Manish Saggar

Principal investigator
Google Scholar
  • Assistant Professor, Department of Psychiatry & Behavioral Sciences
  • Tashia and John Morgridge Endowed Faculty Scholar in Pediatric Translational Medicine, MCHRI
  • Member, Bio-X
  • Member, Child Health Research Institute
  • Member, Stanford Neurosciences Institute
  • Member, Stanford Biophysics Program
  • Member, Stanford Biomedical Informatics Program
  • Bio-design Faculty Fellow (2017)
  • Faculty, Hasso Plattner Institute of Design (

I am a computational neuroscientist who is trained in machine learning, neuroscience and psychiatry. The overarching goal of my research is to develop reliable computational methods that will allow for characterizing and modeling temporal dynamics of brain activity, without averaging data in either space or time. I firmly believe that the spatiotemporal richness in brain activity might hold the key to finding the person- and disorder-centric biomarkers. Currently, funded by a New Innovator Award (DP2; NIH) and a NIH R01, we are developing methods to model the temporal dynamics of brain activity in individuals with psychiatric disorders and healthy controls.

I received my bachelor’s degree from the Indian Institute of Information Technology (Allahabad) and my Masters and PhD from the University of Texas at Austin, advised by Risto Miikkulainen and Clifford Saron. Following my PhD, I did my Postdoctoral Fellowship at the Stanford University School of Medicine, mentored by Allan Reiss.


Densely sampled stimulus-response map of human cortex with single pulse TMS-EEG and its relation to whole brain neuroimaging measures (2024). BioRxiv

A Data-Driven Latent Variable Approach to Validating the Research Domain Criteria (RDoC) Framework (2024). BioRxiv

The control costs of human brain dynamics (2024). BioRxiv

Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data (2023). BioRxiv

NeuroDesign - Greater than the Sum of Its Parts (2023). Springer

Cross-attractor modeling of resting-state functional connectivity in psychiatric disorders (2023). NeuroImage

Brain mitochondrial diversity and network organization predict anxiety-like behavior in male mice (2023). Nature Communications

Network effects of Stanford Neuromodulation Therapy (SNT) in treatment-resistant major depressive disorder a randomized, controlled trial (2023). Translational Psychiatry

Development of top-down cortical propagations in youth (2023). Neuron

Current opinions on the present and future use of functional near-infrared spectroscopy in psychiatry (2023). NeuroPhotonics

Dynamic autonomic nervous system states arise during emotions and manifest in basal physiology (2022). Psychophysiology

Cross-attractor modeling of resting-state functional connectivity in psychiatric disorders reveals disturbances in excitation, inhibition, and energy gaps (2022). BioRxiv

Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest (2022). Nature Communications

Temporal Mapper transition networks in simulated and real neural dynamics (2022). Network Neuroscience

Brief intensive social gaze training normalizes functional brain connectivity in boys with fragile X syndrome (2022). Cerebral Cortex

Cross-attractor repertoire provides new perspective on structure-function relationship in the brain (2022). NeuroImage

Dysfunctional cortical gradient topography in treatment resistant major depression (2022). Biological Psychiatry Cognitive Neuroscience and Neuroimaging

Neural resources shift under Methylphenidate a computational approach to examine anxiety-cognition interplay (2022). NeuroImage

NeuMapper - A scalable computational framework for multiscale exploration of the brains dynamical organization (2022). Network Neuroscience

Altered canonical and striatal-frontal resting state functional connectivity in children with pathogenic variants in the Ras/mitogen-activated protein kinase pathway (2022). Molecular Psychiatry

Simplicial and topological descriptions of human brain dynamics. (2021). Network Neuroscience

Thalamocortical connectivity is associated with autism symptoms in high-functioning adults with autism and typically developing adults. (2021). Translational Psychiatry

Mouse brain-wide mitochondrial connectivity anchored in gene, brain and behavior. (2021). BioRxiv

NeuroDesign From Neuroscience Research to Design Thinking Practice. (2021). Design Thinking Research

Creativity and the brain An editorial introduction to the special issue on the neuroscience of creativity. (2021). NeuroImage

Spontaneous and deliberate modes of creativity - Multitask eigen-connectivity analysis captures latent cognitive modes during creative thinking (2021). NeuroImage

Finding the neural correlates of collaboration using a three-person fMRI hyperscanning paradigm. (2020). PNAS

Mining the Role of Design Reflection and Associated Brain Dynamics in Creativity (2020). Design Thinking Research

Thalamic and prefrontal GABA concentrations but not GABA A receptor densities are altered in high-functioning adults with autism spectrum disorder (2020). Molecular Psychiatry

Complexity of resting brain dynamics shaped by multiscale structural constraints (2020). biorxiv

Pushing the Boundaries of Psychiatric Neuroimaging to Ground Diagnosis in Biology (2019). eNeuro

Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis (2019). Network Neuroscience

Creativity slumps and bumps - Examining the neurobehavioral basis of creativity development during middle childhood (2019). NeuroImage

Towards a new approach to reveal dynamical organization of the brain using topological data analysis (2018). Nature Communications

X-Chromosome Effects on Attention Networks: Insights from Imaging Resting-State Networks in Turner Syndrome (2017). Cerebral Cortex

Identification of biotypes in Attention-Deficit/Hyperactivity Disorder, a report from a randomized, controlled trial (2017). Personalized Medicine in Psychiatry

Compensatory Hyperconnectivity in Developing Brains of Young Children With Type 1 Diabetes (2017). Diabetes

Changes in Brain Activation Associated with Spontaneous Improvization and Figural Creativity After Design-Thinking-Based Training: A Longitudinal fMRI Study (2017). Cerebral Cortex

Sex differences in neural and behavioral signatures of cooperation revealed by fNIRS hyperscanning (2016). Scientific Reports

Altered Brain Network Segregation in Fragile X Syndrome Revealed by Structural Connectomics (2016). Cerebral Cortex

Surface‐based morphometry reveals distinct cortical thickness and surface area profiles in Williams syndrome (2016). Am J Med Genet Part B

Understanding the influence of personality on dynamic social gesture processing: An fMRI study (2016). Neuropsychologia

Estimating individual contribution from group-based structural correlation networks (2015). NeuroImage

Examining the neural correlates of emergent equivalence relations in fragile X syndrome (2015). Psychiatry Research: Neuroimaging

Neural correlates of self‐injurious behavior in Prader–Willi syndrome (2015). Human Brain Mapping

Mean-field thalamocortical modeling of longitudinal EEG acquired during intensive meditation training (2015). NeuroImage

Pictionary-based fMRI paradigm to study the neural correlates of spontaneous improvisation and figural creativity (2015). Scientific Reports

Targeted intervention to increase creative capacity and performance: A randomized controlled pilot study (2014). Thinking Skills & Creativity

Creativity training enhances goal-directed attention and information processing (2014). Thinking Skills & Creativity

Early signs of anomalous neural functional connectivity in healthy offspring of parents with bipolar disorder (2014). Bipolar Disorders

Revealing the neural networks associated with processing of natural social interaction and the related effects of actor-orientation and face-visibility (2014). NeuroImage

Intensive training induces longitudinal changes in meditation state-related EEG oscillatory activity (2012). Frontiers Human Neuroscience

Behavioral, neuroimaging, and computational evidence for perceptual caching in repetition priming (2010). Brain Research

Memory Processes in Perceptual Decision Making (2008). Proceedings of the Cognitive Science Society Meeting (2007)

System Identification for the Hodgkin-Huxley Model using Artificial Neural Networks (2007). Proceedings of the IEEE IJCNN Conference (2007)

Autonomous Learning of Stable Quadruped Locomotion (2007). Lecture Notes in Computer Science

A Computational Model of the Motivation-learning Interface (2007). Proceedings of the Cognitive Science Society Meeting (2007)

Optimization of association rule mining using improved genetic algorithms (2004). Proceedings of the IEEE SMC Conference (2004)


Data-driven validation of the NIMH RDoC framework

Computational Mitochondrial PsychoBiology

Quantifying changes in brain dynamics associated with non-invasive brain stimulation

Examining the neural basis of applied creativity in entrepreneurs

Only time will tell - a computational psychiatry approach to model temporal transitions in brain activity as a lens towards developing better diagnostic nosology for psychiatric illness

Understanding the role of design reflection (vs rumination) in creative thinking

Deciphering “ongoing” cognition using concurrent multimodal neuroimaging and continuous multitask paradigm

Quantifying and capturing transitions in intrinsic brain activity in healthy and patient populations

Creative brain development

Examining the neural correlates of creative capacity enhancement using targetted training.

Brain dynamics associated with intensive meditation training


Using TDA-based Mapper to understand the anxiety-cognition interplay

Topological Data Analysis of fMRI data