From mathematics to medicine: A practical primer on topological data analysis (TDA) and the development of related analytic tools for the functional discovery of latent structure in fMRI data

Spectral and topological analyses of the cortical representation of the head position: Does hypnotizability matter?

(2019) Esther Ibáñez‐Marcelo et al.   Brain and Behavior

A deep learning framework for neuroscience

(2019) Blake A. Richards et al.   NATURE NEUROSCIENCE

Topology highlights mesoscopic functional equivalence between imagery and perception: The case of hypnotizability

(2019) Esther Ibáñez-Marcelo et al.   NEUROIMAGE

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

(2018) Manish Saggar et al.   Nature Communications

Functional dynamics of hippocampal glutamate during associative learning assessed with in vivo 1 H functional magnetic resonance spectroscopy

(2017) Jeffrey A. Stanley et al.   NEUROIMAGE

A roadmap for the computation of persistent homology

(2017) Nina Otter et al.   EPJ Data Science

Potentiation of motor sub-networks for motor control but not working memory: Interaction of dACC and SMA revealed by resting-state directed functional connectivity

(2017) Vaibhav A. Diwadkar et al.   PLoS One

Cortical-hippocampal functional connectivity during covert consolidation sub-serves associative learning: Evidence for an active “rest” state

(2017) Mathura Ravishankar et al.   BRAIN AND COGNITION

Chronological age and its impact on associative learning proficiency and brain structure in middle adulthood

(2016) Vaibhav A. Diwadkar et al.   BEHAVIOURAL BRAIN RESEARCH

Metabolic demands of neural-hemodynamic associated and disassociated areas in brain

(2016) Basavaraju G Sanganahalli et al.   JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM

Two’s company, three (or more) is a simplex

(2016) Chad Giusti et al.   JOURNAL OF COMPUTATIONAL NEUROSCIENCE

Principal component analysis of persistent homology rank functions with case studies of spatial point patterns, sphere packing and colloids

(2016) Vanessa Robins et al.   PHYSICA D-NONLINEAR PHENOMENA

Using persistent homology and dynamical distances to analyze protein binding

(2016) Violeta Kovacev-Nikolic et al.   Statistical Applications in Genetics and Molecular Biology

Using persistent homology and dynamical distances to analyze protein binding

(2016) Violeta Kovacev-Nikolic et al.   Statistical Applications in Genetics and Molecular Biology

Inferring the Dysconnection Syndrome in Schizophrenia: Interpretational Considerations on Methods for the Network Analyses of fMRI Data

(2016) Brian H. Silverstein et al.   Frontiers in Psychiatry

The dorsal prefrontal and dorsal anterior cingulate cortices exert complementary network signatures during encoding and retrieval in associative memory

(2015) Eric A. Woodcock et al.   BEHAVIOURAL BRAIN RESEARCH

Persistent Homology in Sparse Regression and Its Application to Brain Morphometry

(2015) Moo K. Chung et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Architectonic Mapping of the Human Brain beyond Brodmann

(2015) Katrin Amunts et al.   NEURON

Clique topology reveals intrinsic geometric structure in neural correlations

(2015) Chad Giusti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Controllability of structural brain networks

(2015) Shi Gu et al.   Nature Communications

Persistent homology analysis of protein structure, flexibility, and folding

(2014) Kelin Xia et al.   International Journal for Numerical Methods in Biomedical Engineering

A topological measurement of protein compressibility

(2014) Marcio Gameiro et al.   JAPAN JOURNAL OF INDUSTRIAL AND APPLIED MATHEMATICS

Valentino Braitenberg: From neuroanatomy to behavior and back

(2013) Mario Negrello   BIOLOGICAL CYBERNETICS

Function–structure associations of the brain: Evidence from multimodal connectivity and covariance studies

(2013) Jing Sui et al.   NEUROIMAGE

Structural foundations of resting-state and task-based functional connectivity in the human brain

(2013) A. M. Hermundstad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topology of viral evolution

(2013) J. M. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network dysfunction during associative learning in schizophrenia: Increased activation, but decreased connectivity: An fMRI study

(2013) Sunali Wadehra et al.   SCHIZOPHRENIA RESEARCH

Structural and Functional Brain Networks: From Connections to Cognition

(2013) H.-J. Park et al.   SCIENCE

Resting brains never rest: computational insights into potential cognitive architectures

(2013) Gustavo Deco et al.   TRENDS IN NEUROSCIENCES

Persistent Brain Network Homology From the Perspective of Dendrogram

(2012) Hyekyoung Lee et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Dynamic models of BOLD contrast

(2012) Richard B. Buxton   NEUROIMAGE

Probability measures on the space of persistence diagrams

(2011) Yuriy Mileyko et al.   INVERSE PROBLEMS

Model-based dynamical analysis of functional disconnection in schizophrenia

(2011) Mihály Bányai et al.   NEUROIMAGE

Shared impairment in associative learning in schizophrenia and bipolar disorder

(2011) Paolo Brambilla et al.   PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY

Anatomical and Functional Connectivity of Cytoarchitectonic Areas within the Human Parietal Operculum

(2010) S. B. Eickhoff et al.   JOURNAL OF NEUROSCIENCE

Network discovery with DCM

(2010) Karl J. Friston et al.   NEUROIMAGE

Topology and data

(2009) Gunnar Carlsson   BULLETIN OF THE AMERICAN MATHEMATICAL SOCIETY

Induced Gamma activity in primary visual cortex is related to luminance and not color contrast: An MEG study

(2009) Peyman Adjamian et al.   JOURNAL OF VISION

How not to study spontaneous activity

(2009) Nikos K. Logothetis et al.   NEUROIMAGE

Impaired associative learning in schizophrenia: behavioral and computational studies

(2008) Vaibhav A. Diwadkar et al.   Cognitive Neurodynamics

Topological analysis of population activity in visual cortex

(2008) G. Singh et al.   JOURNAL OF VISION

What we can do and what we cannot do with fMRI

(2008) Nikos K. Logothetis   NATURE

Spatiotemporal frequency tuning of BOLD and gamma band MEG responses compared in primary visual cortex

(2008) Suresh D. Muthukumaraswamy et al.   NEUROIMAGE