Anton Arkhipov, Ph.D.
Associate Investigator
Download CV | antona@alleninstitute.org
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
Research Interests
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.
Expertise
- Computational Neuroscience
- Theoretical and Computational Biophysics
- High-performance Computing
Research Programs
- Modeling, Analysis & Theory
Selected Publications
Neuron
March 5, 2020
Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A
The SONATA data format for efficient description of large-scale network models
PLoS Computational Biology
February 24, 2020
Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol JD, Arkhipov A
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Cell
November 12, 2020
Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H
Classification of electrophysiological and morphological neuron types in mouse visual cortex
Nature Neuroscience
June 17, 2019
Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin S, Feng D, Anastassiou C, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle T, Dalley R, Dee N, Desta T, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris J, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina C, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips J, Zeng H, Koch C
BioNet: A Python interface to NEURON for modeling large-scale networks
PLOS | ONE
August 2, 2018
Gratiy SL, Billeh YN, Dai K, Mitelut C, Feng D, Gouwens NW, Cain N, Koch C, Anastassiou CA, Arkhipov A
Systematic generation of biophysically detailed models for diverse cortical neuron types
Nature Communications
February 19, 2018
Gouwens NW, Berg J, Feng D, Sorensen SA, Zeng H, Hawrylycz MJ, Koch C, and Arkhipov A
Visual physiology of the Layer 4 cortical circuit in silico
PLoS Computational Biology
November 12, 2018
Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-LLavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C
Inferring cortical function in the mouse visual system through large-scale systems neuroscience
PNAS
July 5, 2016
Hawrylycz M, Anastassiou C, Arkhipov A, Berg J, Buice M, et al.
Architecture and membrane interactions of the EGF receptor
Cell
January 2013
Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, et al
Conformational coupling across the plasma membrane in activation of the EGF receptor
Cell
January 2013
Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, et al
Cell
May 2012
Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, et al