INSPIRE Lab Imaging- and Neuro-computations for Precision Informatics Research

Publications

2024

Variation in the distribution of large-scale spatiotemporal patterns of activity across brain states
Variation in the distribution of large-scale spatiotemporal patterns of activity across brain states
Lisa Meyer-Baese, Nmachi Anumba, T. Bolt, L. Daley, T. J. LaGrow, Xiaodi Zhang, Nan Xu, Wen-Ju Pan, E. H. Schumacher, Shella Keilholz
Frontiers in Systems Neuroscience  ·  02 Aug 2024  · doi:10.3389/fnsys.2024.1425491
Time-varying causal interactions in the functional brain networks: Modeling and Validation
Time-varying causal interactions in the functional brain networks: Modeling and Validation
Nan Xu, Xiaodi Zhang, Wenju Pan, Jeremy L. Smith, Jason W. Allen, Vince D. Calhoun, Shella D. Keilholz
Organization for Human Brain Mapping 2024 Annual Meeting  ·  23 Jun 2024
The effects of locus coeruleus stimulation on quasi-periodic patterns in rats
The effects of locus coeruleus stimulation on quasi-periodic patterns in rats
Nmachi Anumba, Michael A. Keilberman, Wenju Pan, Alexia Marriott, Nan Xu, David Weinshenker, Shella Keilholz
Organization for Human Brain Mapping 2024 Annual Meeting  ·  23 Jun 2024
Modeling and Validation of Dynamic Causal Interactions in Functional Brain Network
Modeling and Validation of Dynamic Causal Interactions in Functional Brain Network
Nan Xu, Xiaodi Zhang, Wenju Pan, Jeremy L. Smith, Jason W. Allen, Vince D. Calhoun, Shella D. Keilholz
10th Annual BRAIN Initiative Conference  ·  18 Jun 2024
Time-varying functional connectivity predicts fluctuations in sustained attention in a serial tapping task
Time-varying functional connectivity predicts fluctuations in sustained attention in a serial tapping task
Dolly T. Seeburger, Nan Xu, Marcus Ma, Sam Larson, Christine Godwin, Shella D. Keilholz, Eric H. Schumacher
Cognitive, Affective, & Behavioral Neuroscience  ·  22 Jan 2024  · doi:10.3758/s13415-024-01156-1
The Effects of Locus Coeruleus Optogenetic Stimulation on Global Spatiotemporal Patterns in Rats
The Effects of Locus Coeruleus Optogenetic Stimulation on Global Spatiotemporal Patterns in Rats
Nmachi Anumba, Michael A. Kelberman, Wenju Pan, Alexia Marriott, Xiaodi Zhang, Nan Xu, David Weinshenker, Shella Keilholz
Imaging Neuroscience  ·  01 Jan 2024  · doi:10.1162/imag_a_00314

2023

``Hyperconnected'' Vestibular State in Subacute and Chronic Post-Concussive Vestibular Dysfunction Using Dynamic Whole Brain Functional Connectivity Analysis
``Hyperconnected'' Vestibular State in Subacute and Chronic Post-Concussive Vestibular Dysfunction Using Dynamic Whole Brain Functional Connectivity Analysis
Anna Trofimova, Jeremy Smith, Nan Xu, Shella Keilholz, Russell Gore, Jason W. Allen
The 16th Annual Meeting of the American Society of Functional Neuroradiology  ·  07 Oct 2023
Oral Presentation.
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity
QPPLab: A generally applicable software package for detecting, analyzing, and visualizing large-scale quasiperiodic spatiotemporal patterns (QPPs) of brain activity
Nan Xu, Behnaz Yousefi, Nmachi Anumba, Theodore J. LaGrow, Xiaodi Zhang, Shella Keilholz
Cold Spring Harbor Laboratory  ·  25 Sep 2023  · doi:10.1101/2023.09.25.559086
Spatial and Spectral Components of the <scp>BOLD</scp> Global Signal in Rat <scp>Resting‐State</scp> Functional <scp>MRI</scp>
Spatial and Spectral Components of the BOLD Global Signal in Rat Resting‐State Functional MRI
Nmachi Anumba, Eric Maltbie, Wen‐Ju Pan, Theodore J. LaGrow, Nan Xu, Shella Keilholz
Magnetic Resonance in Medicine  ·  15 Aug 2023  · doi:10.1002/mrm.29824
Rodent Whole-Brain fMRI Data Preprocessing Toolbox
Rodent Whole-Brain fMRI Data Preprocessing Toolbox
Nan Xu, Leo Zhang, Sam Larson, Zengmin Li, Nmachi Anumba, Lauren Daley, Wen-Ju Pan, Kai-Hsiang Chuang, Shella D. Keilholz
Aperture Neuro  ·  09 Aug 2023  · doi:10.52294/001c.85075
Featured at the Aperture Symposium of the OHBM 2024 Annual Meeting!
The interaction between random and systematic visual stimulation and
                    infraslow quasi-periodic spatiotemporal patterns of whole-brain
                    activity
The interaction between random and systematic visual stimulation and infraslow quasi-periodic spatiotemporal patterns of whole-brain activity
Nan Xu, Derek M. Smith, George Jeno, Dolly T. Seeburger, Eric H. Schumacher, Shella D. Keilholz
Imaging Neuroscience  ·  01 Aug 2023  · doi:10.1162/imag_a_00002
Employed the statistical inferences techniques to study the interplay between infraslow dynamic processes and visual perceptions. Discovered that these intrinsic dynamic processes are notably resilient in humans, as contrast with anesthetized rodents (Belloy et al., 2021). Yet, their stability can still be affected in diverse ways: they can swamp an overlapping BOLD response evoked by the flickering checkerboard, but their phase-locked waveform can still be modulated by different sequences of stimuli that affects the reaction time and sustained attention.
The interaction between visual stimulation and intrinsic infraslow whole brain activity in humans
The interaction between visual stimulation and intrinsic infraslow whole brain activity in humans
Nan Xu, Derek Smith, George Geno, Dolly T. Seeburger, Eric H. Schumacher, Shella D. Keilholz
Organization for Human Brain Mapping 2023 Annual Meeting  ·  22 Jul 2023
Distribution of large-scale spatiotemporal patterns within and across individuals
Distribution of large-scale spatiotemporal patterns within and across individuals
Taylor Bolt, Nan Xu, Laren Daley, T.J. LaGrow, W-J Pan, Eric Schumacher, Shella Keilholz
Organization for Human Brain Mapping 2023 Annual Meeting  ·  22 Jul 2023

2022

The effects of locus coeruleus stimulation on the BOLD global signal in TgF344‐AD rats
The effects of locus coeruleus stimulation on the BOLD global signal in TgF344‐AD rats
Nmachi Anumba, Michael Kelberman, Corrie Smith, Wen Ju Pan, Perrin G Clavijo, Nan Xu, Alexia Marriott, Ellen Kim, David Weinshenker, Shella Keilholz
Alzheimer's & Dementia  ·  01 Dec 2022  · doi:10.1002/alz.061608
Dynamic spatiotemporal interactions in vestibular networks affected by concussive syndromes
Dynamic spatiotemporal interactions in vestibular networks affected by concussive syndromes
Nan Xu, Jeremy Smith, Jason Allen, Shella Keilholz
Organization for Human Brain Mapping 2022 Annual Meeting  ·  19 Jun 2022
Identifying the neural mechanisms of zone state performance using time-varying functional connectivity methods.
Identifying the neural mechanisms of zone state performance using time-varying functional connectivity methods.
Dolly T. Seeburger, Nan Xu, C Godwin, Marcus Ma, Shella D. Keilholz, Eric H. Schumacher
Cognitive Neuroscience Society 2022 Annual Meeting  ·  23 Apr 2022
Oral Presentation.
Investigating the relationship between sustained attention and quasi-periodic brain activity patterns with the psychomotor vigilance task.
Investigating the relationship between sustained attention and quasi-periodic brain activity patterns with the psychomotor vigilance task.
Yunji Lee, Dolly T. Seeburger, Sakshi Dhawan, Tiffany Nguyen, Nan Xu, …, Anzar Abbas, Waqas Majeed, Garth Thompson, Shella D. Keilholz, Eric H. Schumacher
Cognitive Neuroscience Society 2022 Annual Meeting  ·  23 Apr 2022
Functional Connectivity of the Brain Across Rodents and Humans
Functional Connectivity of the Brain Across Rodents and Humans
Nan Xu, Theodore J. LaGrow, Nmachi Anumba, Azalea Lee, Xiaodi Zhang, …, Eric Maltbie, Lisa Meyer-Baese, Maysam Nezafati, Wen-Ju Pan, Shella Keilholz
Frontiers in Neuroscience  ·  08 Mar 2022  · doi:10.3389/fnins.2022.816331

2021

Quasiperiodic patterns and BOLD response entrained by visual stimulation in the human brain.
Quasiperiodic patterns and BOLD response entrained by visual stimulation in the human brain.
Nan Xu, Derek M. Smith, George Jeno, Dolly T. Seeburger, Eric H. Schumacher, Shella D. Keilholz
Organization for Human Brain Mapping 2021 Annual Meeting  ·  30 May 2021
Spatiotemporal functional interactivity among large-scale brain networks
Spatiotemporal functional interactivity among large-scale brain networks
Nan Xu, Peter C. Doerschuk, Shella D. Keilholz, R. Nathan Spreng
NeuroImage  ·  01 Feb 2021  · doi:10.1016/j.neuroimage.2020.117628

2020

Relationship Between Basic Properties of BOLD Fluctuations and Calculated Metrics of Complexity in the Human Connectome Project
Relationship Between Basic Properties of BOLD Fluctuations and Calculated Metrics of Complexity in the Human Connectome Project
Shella Keilholz, Eric Maltbie, Xiaodi Zhang, Behnaz Yousefi, Wen-Ju Pan, Nan Xu, Maysam Nezafati, Theodore J. LaGrow, Ying Guo
Frontiers in Neuroscience  ·  15 Sep 2020  · doi:10.3389/fnins.2020.550923
Investigation of spatiotemporal functional interactivity among large-scale brain networks
Investigation of spatiotemporal functional interactivity among large-scale brain networks
Nan Xu, R Nathan Spreng, Shella D. Keilholz
Organization for Human Brain Mapping 2020 Annual Meeting  ·  23 Jun 2020
Oral Presentation; Selected 4% of Accepted Abstract Papers.

2019

Reconstruction of Stochastic 3D Signals With Symmetric Statistics From 2D Projection Images Motivated by Cryo-Electron Microscopy
Reconstruction of Stochastic 3D Signals With Symmetric Statistics From 2D Projection Images Motivated by Cryo-Electron Microscopy
Nan Xu, Peter C. Doerschuk
IEEE Transactions on Image Processing  ·  01 Nov 2019  · doi:10.1109/tip.2019.2915631
Using cryo-EM, we transform highly noisy and randomly-oriented projection images of 103─106 virus particles into a 3D model of the virus. Unlike traditional methods that assume strict geometric symmetry, we adopted a more realistic approach, allowing individual particles to be asymmetric while maintaining symmetry in the overall mean and covariance. This novel method eliminates long-standing distortions along the symmetry axes.
Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans
Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans
Nan Xu+, Dhaval S Patel+, Hang Lu
Lab Animal  ·  19 Jun 2019  · doi:10.1038/s41684-019-0326-6
+equal contributions

2018

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data
Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data
Nan Xu, David Veesler, Peter C. Doerschuk, John E. Johnson
Journal of Structural Biology  ·  01 May 2018  · doi:10.1016/j.jsb.2017.12.013
We developed a cyro-EM image reconstruction algortihm for virus particles, allowing for asymmetry and eliminating distortions along symmetry axes (Xu & Doerschuk, 2019). In collaboration with virologists from the Scripps Institute, we uncovered allosteric effects along the symmetry axes of the bacteriophage HK97.

2017

Initial Validation for the Estimation of Resting-State fMRI Effective Connectivity by a Generalization of the Correlation Approach
Initial Validation for the Estimation of Resting-State fMRI Effective Connectivity by a Generalization of the Correlation Approach
Nan Xu, R. Nathan Spreng, Peter C. Doerschuk
Frontiers in Neuroscience  ·  16 May 2017  · doi:10.3389/fnins.2017.00271
We developed p-corr, an innovative algorithm enhancing traditional correlation analysis with a causal dynamic model. P-corr identifies information flow in functional connectivity, maintains sensitivity in detecting modular architecture, and scales to handle hundreds of ROIs for comprehensive whole-brain connectivity assessments.

2016

What are the most talkative brain regions?
What are the most talkative brain regions?
Nan Xu, Peter C. Doerschuk, R Nathan Spreng
IEEE Engineering In Medicine And Biology Society Annual International Conference  ·  01 Aug 2016
Late-breaking Research Paper!
Statistical characterization of ensembles of symmetric virus particles: 3-D stochastic signal reconstruction from electron microscope images
Statistical characterization of ensembles of symmetric virus particles: 3-D stochastic signal reconstruction from electron microscope images
Nan Xu, Peter C. Doerschuk
IEEE Engineering In Medicine And Biology Society Annual International Conference  ·  01 Aug 2016  · doi:10.1109/embc.2016.7591598
EMBS Student Paper Competition Finalist - Top 0.4% conference proceedings!
Virus particle dynamics derived from CryoEM studies
Virus particle dynamics derived from CryoEM studies
Peter C Doerschuk, Yunye Gong, Nan Xu, Tatiana Domitrovic, John E Johnson
Current Opinion in Virology  ·  01 Jun 2016  · doi:10.1016/j.coviro.2016.02.011

2015

Characterizing heterogeneity among virus particles by stochastic 3D signal reconstruction
Characterizing heterogeneity among virus particles by stochastic 3D signal reconstruction
Nan Xu, Yunye Gong, Qiu Wang, Yili Zheng, Peter C. Doerschuk
SPIE Proceedings  ·  21 Sep 2015  · doi:10.1117/12.2193791
Top 10% Paper Recognition; Top 34 papers demonstrated in the Show & Tell session!
Reconstruction for stochastic 3-D signals with symmetric statistics in noise: Electron microscopy of virus particles
Reconstruction for stochastic 3-D signals with symmetric statistics in noise: Electron microscopy of virus particles
Nan Xu, Peter C. Doerschuk
2015 IEEE International Conference on Image Processing (ICIP)  ·  01 Sep 2015  · doi:10.1109/ICIP.2015.7351039

2014

Directed interactivity of large-scale brain networks: Introducing a new method for estimating resting-state effective connectivity MRI
Directed interactivity of large-scale brain networks: Introducing a new method for estimating resting-state effective connectivity MRI
Nan Xu, R. Nathan Spreng, Peter C. Doerschuk
2014 IEEE International Conference on Image Processing (ICIP)  ·  01 Oct 2014  · doi:10.1109/ICIP.2014.7025712
Directed interactivity of large-scale brain networks: Introducing a new method for estimating brain connectivity MRI
Directed interactivity of large-scale brain networks: Introducing a new method for estimating brain connectivity MRI
Nan Xu, R Nathan Spreng, Peter C. Doerschuk
Cognitive Neuroscience Society 2014 Annual Meeting  ·  07 Apr 2014
3-D statistical characterization of the heterogeneity of biological macromolecular complexes by electron microscopy
3-D statistical characterization of the heterogeneity of biological macromolecular complexes by electron microscopy
Nan Xu, Yunye Gong, Yili Zheng, Qiu Wang, Peter C. Doerschuk
Imaging and Applied Optics 2014  ·  01 Jan 2014  · doi:10.1364/srs.2014.stu3f.4