Christoph Kirst, PhD, MS, BS | Neuroscience Graduate Program

Assistant Professor

M_Anatomy-General

415-502-7372

Research Description

We develop theory and dynamical systems tools, machine learning and data analysis algorithms, and whole brain mapping methods to characterize and understand flexible brain function

Current Projects

Theoretical frameworks for functional self-reconfiguration processes in neuronal networks.
Analysis and machine learning tools for high-dimensional, multi-scale network dynamics from experimental data investigating flexible function and functional coordination in brain circuits
Whole brain structure and activity mapping
Neuro-modulation and AI

Publications

Resolving non-identifiability mitigates systematic errors in simultaneous models of neural tuning and functional coupling.

Journal of computational neuroscience

Sachdeva P, Bak JH, Livezey J, Kirst C, Frank L, Bhattacharyya S, Bouchard KE

Regional specialization in prefrontal cortex manifests in the reliability of task progression codes.

Neuron

Guidera JA, Gramling DP, Comrie AE, Joshi A, Tseng SY, Denovellis EL, Smyth CN, Lee KH, Zhou J, Thompson P, Hernandez J, Yorita A, Haque R, Kirst C, Frank LM

Extracellular matrix proteolysis maintains synapse plasticity during brain development.

Nature Neuroscience

Nakajo H, Cao R, Mula SA, McKetney J, Silva NJ, Li KH, Chalkley RJ, Randolph LK, Shah M, Rose IVL, Kampmann M, Swaney DL, Kirst C, Molofsky AV

Identity-stable multi-animal tracking using bidirectional segmentation with object-level memory.

bioRxiv : the preprint server for biology

Wang S, Quine K, Jordan A, Dasari S, Manoli DS, Kirst C

Design of Hopfield Networks Based on Superconducting Coupled Oscillators.

Ran Cheng, Christoph Kirst, Dilip Vasudevan

Extracellular matrix proteolysis maintains synapse plasticity during brain development.

bioRxiv : the preprint server for biology

Nakajo H, Cao R, Mula SA, McKetney J, Silva NJ, Shah M, Rose IVL, Kampmann M, Swaney DL, Kirst C, Molofsky AV

Publisher Correction: Network-level encoding of local neurotransmitters in cortical astrocytes.

Cahill MK, Collard M, Tse V, Reitman ME, Etchenique R, Kirst C, Poskanzer KE

Network-level encoding of local neurotransmitters in cortical astrocytes.

Nature

Cahill MK, Collard M, Tse V, Reitman ME, Etchenique R, Kirst C, Poskanzer KE

Super-Tsetlin: Superconducting Tsetlin Machines.

Ran Cheng, Dilip Vasudevan, Christoph Kirst

Regional specialization manifests in the reliability of neural population codes.

Guidera JA, Gramling DP, Comrie AE, Joshi A, Denovellis EL, Lee KH, Zhou J, Thompson P, Hernandez J, Yorita A, Haque R, Kirst C, Frank LM

Network-level encoding of local neurotransmitters in cortical astrocytes.

Cahill MK, Collard M, Tse V, Reitman ME, Etchenique R, Kirst C, Poskanzer KE

Resolving Non-identifiability Mitigates Bias in Models of Neural Tuning and Functional Coupling.

Sachdeva P, Bak JH, Livezey J, Kirst C, Frank L, Bhattacharyya S, Bouchard KE

Superconducting-Oscillatory Neural Network With Pixel Error Detection for Image Recognition.

Ran Cheng, Christoph Kirst, Dilip Vasudevan

Edinger-Westphal peptidergic neurons enable maternal preparatory nesting.

Topilko T, Diaz SL, Pacheco CM, Verny F, Rousseau CV, Kirst C, Deleuze C, Gaspar P, Renier N

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature.

M_Anatomy-General

Kirst C, Skriabine S, Vieites-Prado A, Topilko T, Bertin P, Gerschenfeld G, Verny F, Topilko P, Michalski N, Tessier-Lavigne M, Renier N

WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids.

M_PEDS-NEONATOLOGY

Yoney A, Etoc F, Ruzo A, Carroll T, Metzger JJ, Martyn I, Li S, Kirst C, Siggia ED, Brivanlou AH

hPSC Modeling Reveals that Fate Selection of Cortical Deep Projection Neurons Occurs in the Subplate.

Ozair MZ, Kirst C, van den Berg BL, Ruzo A, Rito T, Brivanlou AH

Neuromodulatory Control of Long-Term Behavioral Patterns and Individuality across Development.

M_Anatomy-General

Stern S, Kirst C, Bargmann CI

Transition to reconstructibility in weakly coupled networks.

Lünsmann BJ, Kirst C, Timme M

Shifting attention to dynamics: Self-reconfiguration of neural networks.

Christoph Kirst, Carl D. Modes, Marcelo O. Magnasco

Convergence of Self-Organizing Pulse-Coupled Oscillator Synchronization in Dynamic Networks.

Johannes Klinglmayr, Christian Bettstetter, Marc Timme, Christoph Kirst

A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization.

Etoc F, Metzger J, Ruzo A, Kirst C, Yoney A, Ozair MZ, Brivanlou AH, Siggia ED

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes.

M_Anatomy-General

Renier N, Adams EL, Kirst C, Wu Z, Azevedo R, Kohl J, Autry AE, Kadiri L, Umadevi Venkataraju K, Zhou Y, Wang VX, Tang CY, Olsen O, Dulac C, Osten P, Tessier-Lavigne M