Staff Profiles

Sergey Gratiy, Ph.D.

Software Engineer II

Sergey develops and supports the analysis pipeline and the corresponding software for computing cell features from electrophysiology data. He joined the Allen Institute in 2014 developing theoretical and computational techniques for investigating the biophysical origins of extracellular potential. As a part of this research direction, he contributed to the development of the software tools (e.g, Brain Modeling Toolkit) that facilitate modeling large-scale networks of biophysically/morphologically realistic neurons and that enable the simulation of extracellular potential recordings. Prior to joining the Allen Institute, he conducted postdoctoral research at the University of California, San Diego where he developed models for inferring population-level synaptic currents from Local Field Potential recordings. Sergey earned his PhD in Aerospace Engineering from the Pennsylvania State University, a MS in Physics from the University of Louisville and a BS in Physics from Perm State University, Russia.

Selected Publications View Publications

Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex

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

Brain Modeling ToolKit: an Open Source Software Suite for Multiscale Modeling of Brain Circuits

PLoS Computational Biology
November 30, 2020

Dai K, Gratiy SL, Billeh YN, Xu R, Cai B, Cain N, Rimehaug AE, Stasik AJ, Einevoll GT, Mihalas S, Koch C, Arkhipov A

BioNet: A Python interface to NEURON for modeling large-scale networks

August 2, 2018

Gratiy SL, Billeh YN, Dai K, Mitelut C, Feng D, Gouwens NW, Cain N, Koch C, Anastassiou CA, 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

From Maxwell's equations to the theory of current-source density analysis

European Journal of Neuroscience
February 8, 2017

Gratiy SL, Halnes G, Denman D, Hawrylycz MJ, Koch C, Einevoll GT, Anastassiou CA

Fully integrated silicon probes for high-density recording of neural activity

November 8, 2017

Jun JJ, Steinmetz NA, Siegle JH, Denman DJ, Bauza M, Barbarits B, Lee AK, Anastassiou CA, Andrei A, Aydın Ç, Barbic M, Blanche TJ, Bonin V, Couto J, Dutta B, Gratiy SL, Gutnisky DA, Häusser M, Karsh B, Ledochowitsch P, Lopez CM, Mitelut C, Musa S, Okun M, Pachitariu M, Putzeys J, Rich PD, Rossant C, Sun WL, Svoboda K, Carandini M, Harris KD, Koch C5 O'Keefe J, Harris TD

In vivo stimulus-induced vasodilation occurs without IP3 receptor activation and may precede astrocytic calcium increase

Journal of Neuroscience
May 8, 2013

Nizar K, Uhlirova H, Tian P, Saisan PA, Cheng Q, Reznichenko L, Weldy KL, Steed TC, Sridhar VB, MacDonald CL, Cui J, Gratiy SL, Sakadzić S, Boas DA, Beka TI, Einevoll GT, Chen J, Masliah E, Dale AM, Silva GA, Devor A

Pitfalls in the interpretation of multielectrode data: on the infeasibility of the neuronal current-source monopoles

Journal of Neurophysiology
March 15, 2013

Gratiy SL, Pettersen KH, Einevoll GT, Dale AM

On the estimation of population-specific synaptic currents from laminar multielectrode recordings

Frontiers in Neuroinformatics
December 20, 2011

Gratiy SL, Devor A, Einevoll GT, Dale AM