brain dynamics lab / papers | Brain Dynamics Lab

2026

Neurophysiological signatures of Stanford Neuromodulation Therapy in treatment resistant depression

Momi D., Buchanan D., Wada M., Geoly A.D., Johnson N.J., Cole E.J., Maron-Katz A., Tischler C., Cline C.C., Pizzagalli D.A., Saggar M., Voineskos D., Griffiths J.D., Rolle C.E., Keller C.J., Williams N.

Molecular Psychiatry

depressionTMSmodeling

Dynamic Substates of the Default Mode Network Are Associated with Mystical Experiences and Clinical Outcomes after Magnesium-Ibogaine Treatment in Veterans with Traumatic Brain Injury

Shinozuka K., Olash C., Han T., Azeez A., Sridhar M., Geoly A.D., Daye C., Hunegnaw S., Cherian K.N., Keynan J.N., Brown R.E., Buchanan D.M., Coetzee J.P., Kratter I.H., Airan R.D., Arns M., Adamson M.M., Saggar M., Rolle C.

medRxiv

psychedelicsbrain-dynamics

Efficient Deep Learning Models for Predicting Individualized Task Activation From Resting-State Functional Connectivity

Madsen S.*, Lee Y.*, Quah S.K.L., Uddin L.Q., Mumford J.A., Barch D.M., Fair D.A., Gotlib I.H., Poldrack, R.A., Kuceyeski A., Saggar M. (* co-first)

Human Brain Mapping

methodspsychiatry

Global topology of brain-wide co-fluctuations links task states, personality, and behavioral symptom dimensions

Siu C., Pirzada S., Glick C., Betzel R., Petri G., Manning J.R., Williams L., Saggar M.

bioRxiv

TDAbrain-dynamics

A fully remote randomized controlled trial of an ultra-brief digital meditation intervention reduces internalizing symptoms

Glick C.C., Pirzada S.T., Quah S.K., Feldman S., Enabulele I., Madsen S., Billimoria N., Feldman S., Bhatia R., Spiegel D., Saggar M.

medRxiv

meditation

Increased cortical thickness and decreased brain age among special operations veterans with blast TBI after a magnesium-ibogaine protocol

Geoly A.D., Coetzee J.P., Buchanan D.M., Struckmann W., Kim B., Sridhar M., Azeez A., Lissemore J.I., Cherian K., Faerman A., Keynan J.N., Singal P., Shanbour A., Bandeira I.D., Kratter I.H., Adamson M.M., Saggar M., Rolle C., Williams N.R.

iScience

psychedelics

Neural correlates of ibogaine Evidence from functional neuroimaging of military veterans

Sridhar M., Azeez A., Geoly A.D., Lissemore J.I., Faerman A., Cherian K., Buchanan D.M., Hunegnaw S., Keynan J.N., Kratter I.H., Rolle C., Saggar M., Williams N.R.

Biological Psychiatry Cognitive Neuroscience and Neuroimaging

psychedelics

Evolution With Purpose Hierarchy-Informed Optimization of Whole-Brain Models

Shahrzad H., Gajawelli N., Maile K., Saggar M., Miikkulainen R.

arXiv

modeling

2025

Topological data analysis reveals rigid brain-state dynamics during self-viewing in trait rumination

Geniesse C., Jahanikia S., Xie H., Sonalkar N., Williams L.M., Saggar M.

BioRxiv

TDAbrain-dynamicspsychiatry

Refining RDoC Using Individual-Level Task fMRI Factor Models Reveals Reproducible Brain-wide Motifs

Quah S.K.L., Madsen S., Pirzada S., Jo B., Uddin L.Q., Mumford J.A., Barch D.M., Gotlib I.H., Fair D.A., Poldrack, R.A., Saggar M.

BioRxiv

psychiatry

The Role of Meditation in Coping with Stress during the COVID-19 Lockdown A Cross-sectional Study of Undergraduates in India

Munjal P., Khurana N., Saggar M., Kumar L.

Frontiers in Psychiatry

meditation

Magnesium–ibogaine therapy effects on cortical oscillations and neural complexity in veterans with traumatic brain injury

Lissemore J.I., Chaiken A., Cherian K.N., Buchanan D., Espil F., Keynan J.N., Sridhar M., Rolle C.E., Saggar M., Keller C.J., Williams N.

Nature Mental Health

psychedelics

Concurrent single-pulse TMS-fMRI dataset to reveal the causal connectome in healthy and patient populations

Glick C., Gajawelli N., Sun Y., Badami F., Saggar M. Etkin A.

Scientific Data

TMSmethods

The topological architecture of brain identity

Poetto S., Merritt H., Santoro A., Rabuffo G., Battaglia D.A., Vaccarino F., Saggar M., Brovelli A., Petri G.

BioRxiv

TDAbrain-dynamics

Artificial Intelligence in Obsessive-Compulsive Disorder - A Systematic Review

Kim J., Pacheco J.P.G., Golden A., Aboujaoude E., Roessel P., Gandhi A., Mukunda P., Avanesyan T., Xue H., Adeli E., Kim J.P., Saggar M., Stirman S.W., Kuhn E., Supekar K., Pohl K.M., Rodriguez C.I.

Current Treatment Options in Psychiatry

psychiatrymethods

A data-driven approach exploring the entrepreneurialmanagerial spectrum

Booras A., Auernhammer J., Monlux K., Bruno J., Jahanikia S., Xie H., Sonalkar N., Saggar M.

Frontiers in Organizational Psychology

creativity

$Excitation-Inhibition Balance and Fronto-Limbic Connectivity Drive TMS Treatment Outcomes in Refractory Depression$

Excitation-Inhibition Balance and Fronto-Limbic Connectivity Drive TMS Treatment Outcomes in Refractory Depression

Momi D., Wang Z., Oveisi M.P., Kadak K., Bastiaens S.P., Lissemore J.I., Noda Y., Downar J., Rodriguez F.V., Strafella R., Daskalakis Z.J., Zrenner C., Zomorrodi R., Rolle C.E., Saggar M., Williams N., Keller C.J., Blumberger D.M., Voineskos D., Griffiths J.D.

BioRxiv

depressionTMSmodeling

Revealing Changes in Linear and Nonlinear Functional Connectivity After Psilocybin and Escitalopram Treatment in Patients with Depression

Quah S.K.L., Glick C., Roseman L., Pasquini L., Carhart-Harris R.L., Saggar M.

BioRxiv

psychedelicsdepression

Quantitative T1 mapping indicates elevated white matter myelin in children with RASopathies

Plank J.R., Gozdas E., Bruno J., McGhee C.A., Wu H., Raman M.M., Saggar M., Green G.

Biological Psychiatry

geneticsdevelopment

A Data-Driven Latent Variable Approach to Validating the Research Domain Criteria Framework

Quah S.K.L., Jo B., Geniesse C., Uddin L.Q., Mumford J.A., Barch D.M., Fair D.A., Gotlib I.H., Poldrack, R.A., Saggar M.

Nature Communications

psychiatry

2024

Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data

Hasegan D., Geniesse C., Chowdhury S., Saggar M.

Network Neuroscience

TDAmethods

Increased anti-correlation between the left dorsolateral prefrontal cortex and the default mode network following Stanford Neuromodulation Therapy (SNT) analysis of a double-blinded, randomized, sham-controlled trial

Gajawelli N., Geoly A. D., Batail JM, Xiao X., Maron-Katz A., Cole E., Azeez A., Kratter I.H., Saggar M., Williams N.R.

Mental Health Research

depressionTMS

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

Sun Y., Lucas M. V., Cline C. C., Menezes M. C., Kim S., Badami F. S., Narayan M., Wu W., Daskalakis Z. J., Etkin A., Saggar M.

BioRxiv

TMSmethods

The control costs of human brain dynamics

Ceballos E.G., Luppi A.I., Castrillon G., Saggar M., Misic B., Riedl V.

Network Neuroscience

brain-dynamicsmodeling

2023

NeuroDesign - Greater than the Sum of Its Parts

Auernhammer J., Bruno J., Booras A., McIntyre C., Hasegan D., Saggar M.

Springer

creativity

Cross-attractor modeling of resting-state functional connectivity in psychiatric disorders

Sun Y.,Zhang M.,Saggar M.

NeuroImage

modelingpsychiatry

Brain mitochondrial diversity and network organization predict anxiety-like behavior in male mice

Rosenberg A., Saggar M., Rogu P., Sandi C., Dumitriu D., Anacker C., Picard M.

Nature Communications

mitochondria

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

Batail J.M., Xiao X., Azeez A., Tischler C., Kratter I.H., Bishop J.H., Saggar M., Williams N.R.

Translational Psychiatry

depressionTMS

Development of top-down cortical propagations in youth

Pines A., Keller A.S., Larsen B., Bertolero M., Ashourvan A., Bassett D.S., Cieslak M., Covitz S., Fan Y., Feczko E., Houghton A., Rueter A.R., Saggar M., Shafiei G., Tapera T.M., Vogel J., Weinstein S.M., Shinohara R.T., Williams L.M., Fair D.A., Satterthwaite T.D.

Neuron

developmentbrain-dynamics

Current opinions on the present and future use of functional near-infrared spectroscopy in psychiatry

Li R., Hosseini H., Saggar M., Balters S.C., Reiss A.L.

NeuroPhotonics

psychiatrymethods

2022

Dynamic autonomic nervous system states arise during emotions and manifest in basal physiology

Pasquini L., Noohi F., Veziris C. R., Kosik E. L., Holley S. R., Lee A., ..., Saggar M., Seeley W., & Sturm, V. E.

Psychophysiology

brain-dynamics

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

Sun Y., Zhang M., Saggar M.

BioRxiv

modelingpsychiatry

Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest

Saggar M., Shine J.M., Liegeois R., Dosenbach N.U.F., Fair D.

Nature Communications

TDAbrain-dynamics

Temporal Mapper transition networks in simulated and real neural dynamics

Zhang M., Chowdhury S., Saggar M.

Network Neuroscience

TDAbrain-dynamics

Brief intensive social gaze training normalizes functional brain connectivity in boys with fragile X syndrome

Saggar M., Bruno J., Hall S.

Cerebral Cortex

geneticssocial

Cross-attractor repertoire provides new perspective on structure-function relationship in the brain

Zhang M., Sun Y., Saggar M.

NeuroImage

brain-dynamicsmodeling

Dysfunctional cortical gradient topography in treatment resistant major depression

Pasquini L. Fryer S.L., Eisendrath S.J., Segal Z.V., Lee A.J., Brown J.A., Saggar M., Mathalon D.H.

Biological Psychiatry Cognitive Neuroscience and Neuroimaging

depression

Neural resources shift under Methylphenidate a computational approach to examine anxiety-cognition interplay

Saggar M., Bruno J., Gaillard C., Claudino L., Ernst M.

NeuroImage

psychiatry

NeuMapper - A scalable computational framework for multiscale exploration of the brains dynamical organization

Geniesse C., Chowdhury S., Saggar M.

Network Neuroscience

TDAmethods

Altered canonical and striatal-frontal resting state functional connectivity in children with pathogenic variants in the Ras/mitogen-activated protein kinase pathway

Bruno J., Shrestha S., Reiss A., Saggar M., Green T.

Molecular Psychiatry

geneticsdevelopment

2021

Simplicial and topological descriptions of human brain dynamics.

Billings J., Saggar M., Hlinka J., Keilholz S., & Petri G.

Network Neuroscience

TDAbrain-dynamics

Thalamocortical connectivity is associated with autism symptoms in high-functioning adults with autism and typically developing adults.

Ayub R., Sun K. L., Flores R. E., Lam V. T., Jo B., Saggar M., & Fung L. K.

Translational Psychiatry

psychiatry

Mouse brain-wide mitochondrial connectivity anchored in gene, brain and behavior.

Rosenberg A., Saggar M., Rogu P., Limoges A. W., Sandi C., Mosharov E. V., ... & Picard M.

BioRxiv

mitochondria

NeuroDesign From Neuroscience Research to Design Thinking Practice.

Auernhammer J., Sonalkar N., & Saggar M.

Design Thinking Research

creativity

Creativity and the brain An editorial introduction to the special issue on the neuroscience of creativity.

Saggar M., Volle E., Uddin L. Q., Chrysikou E. G., & Green A. E.

NeuroImage

creativity

Spontaneous and deliberate modes of creativity - Multitask eigen-connectivity analysis captures latent cognitive modes during creative thinking

Xie H., Beaty R. E., Jahanikia S., Geniesse C., Sonalkar N. S., & Saggar M.

NeuroImage

creativity

2020

Finding the neural correlates of collaboration using a three-person fMRI hyperscanning paradigm.

Xie H., Karipidis, I. I., Howell A., Schreier M., Sheau K. E., Manchanda M. K., ... & Saggar M.

PNAS

social

Mining the Role of Design Reflection and Associated Brain Dynamics in Creativity

Sonalkar N., Jahanikia S., Xie H., Geniesse C., Ayub R., Beaty R., & Saggar M.

Design Thinking Research

creativitybrain-dynamics

Thalamic and prefrontal GABA concentrations but not GABA A receptor densities are altered in high-functioning adults with autism spectrum disorder

Fung L.K., Flores R.E., Gu M., Sun K.L., James D., Schuck R.K., Jo B., Park J.H., Lee B.C., Jung J.H., Kim S.E., Saggar M., Sacchet M.D., Warnock G., Khalighi M.M., Spielman D., Chin F.T., Hardan A.Y.

Molecular Psychiatry

psychiatry

Complexity of resting brain dynamics shaped by multiscale structural constraints

Zhang M., Saggar M.

biorxiv

brain-dynamicsmodeling

2019

Pushing the Boundaries of Psychiatric Neuroimaging to Ground Diagnosis in Biology

Saggar M. and Uddin L. Q.

eNeuro

psychiatry

Large expert-curated database for benchmarking document similarity detection in biomedical literature search.

Brown, P., Tan, A. C., El-Esawi, M. A., Liehr, T., Blanck, O., Gladue, D. P., ... & Shabalin, I. G.

Database

methods

Implementing evolutionary optimization to model neural functional connectivity

Maile, K., Saggar, M., & Miikkulainen, R.

GECCO

modelingmethods

Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis

Geniesse C., Sporns O., Petri G., and Saggar M.

Network Neuroscience

TDAmethods

Creativity slumps and bumps - Examining the neurobehavioral basis of creativity development during middle childhood

Saggar M., Xie H., Beaty R.E., Stankov A.D., Schreier M., and Reiss A.L.

NeuroImage

creativitydevelopment

2018

Creativity in the twenty-first century - The added benefit of training and cooperation

Mayseless, N., Saggar, M., Hawthorne, G., & Reiss, A.

Design thinking research

creativitysocial

Towards a new approach to reveal dynamical organization of the brain using topological data analysis

Saggar M., Sporns O., Gonzalez-Castillo J., Bandettini P.A., Carlsson G., Glover G., Reiss A.L.

Nature Communications

TDAbrain-dynamics

2017

X-Chromosome Effects on Attention Networks: Insights from Imaging Resting-State Networks in Turner Syndrome

Green T.*, Saggar M.*, Ishak A., Hong D.S., Reiss A.L.

Cerebral Cortex

genetics

Identification of biotypes in Attention-Deficit/Hyperactivity Disorder, a report from a randomized, controlled trial

Leikauf J.E., Griffiths K.R., Saggar M., Hong D.S., Clarke S., Efron D., Tsang T.W., Hermens D.F., Kohn M.R., Williams L.M.

Personalized Medicine in Psychiatry

psychiatry

Compensatory Hyperconnectivity in Developing Brains of Young Children With Type 1 Diabetes

Saggar M., Tsalikian E., Mauras N., Mazaika P., White N., Weinzimer S., Buckingham B., Hershey T., Reiss A.L

Diabetes

development

Changes in Brain Activation Associated with Spontaneous Improvization and Figural Creativity After Design-Thinking-Based Training: A Longitudinal fMRI Study

Saggar M., Quintin E-M, Bott N., Kienitz E., Chien Y.H., Hong D.W.C., Liu N., Royalty A., Hawthorne G., Reiss A.L.

Cerebral Cortex

creativity

2016

Sex differences in neural and behavioral signatures of cooperation revealed by fNIRS hyperscanning

Baker J.M., Liu N., Cui X., Vrticka P., Saggar M., Hosseini H., Reiss A.L.

Scientific Reports

social

Altered Brain Network Segregation in Fragile X Syndrome Revealed by Structural Connectomics

Bruno J., Hosseini H., Saggar M., Quintin EM, Raman M., Reiss A.L.

Cerebral Cortex

genetics

Surface‐based morphometry reveals distinct cortical thickness and surface area profiles in Williams syndrome

Green T., Fierro K., Raman M., Saggar M., Sheau K., Reiss A.L.

Am J Med Genet Part B

genetics

Understanding the influence of personality on dynamic social gesture processing: An fMRI study

Saggar M.*, Vrticka P.*, & Reiss A.L.

Neuropsychologia

social

2015

Estimating individual contribution from group-based structural correlation networks

Saggar M., Hosseini S. M. H., Bruno J., Quintin E.-M., Raman M. M., Kesler S. R., Reiss A. L.

NeuroImage

methods

$Examining the neural correlates of emergent equivalence relations in fragile X syndrome$

Examining the neural correlates of emergent equivalence relations in fragile X syndrome

Klabunde M., Saggar M., Hustyi K. M., Kelley R. G., Reiss A. L., Hall S. S.

Psychiatry Research: Neuroimaging

genetics

Neural correlates of self‐injurious behavior in Prader–Willi syndrome

Klabunde M., Saggar M., Hustyi K. M., Hammond J. L., Reiss A. L., Hall S. S.

Human Brain Mapping

genetics

Mean-field thalamocortical modeling of longitudinal EEG acquired during intensive meditation training

Saggar M., Zanesco A. P., King B. G., Bridwell D. A., MacLean K. A., Aichele S. R., Jacobs T.L., Wallace B.A., Saron C.D., Miikkulainen R.

NeuroImage

meditationmodeling

Pictionary-based fMRI paradigm to study the neural correlates of spontaneous improvisation and figural creativity

Saggar M., Quintin E.-M., Kienitz E., Bott N. T., Sun Z., Hong D.W.C., Chien Y.H., Liu N., Dougherty R.F., Royalty A., Hawthorne G., Reiss A.L.

Scientific Reports

creativity

2014

Targeted intervention to increase creative capacity and performance: A randomized controlled pilot study

Kienitz E., Quintin E.-M., Saggar M., Bott N., Royalty A., Hong D. W.C., Liu N., Chien Y.H., Hawthorne G., Reiss A.L.

Thinking Skills & Creativity

creativity

Creativity training enhances goal-directed attention and information processing

Bott N., Quintin E.-M., Saggar M., Kienitz E., Royalty A., Hong D. W.C., Liu N., Chien Y.H., Hawthorne G., Reiss A.L.

Thinking Skills & Creativity

creativity

Early signs of anomalous neural functional connectivity in healthy offspring of parents with bipolar disorder

Singh M., Chang K. D., Kelley R. G., Saggar M., Reiss A., Gotlib I. H.

Bipolar Disorders

psychiatrydevelopment

Revealing the neural networks associated with processing of natural social interaction and the related effects of actor-orientation and face-visibility

Saggar M., Shelly E. W., Lepage J.-F., Hoeft F., Reiss A.L.

NeuroImage

social

2012 and earlier

Intensive training induces longitudinal changes in meditation state-related EEG oscillatory activity

Saggar M., King B. G., Zanesco A. P., MacLean K. A., Aichele S. R., Jacobs T. L., Bridwell D.A., Shaver P.R., Rosenberg E.L., Sahdra B.K., Ferrer E., Tang A.C., Mangun G.R., Wallace B.A., Miikkulainen R., Saron C.D.

Frontiers Human Neuroscience

meditation