Ashish Raj, PhD

Professor
Professor in Residence
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Biography

I have more than 15 years experience in computer vision, signal processing, graph theory, medical imaging and informatics. I have had continuous and successive experiences in forming and leading research teams comprising of basic and clinical scientists in executing NIH-funded research projects. I have published more than 70 peer reviewed papers ranging from microwave engineering, superconductivity, image/signal processing, vision, graph theory and neuroscience, and two US patents. I have attracted several NIH grants, on graph algorithms for accelerated MRI, theoretical neuroscience and network modeling of dementia and Parkinson’s.

The defining characteristic of my work has been inter-disciplinarity: finding innovative ways to apply computation and algorithms to biomedical applications. My group was an early adopter of mathematical models of brain connectivity networks, a subject that marries computer science with neuroradiology. I have deep interest in the graph properties of brain networks, and how they are altered in neurological disorders like epilepsy, dementia, movement disorders, traumatic brain injury and stroke. A recent project on dementia modeling was selected by the NIH for the prestigious EUREKA award that supports highly innovative but risky research, and another by the BRAIN Initiative. My team has developed novel image reconstruction algorithms for fast MRI, motion correction for MR angiography, and new methods in tractography, Q-ball imaging, brain connectivity networks and computational neurology.

My research program is now perfectly poised to help bring the fields of neurology and radiology into the era of personalized, precision medicine, using mathematical modeling and data science.

Education

PhD, 05/2005 - Electrical and Computer Engineering, Cornell University
BE, 12/1998 - Electrical Engineering, University of Auckland

Publications

Raj A, Sipes BS, Verma P, Mathalon DH, Biswal BB, Nagarajan SS. Spectral graph model for fMRI: a biophysical, connectivity-based generative model for the analysis of frequency-resolved resting state fMRI. bioRxiv. 2024 Mar 27.
Verma P, Ranasinghe K, Prasad J, Cai C, Xie X, Lerner H, Mizuiri D, Miller B, Rankin K, Vossel K, Cheung SW, Nagarajan SS, Raj A. Impaired long-range excitatory time scale predicts abnormal neural oscillations and cognitive deficits in Alzheimer's disease. Alzheimers Res Ther. 2024 Mar 19; 16(1):62.
Raj A, Torok J. Understanding the complex interplay between tau, amyloid and the network in the spatiotemporal progression of Alzheimer's Disease. bioRxiv. 2024 Mar 11.
Anand C, Torok J, Abdelnour F, Maia PD, Raj A. Selective vulnerability and resilience to Alzheimer's disease tauopathy as a function of genes and the connectome. bioRxiv. 2024 Mar 08.
Torok J, Maia PD, Anand C, Raj A. Cellular underpinnings of the selective vulnerability to tauopathic insults in Alzheimer's disease. bioRxiv. 2023 Nov 29.
Fan JM, Kudo K, Verma P, Ranasinghe KG, Morise H, Findlay AM, Vossel K, Kirsch HE, Raj A, Krystal AD, Nagarajan SS. Cortical Synchrony and Information Flow during Transition from Wakefulness to Light Non-Rapid Eye Movement Sleep. J Neurosci. 2023 11 29; 43(48):8157-8171.
Verma P, Ranasinghe K, Prasad J, Cai C, Xie X, Lerner H, Mizuiri D, Miller B, Rankin K, Vossel K, Cheung SW, Nagarajan S, Raj A. Impaired long-range excitatory time scale predicts abnormal neural oscillations and cognitive deficits in Alzheimer's disease. Res Sq. 2023 Nov 01.
Sun S, Torok J, Mezias C, Ma D, Raj A. Spatial cell-type enrichment predicts mouse brain connectivity. Cell Rep. 2023 10 31; 42(10):113258.
Jin H, Ranasinghe KG, Prabhu P, Dale C, Gao Y, Kudo K, Vossel K, Raj A, Nagarajan SS, Jiang F. Dynamic functional connectivity MEG features of Alzheimer's disease. Neuroimage. 2023 Nov 01; 281:120358.
Jin H, Verma P, Jiang F, Nagarajan SS, Raj A. Bayesian inference of a spectral graph model for brain oscillations. Neuroimage. 2023 10 01; 279:120278.
Jin H, Verma P, Jiang F, Nagarajan S, Raj A. Bayesian Inference of a Spectral Graph Model for Brain Oscillations. bioRxiv. 2023 Mar 11.
Ghosh S, Raj A, Nagarajan SS. A joint subspace mapping between structural and functional brain connectomes. Neuroimage. 2023 05 15; 272:119975.
Verma P, Nagarajan S, Raj A. Stability and dynamics of a spectral graph model of brain oscillations. Netw Neurosci. 2023; 7(1):48-72.
Anand C, Maia PD, Torok J, Mezias C, Raj A. The effects of microglia on tauopathy progression can be quantified using Nexopathy in silico (Nexis) models. Sci Rep. 2022 Dec 07; 12(1):21170.
Abdelnour F, Kuceyeski A, Raj A, Iturria-Medina Y, Deslauriers-Gauthier S. Editorial: Advances in brain functional and structural networks modeling via graph theory. Front Neurosci. 2022; 16:1031280.
Raj A, Verma P, Nagarajan S. Structure-function models of temporal, spatial, and spectral characteristics of non-invasive whole brain functional imaging. Front Neurosci. 2022; 16:959557.
Torok J, Anand C, Verma P, Raj A. Connectome-based biophysics models of Alzheimer's disease diagnosis and prognosis. Transl Res. 2023 04; 254:13-23.
Ranasinghe KG, Verma P, Cai C, Xie X, Kudo K, Gao X, Lerner H, Mizuiri D, Strom A, Iaccarino L, La Joie R, Miller BL, Gorno-Tempini ML, Rankin KP, Jagust WJ, Vossel K, Rabinovici GD, Raj A, Nagarajan SS. Altered excitatory and inhibitory neuronal subpopulation parameters are distinctly associated with tau and amyloid in Alzheimer's disease. Elife. 2022 05 26; 11.
Zarei M, Xie D, Jiang F, Bagirov A, Huang B, Raj A, Nagarajan S, Guo S. High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains. BMC Biol. 2022 04 11; 20(1):84.
Mezias C, Torok J, Maia PD, Markley E, Raj A. Matrix Inversion and Subset Selection (MISS): A pipeline for mapping of diverse cell types across the murine brain. Proc Natl Acad Sci U S A. 2022 04 05; 119(14):e2111786119.
Jiang F, Jin H, Gao Y, Xie X, Cummings J, Raj A, Nagarajan S. Time-varying dynamic network model for dynamic resting state functional connectivity in fMRI and MEG imaging. Neuroimage. 2022 07 01; 254:119131.
Cummings JA, Sipes B, Mathalon DH, Raj A. Predicting Functional Connectivity From Observed and Latent Structural Connectivity via Eigenvalue Mapping. Front Neurosci. 2022; 16:810111.
Pandya S, Maia PD, Freeze B, Menke RAL, Talbot K, Turner MR, Raj A. Modeling seeding and neuroanatomic spread of pathology in amyotrophic lateral sclerosis. Neuroimage. 2022 05 01; 251:118968.
Verma P, Nagarajan S, Raj A. Spectral graph theory of brain oscillations--Revisited and improved. Neuroimage. 2022 04 01; 249:118919.
Torok J, Maia PD, Verma P, Mezias C, Raj A. Emergence of directional bias in tau deposition from axonal transport dynamics. PLoS Comput Biol. 2021 07; 17(7):e1009258.
Raj A, Tora V, Gao X, Cho H, Choi JY, Ryu YH, Lyoo CH, Franchi B. Combined Model of Aggregation and Network Diffusion Recapitulates Alzheimer's Regional Tau-Positron Emission Tomography. Brain Connect. 2021 10; 11(8):624-638.
Powell F, Tosun D, Raj A, Alzheimer’s Disease Neuroimaging Initiative. Network-constrained technique to characterize pathology progression rate in Alzheimer's disease. Brain Commun. 2021; 3(3):fcab144.
Raj A. Graph Models of Pathology Spread in Alzheimer's Disease: An Alternative to Conventional Graph Theoretic Analysis. Brain Connect. 2021 12; 11(10):799-814.
Xie X, Cai C, Damasceno PF, Nagarajan SS, Raj A. Emergence of canonical functional networks from the structural connectome. Neuroimage. 2021 08 15; 237:118190.
Akerele MI, Zein SA, Pandya S, Nikolopoulou A, Gauthier SA, Raj A, Henchcliffe C, Mozley PD, Karakatsanis NA, Gupta A, Babich J, Nehmeh SA. Population-based input function for TSPO quantification and kinetic modeling with [11C]-DPA-713. EJNMMI Phys. 2021 Apr 29; 8(1):39.
Raj A, Powell F. Network model of pathology spread recapitulates neurodegeneration and selective vulnerability in Huntington's Disease. Neuroimage. 2021 07 15; 235:118008.
Abdelnour F, Dayan M, Devinsky O, Thesen T, Raj A. Algebraic relationship between the structural network's Laplacian and functional network's adjacency matrix is preserved in temporal lobe epilepsy subjects. Neuroimage. 2021 03; 228:117705.
Ivanidze J, Skafida M, Pandya S, Patel D, Osborne JR, Raj A, Gupta A, Henchcliffe C, Dyke JP. Molecular Imaging of Striatal Dopaminergic Neuronal Loss and the Neurovascular Unit in Parkinson Disease. Front Neurosci. 2020; 14:528809.
Xu J, Pannetier N, Raj A. A dictionary-based graph-cut algorithm for MRI reconstruction. NMR Biomed. 2020 12; 33(12):e4344.
Maia PD, Pandya S, Freeze B, Torok J, Gupta A, Zeighami Y, Raj A. Origins of atrophy in Parkinson linked to early onset and local transcription patterns. Brain Commun. 2020; 2(2):fcaa065.
Freeze B, Maia P, Pandya S, Raj A. Network mediation of pathology pattern in sporadic Creutzfeldt-Jakob disease. Brain Commun. 2020; 2(1):fcaa060.
Raj A, Cai C, Xie X, Palacios E, Owen J, Mukherjee P, Nagarajan S. Spectral graph theory of brain oscillations. Hum Brain Mapp. 2020 08 01; 41(11):2980-2998.
Johnson PJ, Pascalau R, Luh WM, Raj A, Cerda-Gonzalez S, Barry EF. Stereotaxic Diffusion Tensor Imaging White Matter Atlas for the in vivo Domestic Feline Brain. Front Neuroanat. 2020; 14:1.
Nguyen AA, Maia PD, Gao X, F Damasceno P, Raj A. Dynamical Role of Pivotal Brain Regions in Parkinson Symptomatology Uncovered with Deep Learning. Brain Sci. 2020 Jan 30; 10(2).
Mezias C, Rey N, Brundin P, Raj A. Neural connectivity predicts spreading of alpha-synuclein pathology in fibril-injected mouse models: Involvement of retrograde and anterograde axonal propagation. Neurobiol Dis. 2020 02; 134:104623.
Freeze B, Pandya S, Zeighami Y, Raj A. Regional transcriptional architecture of Parkinson's disease pathogenesis and network spread. Brain. 2019 10 01; 142(10):3072-3085.
Kuceyeski AF, Jamison KW, Owen JP, Raj A, Mukherjee P. Longitudinal increases in structural connectome segregation and functional connectome integration are associated with better recovery after mild TBI. Hum Brain Mapp. 2019 10 15; 40(15):4441-4456.
Maia PD, Raj A, Kutz JN. Slow-gamma frequencies are optimally guarded against effects of neurodegenerative diseases and traumatic brain injuries. J Comput Neurosci. 2019 08; 47(1):1-16.
Raj A, Iturria-Medina Y. Editorial: Network Spread Models of Neurodegenerative Diseases. Front Neurol. 2018; 9:1159.
Barry EF, Cerda-Gonzalez S, Luh WM, Daws RE, Raj A, Johnson PJ. Normal diffusivity of the domestic feline brain. J Comp Neurol. 2019 04 01; 527(5):1012-1023.
Raj A, Powell F. Models of Network Spread and Network Degeneration in Brain Disorders. Biol Psychiatry Cogn Neurosci Neuroimaging. 2018 09; 3(9):788-797.
Torok J, Maia PD, Powell F, Pandya S, Raj A. A method for inferring regional origins of neurodegeneration. Brain. 2018 03 01; 141(3):863-876.
Abdelnour F, Dayan M, Devinsky O, Thesen T, Raj A. Functional brain connectivity is predictable from anatomic network's Laplacian eigen-structure. Neuroimage. 2018 05 15; 172:728-739.
Freeze B, Acosta D, Pandya S, Zhao Y, Raj A. Regional expression of genes mediating trans-synaptic alpha-synuclein transfer predicts regional atrophy in Parkinson disease. Neuroimage Clin. 2018; 18:456-466.
Acosta D, Powell F, Zhao Y, Raj A. Regional vulnerability in Alzheimer's disease: The role of cell-autonomous and transneuronal processes. Alzheimers Dement. 2018 06; 14(6):797-810.
Powell F, Tosun D, Sadeghi R, Weiner M, Raj A, Alzheimer’s Disease Neuroimaging Initiative. Preserved Structural Network Organization Mediates Pathology Spread in Alzheimer's Disease Spectrum Despite Loss of White Matter Tract Integrity. J Alzheimers Dis. 2018; 65(3):747-764.
Pandya S, Mezias C, Raj A. Predictive Model of Spread of Progressive Supranuclear Palsy Using Directional Network Diffusion. Front Neurol. 2017; 8:692.
Mezias C, Raj A. Analysis of Amyloid-β Pathology Spread in Mouse Models Suggests Spread Is Driven by Spatial Proximity, Not Connectivity. Front Neurol. 2017; 8:653.
Powell F, LoCastro E, Acosta D, Ahmed M, O'Donoghue S, Forde N, Cannon D, Scanlon C, Rao T, McDonald C, Raj A. Age-Related Changes in Topological Degradation of White Matter Networks and Gene Expression in Chronic Schizophrenia. Brain Connect. 2017 11; 7(9):574-589.
Sudarov A, Zhang XJ, Braunstein L, LoCastro E, Singh S, Taniguchi Y, Raj A, Shi SH, Moore H, Ross ME. Mature Hippocampal Neurons Require LIS1 for Synaptic Integrity: Implications for Cognition. Biol Psychiatry. 2018 03 15; 83(6):518-529.
Mezias C, LoCastro E, Xia C, Raj A. Connectivity, not region-intrinsic properties, predicts regional vulnerability to progressive tau pathology in mouse models of disease. Acta Neuropathol Commun. 2017 08 14; 5(1):61.
Wang MB, Owen JP, Mukherjee P, Raj A. Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease. PLoS Comput Biol. 2017 Jun; 13(6):e1005550.
Dayan M, Hurtado Rúa SM, Monohan E, Fujimoto K, Pandya S, LoCastro EM, Vartanian T, Nguyen TD, Raj A, Gauthier SA. MRI Analysis of White Matter Myelin Water Content in Multiple Sclerosis: A Novel Approach Applied to Finding Correlates of Cortical Thinning. Front Neurosci. 2017; 11:284.
Pandya S, Kuceyeski A, Raj A, Alzheimer’s Disease Neuroimaging Initiative. The Brain's Structural Connectome Mediates the Relationship between Regional Neuroimaging Biomarkers in Alzheimer's Disease. J Alzheimers Dis. 2017; 55(4):1639-1657.
Abdelnour F, Raj A, Devinsky O, Thesen T. Network Analysis on Predicting Mean Diffusivity Change at Group Level in Temporal Lobe Epilepsy. Brain Connect. 2016 10; 6(8):607-620.
Diamond EL, Hatzoglou V, Patel S, Abdel-Wahab O, Rampal R, Hyman DM, Holodny AI, Raj A. Diffuse reduction of cerebral grey matter volumes in Erdheim-Chester disease. Orphanet J Rare Dis. 2016 08 02; 11(1):109.
Kuceyeski A, Navi BB, Kamel H, Raj A, Relkin N, Toglia J, Iadecola C, O'Dell M. Structural connectome disruption at baseline predicts 6-months post-stroke outcome. Hum Brain Mapp. 2016 07; 37(7):2587-601.
Dayan M, Monohan E, Pandya S, Kuceyeski A, Nguyen TD, Raj A, Gauthier SA. Profilometry: A new statistical framework for the characterization of white matter pathways, with application to multiple sclerosis. Hum Brain Mapp. 2016 Mar; 37(3):989-1004.
Abdelnour F, Mueller S, Raj A. Relating Cortical Atrophy in Temporal Lobe Epilepsy with Graph Diffusion-Based Network Models. PLoS Comput Biol. 2015 Oct; 11(10):e1004564.
Vargas WS, Monohan E, Pandya S, Raj A, Vartanian T, Nguyen TD, Hurtado Rúa SM, Gauthier SA. Measuring longitudinal myelin water fraction in new multiple sclerosis lesions. Neuroimage Clin. 2015; 9:369-75.
Nguyen TD, Deh K, Monohan E, Pandya S, Spincemaille P, Raj A, Wang Y, Gauthier SA. Feasibility and reproducibility of whole brain myelin water mapping in 4 minutes using fast acquisition with spiral trajectory and adiabatic T2prep (FAST-T2) at 3T. Magn Reson Med. 2016 08; 76(2):456-65.
Kuceyeski A, Navi BB, Kamel H, Relkin N, Villanueva M, Raj A, Toglia J, O'Dell M, Iadecola C. Exploring the brain's structural connectome: A quantitative stroke lesion-dysfunction mapping study. Hum Brain Mapp. 2015 Jun; 36(6):2147-60.
Raj A, LoCastro E, Kuceyeski A, Tosun D, Relkin N, Weiner M, Alzheimer’s Disease Neuroimaging Initiative (ADNI). Network Diffusion Model of Progression Predicts Longitudinal Patterns of Atrophy and Metabolism in Alzheimer's Disease. Cell Rep. 2015 Jan 20; 10(3):359-369.
Dong J, Liu T, Chen F, Zhou D, Dimov A, Raj A, Cheng Q, Spincemaille P, Wang Y. Simultaneous phase unwrapping and removal of chemical shift (SPURS) using graph cuts: application in quantitative susceptibility mapping. IEEE Trans Med Imaging. 2015 Feb; 34(2):531-40.
Maier-Hein KH, Westin CF, Shenton ME, Weiner MW, Raj A, Thomann P, Kikinis R, Stieltjes B, Pasternak O. Widespread white matter degeneration preceding the onset of dementia. Alzheimers Dement. 2015 May; 11(5):485-493.e2.
Raj A, Pandya S, Shen X, LoCastro E, Nguyen TD, Gauthier SA. Multi-compartment T2 relaxometry using a spatially constrained multi-Gaussian model. PLoS One. 2014; 9(6):e98391.
Goel P, Kuceyeski A, LoCastro E, Raj A. Spatial patterns of genome-wide expression profiles reflect anatomic and fiber connectivity architecture of healthy human brain. Hum Brain Mapp. 2014 Aug; 35(8):4204-18.
Kuceyeski A, Kamel H, Navi BB, Raj A, Iadecola C. Predicting future brain tissue loss from white matter connectivity disruption in ischemic stroke. Stroke. 2014 Mar; 45(3):717-22.
Abdelnour F, Voss HU, Raj A. Network diffusion accurately models the relationship between structural and functional brain connectivity networks. Neuroimage. 2014 Apr 15; 90:335-47.
Liu B, Raj A. Discriminative random field segmentation of lung nodules in CT studies. Comput Math Methods Med. 2013; 2013:683216.
Shen X, Nguyen TD, Gauthier SA, Raj A. Robust myelin quantitative imaging from multi-echo T2 MRI using edge preserving spatial priors. Med Image Comput Comput Assist Interv. 2013; 16(Pt 1):622-30.
Kuceyeski A, Maruta J, Relkin N, Raj A. The Network Modification (NeMo) Tool: elucidating the effect of white matter integrity changes on cortical and subcortical structural connectivity. Brain Connect. 2013; 3(5):451-63.
Kuceyeski A, Meyerhoff DJ, Durazzo TC, Raj A. Loss in connectivity among regions of the brain reward system in alcohol dependence. Hum Brain Mapp. 2013 Dec; 34(12):3129-42.
Ivkovic M, Kuceyeski A, Raj A. Statistics of weighted brain networks reveal hierarchical organization and Gaussian degree distribution. PLoS One. 2012; 7(6):e35029.
Raj A, Kuceyeski A, Weiner M. A network diffusion model of disease progression in dementia. Neuron. 2012 Mar 22; 73(6):1204-15.
Kuceyeski A, Zhang Y, Raj A. Linking white matter integrity loss to associated cortical regions using structural connectivity information in Alzheimer's disease and fronto-temporal dementia: the Loss in Connectivity (LoCo) score. Neuroimage. 2012 Jul 16; 61(4):1311-23.
Kumar D, Nguyen TD, Gauthier SA, Raj A. Bayesian algorithm using spatial priors for multiexponential T₂ relaxometry from multiecho spin echo MRI. Magn Reson Med. 2012 Nov; 68(5):1536-43.
Nguyen TD, Wisnieff C, Cooper MA, Kumar D, Raj A, Spincemaille P, Wang Y, Vartanian T, Gauthier SA. T2 prep three-dimensional spiral imaging with efficient whole brain coverage for myelin water quantification at 1.5 tesla. Magn Reson Med. 2012 Mar; 67(3):614-21.
Raj A, Chen YH. The wiring economy principle: connectivity determines anatomy in the human brain. PLoS One. 2011; 6(9):e14832.
Moore DW, Kovanlikaya I, Heier LA, Raj A, Huang C, Chu KW, Relkin NR. A pilot study of quantitative MRI measurements of ventricular volume and cortical atrophy for the differential diagnosis of normal pressure hydrocephalus. Neurol Res Int. 2012; 2012:718150.
Kuceyeski A, Maruta J, Niogi SN, Ghajar J, Raj A. The generation and validation of white matter connectivity importance maps. Neuroimage. 2011 Sep 01; 58(1):109-21.
Singh G, Raj A, Kressler B, Nguyen TD, Spincemaille P, Zabih R, Wang Y. A fast Edge-preserving Bayesian reconstruction method for Parallel Imaging applications in cardiac MRI. Magn Reson Med. 2011 Jan; 65(1):184-9.
Raj A, Hess C, Mukherjee P. Spatial HARDI: improved visualization of complex white matter architecture with Bayesian spatial regularization. Neuroimage. 2011 Jan 01; 54(1):396-409.
Raj A, Juluru K. Visualization and segmentation of liver tumors using dynamic contrast MRI. Annu Int Conf IEEE Eng Med Biol Soc. 2009; 2009:6985-9.
Raj A, Wang Y, Zabih R. A maximum likelihood approach to parallel imaging with coil sensitivity noise. IEEE Trans Med Imaging. 2007 Aug; 26(8):1046-57.
Raj A, Thakur K. Fast and stable bayesian image expansion using sparse edge priors. IEEE Trans Image Process. 2007 Apr; 16(4):1073-84.
Raj A, Singh G, Zabih R, Kressler B, Wang Y, Schuff N, Weiner M. Bayesian parallel imaging with edge-preserving priors. Magn Reson Med. 2007 Jan; 57(1):8-21.
Raj A, Zhang H, Prince MR, Wang Y, Zabih R. Automatic algorithm for correcting motion artifacts in time-resolved two-dimensional magnetic resonance angiography using convex projections. Magn Reson Med. 2006 Mar; 55(3):649-58.
Singh G, Nguyen T, Kressler B, Spincemaille P, Raj A, Zabih R, Wang Y. Improved signal-to-noise ratio in parallel coronary artery magnetic resonance angiography using graph cuts based Bayesian reconstruction. Conf Proc IEEE Eng Med Biol Soc. 2006; 2006:703-6.
Raj A, Kressler B, Singh G, Zabih R, Wang Y. Statistical aspects of parallel imaging reconstruction. Conf Proc IEEE Eng Med Biol Soc. 2006; 2006:377-80.