov, Amy Bernard, Yazan N. Billeh, Dillan Brown, Michael A. Buice, Nicolas Cain, Shiella Caldejon, Linzy Casal, Andrew Cho, Maggie Chvilicek, Timothy C. Cox, Kael Dai, Daniel J. Denman, Saskia E. J. de Vries, Roald Dietzman, Luke Esposito, Colin Farrell, David Feng, John Galbraith, Marina Garrett, Emily C. Gelfand, Nicole Hancock, Julie A. Harris, Robert Howard, Brian Hu, Ross Hytnen, Ramakrishnan Iyer, Erika Jessett, Katelyn Johnson, India Kato, Justin Kiggins, Sophie Lambert, Jerome Lecoq, Peter Ledochowitsch, Jung Hoon Lee, Arielle Leon, Yang Li, Elizabeth Liang, Fuhui Long, Kyla Mace, Jose Melchior, Daniel Millman, Tyler Mollenkopf, Chelsea Nayan, Lydia Ng, Kiet Ngo, Thuyahn Nguyen, Philip R. Nicovich, Kat North, Gabriel Koch Ocker, Doug Ollerenshaw, Michael Oliver, Marius Pachitariu, Jed Perkins, Melissa Reding, David Reid, Miranda Robertson, Kara Ronellenfitch, Sam Seid, Cliff Slaughterbeck, Michelle Stoecklin, David Sullivan, Ben Sutton, Jackie Swapp, Carol Thompson, Kristen Turner, Wayne Wakeman, Jennifer D. Whitesell, Derric Williams, Ali Williford, Rob Young, Hongkui Zeng, Sarah Naylor, John W. Phillips, R. Clay Reid, Stefan Mihalas, Shawn R. Olsen, Christof Koch
Read MoreNature Computational Science
Consistent cross-modal identification of cortical neurons with coupled autoencoders
Feb 01, 2021
Rohan Gala, Agata Budzillo, Fahimeh Baftizadeh, Jeremy Miller, Nathan Gouwens, Anton Arkhipov, Gabe Murphy, Bosiljka Tasic, Hongkui Zeng, Michael Hawrylycz, Uygar Sümbül
Read MoreCell
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Nov 12, 2020
Nathan W. Gouwens, Staci A. Sorensen, Fahimeh Baftizadeh, Agata Budzillo, Brian R. Lee, Tim Jarsky, Lauren Alfiler, Katherine Baker, Eliza Barkan, Kyla Berry, Darren Bertagnolli, Kris Bickley, Jasmine Bomben, Thomas Braun, Krissy Brouner, Tamara Casper, Kirsten Crichton, Tanya L. Daigle, Rachel Dalley, Rebecca A. de Frates, Nick Dee, Tsega Desta, Samuel Dingman Lee, Nadezhda Dotson, Tom Egdorf, Lauren Ellingwood, Rachel Enstrom, Luke Esposito, Colin Farrell, David Feng, Olivia Fong, Rohan Gala, Clare Gamlin, Amanda Gary, Alexandra Glandon, Jeff Goldy, Melissa Gorham, Lucas Graybuck, Hong Gu, Kristen Hadley, Michael J. Hawrylycz, Alex M. Henry, DiJon Hill, Madie Hupp, Sara Kebede, Tae Kyung Kim, Lisa Kim, Matthew Kroll, Changkyu Lee, Katherine E. Link, Matthew Mallory, Rusty Mann, Michelle Maxwell, Medea McGraw, Delissa McMillen, Alice Mukora, Lindsay Ng, Lydia Ng, Kiet Ngo, Philip R. Nicovich, Aaron Oldre, Daniel Park, Hanchuan Peng, Osnat Penn, Thanh Pham, Alice Pom, Zoran Popović, Lydia Potekhina, Ramkumar Rajanbabu, Shea Ransford, David Reid, Christine Rimorin, Miranda Robertson, Kara Ronellenfitch, Augustin Ruiz, David Sandman, Kimberly Smith, Josef Sulc, Susan M. Sunkin, Aaron Szafer, Michael Tieu, Amy Torkelson, Jessica Trinh, Herman Tung, Wayne Wakeman, Katelyn Ward, Grace Williams, Zhi Zhou, Jonathan T. Ting, Anton Arkhipov, Uygar Sümbül, Ed S. Lein, Christof Koch, Zizhen Yao, Bosiljka Tasic, Jim Berg, Gabe J. Murphy, Hongkui Zeng
Read MorePLoS computational biology
Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
Nov 01, 2020
Kael Dai, Sergey L. Gratiy, Yazan N. Billeh, Richard Xu, Binghuang Cai, Nicholas Cain, Atle E. Rimehaug, Alexander J. Stasik, Gaute T. Einevoll, Stefan Mihalas, Christof Koch, Anton Arkhipov
Read MoreNeuron
Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex
May 06, 2020
Yazan N. Billeh, Binghuang Cai, Sergey L. Gratiy, Kael Dai, Ramakrishnan Iyer, Nathan W. Gouwens, Reza Abbasi-Asl, Xiaoxuan Jia, Joshua H. Siegle, Shawn R. Olsen, Christof Koch, Stefan Mihalas, Anton Arkhipov
Read MorePLoS computational biology
The SONATA data format for efficient description of large-scale network models
Feb 01, 2020
Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K. Dichter, Michael Gevaert, James G. King, Werner A. H. Van Geit, Arseny V. Povolotsky, Eilif Muller, Jean-Denis Courcol, Anton Arkhipov
Read MoreNature Neuroscience
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Jul 01, 2019
Nathan W. Gouwens, Staci A. Sorensen, Jim Berg, Changkyu Lee, Tim Jarsky, Jonathan Ting, Susan M. Sunkin, David Feng, Costas A. Anastassiou, Eliza Barkan, Kris Bickley, Nicole Blesie, Thomas Braun, Krissy Brouner, Agata Budzillo, Shiella Caldejon, Tamara Casper, Dan Castelli, Peter Chong, Kirsten Crichton, Christine Cuhaciyan, Tanya L. Daigle, Rachel Dalley, Nick Dee, Tsega Desta, Song-Lin Ding, Samuel Dingman, Alyse Doperalski, Nadezhda Dotson, Tom Egdorf, Michael Fisher, Rebecca A. de Frates, Emma Garren, Marissa Garwood, Amanda Gary, Nathalie Gaudreault, Keith Godfrey, Melissa Gorham, Hong Gu, Caroline Habel, Kristen Hadley, James Harrington, Julie A. Harris, Alex Henry, DiJon Hill, Sam Josephsen, Sara Kebede, Lisa Kim, Matthew Kroll, Brian Lee, Tracy Lemon, Katherine E. Link, Xiaoxiao Liu, Brian Long, Rusty Mann, Medea McGraw, Stefan Mihalas, Alice Mukora, Gabe J. Murphy, Lindsay Ng, Kiet Ngo, Thuc Nghi Nguyen, Philip R. Nicovich, Aaron Oldre, Daniel Park, Sheana Parry, Jed Perkins, Lydia Potekhina, David Reid, Miranda Robertson, David Sandman, Martin Schroedter, Cliff Slaughterbeck, Gilberto Soler-Llavina, Josef Sulc, Aaron Szafer, Bosiljka Tasic, Naz Taskin, Corinne Teeter, Nivretta Thatra, Herman Tung, Wayne Wakeman, Grace Williams, Rob Young, Zhi Zhou, Colin Farrell, Hanchuan Peng, Michael J. Hawrylycz, Ed Lein, Lydia Ng, Anton Arkhipov, Amy Bernard, John W. Phillips, Hongkui Zeng, Christof Koch
Read MorePLoS computational biology
Visual physiology of the layer 4 cortical circuit in silico
Nov 01, 2018
Anton Arkhipov, Nathan W. Gouwens, Yazan N. Billeh, Sergey Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael Buice, Nicholas Cain, Nuno da Costa, Saskia de Vries, Daniel Denman, Severine Durand, David Feng, Tim Jarsky, Jérôme Lecoq, Brian Lee, Lu Li, Stefan Mihalas, Gabriel K. Ocker, Shawn R. Olsen, R. Clay Reid, Gilberto Soler-Llavina, Staci A. Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch
Read MoreNature Communications
Systematic generation of biophysically detailed models for diverse cortical neuron types
Feb 19, 2018
Nathan W. Gouwens, Jim Berg, David Feng, Staci A. Sorensen, Hongkui Zeng, Michael J. Hawrylycz, Christof Koch, Anton Arkhipov
Read MorePloS One
BioNet: A Python interface to NEURON for modeling large-scale networks
Jan 01, 2018
Sergey L. Gratiy, Yazan N. Billeh, Kael Dai, Catalin Mitelut, David Feng, Nathan W. Gouwens, Nicholas Cain, Christof Koch, Costas A. Anastassiou, Anton Arkhipov
Read MoreProceedings of the National Academy of Sciences of the United States of America
Inferring cortical function in the mouse visual system through large-scale systems neuroscience
Jul 05, 2016
Michael Hawrylycz, Costas Anastassiou, Anton Arkhipov, Jim Berg, Michael Buice, Nicholas Cain, Nathan W. Gouwens, Sergey Gratiy, Ramakrishnan Iyer, Jung Hoon Lee, Stefan Mihalas, Catalin Mitelut, Shawn Olsen, R. Clay Reid, Corinne Teeter, Saskia de Vries, Jack Waters, Hongkui Zeng, Christof Koch, MindScope
Read More