Project:	Biophysics-informed foundational models of brain circuits
Disciplines:	Computation and Neural Systems, Bioengineering
Mentor:	Costas Anastassiou, Associate Professor, (EAS), costas@caltech.edu
Mentor URL:	Anastassioulab.org  (opens in new window)
Background:	We generate a bio-realistic model of human microcircuit models that comprises of several major excitatory and inhibitory cell types connected using human-derived connectivity rules. This model is foundational because it i) unifies multimodal cellular and circuit data into a single, coherent framework; ii) bridges spatiotemporal scales, iii) enables perturbation experiments that are impossible to perform in humans, and iv) generalizes by generating testable hypotheses about dynamics, computations and interventions it did not train on. This foundational model therefore offers a platform for mechanistic understanding -- not by learning what the human cortex does, but by implementing how it works. We use this model to ask questions about how the cellular properties and composition of human circuits shape their collective function and emergent dynamics.
Description:	The student will contribute in developing tools and methods to generate , test , run and interpret large-scale foundational modeling results.
References:	Full View “Cellular classes in the human brain revealed in vivo by heartbeat-related modulation of the extracellular action potential waveform” Clayton P Mosher, Yina Wei, Jan Kamiński, Anirban Nandi, Adam N Mamelak, Costas A Anastassiou, Ueli Rutishauser, Cell reports, 30: 10, 3536-3551. e6 (2020) “Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types” Anirban Nandi, Thomas Chartrand, Werner Van Geit, Anatoly Buchin, Zizhen Yao, Soo Yeun Lee, Yina Wei, Brian Kalmbach, Brian Lee, Ed Lein, Jim Berg, Uygar Sümbül, Christof Koch, Bosiljka Tasic, Costas A Anastassiou Cell reports, 40: 6 (2022) “Multi-modal characterization and simulation of human epileptic circuitry” Anatoly Buchin, Rebecca de Frates, Anirban Nandi, Rusty Mann, Peter Chong, Lindsay Ng, Jeremy Miller, Rebecca Hodge, Brian Kalmbach, Soumita Bose, Ueli Rutishauser, Stephen McConoughey, Ed Lein, Jim Berg, Staci Sorensen, Ryder Gwinn, Christof Koch, Jonathan Ting, Costas A Anastassiou, Cell reports, 41: 13 (2022)
Student Requirements:	Strong coding and data wrangling skills are essential.
Programs:	This AO can be done under the following programs:   Program    Available To        Amgen Scholars    Non-Caltech students only          SURF    both Caltech and non-Caltech students  Click on a program name for program info and application requirements.