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Ashish Raj, PhD

Title(s)Professor, Radiology
SchoolSchool of Medicine
Address400 Parnassus Avenue
San Francisco CA 94117
Phone415-353-3442
ORCID ORCID Icon0000-0003-2414-2444 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Cornell University, Ithaca, NYPhD05/2005Electrical and Computer Engineering
    University of Auckland, Auckland, New ZealandBE12/1998Electrical Engineering

    Collapse Overview 
    Collapse Overview
    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.

    Collapse Research 
    Collapse Research Activities and Funding
    Understanding the dynamic interactions between tau pathology and microglia-mediated inflammation in Alzheimer's Disease
    NIH/NIA R56AG064873Aug 15, 2019 - Jul 31, 2020
    Role: Co-Principal Investigator
    Network Modelling of Multimodal Dynamics in Alzheimer?s Disease and Dementia
    NIH/NIA R01AG062196Mar 1, 2019 - Dec 31, 2023
    Role: Principal Investigator
    Multimodal modeling framework for fusing structural and functional connectome data
    NIH/NIBIB R01EB022717Sep 30, 2016 - Jun 30, 2019
    Role: Principal Investigator
    Predictive model of spread of Parkinson's pathology using network diffusion
    NIH/NINDS R01NS092802Jul 15, 2016 - Apr 30, 2021
    Role: Co-Principal Investigator
    A Novel Network Diffusion Model for Alzheimer's And Other Neurodegenerative Disea
    NIH/NINDS R01NS075425Aug 1, 2011 - Jul 31, 2015
    Role: Principal Investigator
    Bayesian Parallel Imaging For Arbitrarily Sampled MR Data Using Edge-Preserving S
    NIH/NIBIB R21EB008138Sep 30, 2008 - Aug 31, 2011
    Role: Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A dictionary-based graph-cut algorithm for MRI reconstruction. NMR Biomed. 2020 Jul 02; e4344. Xu J, Pannetier N, Raj A. PMID: 32618082.
      View in: PubMed   Mentions:    Fields:    
    2. Origins of atrophy in Parkinson linked to early onset and local transcription patterns. Brain Commun. 2020; 2(2):fcaa065. Maia PD, Pandya S, Freeze B, Torok J, Gupta A, Zeighami Y, Raj A. PMID: 32954322.
      View in: PubMed   Mentions:
    3. Network mediation of pathology pattern in sporadic Creutzfeldt-Jakob disease. Brain Commun. 2020; 2(1):fcaa060. Freeze B, Maia P, Pandya S, Raj A. PMID: 32954308.
      View in: PubMed   Mentions:
    4. Spectral graph theory of brain oscillations. Hum Brain Mapp. 2020 Aug 01; 41(11):2980-2998. Raj A, Cai C, Xie X, Palacios E, Owen J, Mukherjee P, Nagarajan S. PMID: 32202027.
      View in: PubMed   Mentions: 1     Fields:    
    5. Stereotaxic Diffusion Tensor Imaging White Matter Atlas for the in vivo Domestic Feline Brain. Front Neuroanat. 2020; 14:1. Johnson PJ, Pascalau R, Luh WM, Raj A, Cerda-Gonzalez S, Barry EF. PMID: 32116572.
      View in: PubMed   Mentions:
    6. Dynamical Role of Pivotal Brain Regions in Parkinson Symptomatology Uncovered with Deep Learning. Brain Sci. 2020 Jan 30; 10(2). Nguyen AA, Maia PD, Gao X, F Damasceno P, Raj A. PMID: 32019067.
      View in: PubMed   Mentions:
    7. 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. Mezias C, Rey N, Brundin P, Raj A. PMID: 31628991.
      View in: PubMed   Mentions: 6     Fields:    
    8. Regional transcriptional architecture of Parkinson's disease pathogenesis and network spread. Brain. 2019 10 01; 142(10):3072-3085. Freeze B, Pandya S, Zeighami Y, Raj A. PMID: 31359041.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    9. 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. Kuceyeski AF, Jamison KW, Owen JP, Raj A, Mukherjee P. PMID: 31294921.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    10. Slow-gamma frequencies are optimally guarded against effects of neurodegenerative diseases and traumatic brain injuries. J Comput Neurosci. 2019 08; 47(1):1-16. Maia PD, Raj A, Kutz JN. PMID: 31165337.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    11. Editorial: Network Spread Models of Neurodegenerative Diseases. Front Neurol. 2018; 9:1159. Raj A, Iturria-Medina Y. PMID: 30671020.
      View in: PubMed   Mentions:
    12. Normal diffusivity of the domestic feline brain. J Comp Neurol. 2019 04 01; 527(5):1012-1023. Barry EF, Cerda-Gonzalez S, Luh WM, Daws RE, Raj A, Johnson PJ. PMID: 30298687.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    13. Models of Network Spread and Network Degeneration in Brain Disorders. Biol Psychiatry Cogn Neurosci Neuroimaging. 2018 09; 3(9):788-797. Raj A, Powell F. PMID: 30170711.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    14. A method for inferring regional origins of neurodegeneration. Brain. 2018 03 01; 141(3):863-876. Torok J, Maia PD, Powell F, Pandya S, Raj A. PMID: 29409009.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    15. Functional brain connectivity is predictable from anatomic network's Laplacian eigen-structure. Neuroimage. 2018 05 15; 172:728-739. Abdelnour F, Dayan M, Devinsky O, Thesen T, Raj A. PMID: 29454104.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    16. Regional expression of genes mediating trans-synaptic alpha-synuclein transfer predicts regional atrophy in Parkinson disease. Neuroimage Clin. 2018; 18:456-466. Freeze B, Acosta D, Pandya S, Zhao Y, Raj A. PMID: 29868450.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    17. Regional vulnerability in Alzheimer's disease: The role of cell-autonomous and transneuronal processes. Alzheimers Dement. 2018 06; 14(6):797-810. Acosta D, Powell F, Zhao Y, Raj A. PMID: 29306583.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    18. 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. Powell F, Tosun D, Sadeghi R, Weiner M, Raj A. PMID: 29578480.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    19. Predictive Model of Spread of Progressive Supranuclear Palsy Using Directional Network Diffusion. Front Neurol. 2017; 8:692. Pandya S, Mezias C, Raj A. PMID: 29312121.
      View in: PubMed   Mentions:
    20. Analysis of Amyloid-ß Pathology Spread in Mouse Models Suggests Spread Is Driven by Spatial Proximity, Not Connectivity. Front Neurol. 2017; 8:653. Mezias C, Raj A. PMID: 29326640.
      View in: PubMed   Mentions:
    21. Age-Related Changes in Topological Degradation of White Matter Networks and Gene Expression in Chronic Schizophrenia. Brain Connect. 2017 11; 7(9):574-589. Powell F, LoCastro E, Acosta D, Ahmed M, O'Donoghue S, Forde N, Cannon D, Scanlon C, Rao T, McDonald C, Raj A. PMID: 28946750.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    22. Mature Hippocampal Neurons Require LIS1 for Synaptic Integrity: Implications for Cognition. Biol Psychiatry. 2018 03 15; 83(6):518-529. Sudarov A, Zhang XJ, Braunstein L, LoCastro E, Singh S, Taniguchi Y, Raj A, Shi SH, Moore H, Ross ME. PMID: 29150182.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    23. 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. Mezias C, LoCastro E, Xia C, Raj A. PMID: 28807028.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    24. 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. Wang MB, Owen JP, Mukherjee P, Raj A. PMID: 28640803.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    25. 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. Dayan M, Hurtado Rúa SM, Monohan E, Fujimoto K, Pandya S, LoCastro EM, Vartanian T, Nguyen TD, Raj A, Gauthier SA. PMID: 28603479.
      View in: PubMed   Mentions:
    26. The Brain's Structural Connectome Mediates the Relationship between Regional Neuroimaging Biomarkers in Alzheimer's Disease. J Alzheimers Dis. 2017; 55(4):1639-1657. Pandya S, Kuceyeski A, Raj A. PMID: 27911289.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    27. Network Analysis on Predicting Mean Diffusivity Change at Group Level in Temporal Lobe Epilepsy. Brain Connect. 2016 10; 6(8):607-620. Abdelnour F, Raj A, Devinsky O, Thesen T. PMID: 27405726.
      View in: PubMed   Mentions: 1     Fields:    
    28. Diffuse reduction of cerebral grey matter volumes in Erdheim-Chester disease. Orphanet J Rare Dis. 2016 08 02; 11(1):109. Diamond EL, Hatzoglou V, Patel S, Abdel-Wahab O, Rampal R, Hyman DM, Holodny AI, Raj A. PMID: 27484739.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    29. Structural connectome disruption at baseline predicts 6-months post-stroke outcome. Hum Brain Mapp. 2016 07; 37(7):2587-601. Kuceyeski A, Navi BB, Kamel H, Raj A, Relkin N, Toglia J, Iadecola C, O'Dell M. PMID: 27016287.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    30. 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. Dayan M, Monohan E, Pandya S, Kuceyeski A, Nguyen TD, Raj A, Gauthier SA. PMID: 26667008.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    31. Relating Cortical Atrophy in Temporal Lobe Epilepsy with Graph Diffusion-Based Network Models. PLoS Comput Biol. 2015 Oct; 11(10):e1004564. Abdelnour F, Mueller S, Raj A. PMID: 26513579.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    32. Measuring longitudinal myelin water fraction in new multiple sclerosis lesions. Neuroimage Clin. 2015; 9:369-75. Vargas WS, Monohan E, Pandya S, Raj A, Vartanian T, Nguyen TD, Hurtado Rúa SM, Gauthier SA. PMID: 26594620.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    33. 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. Nguyen TD, Deh K, Monohan E, Pandya S, Spincemaille P, Raj A, Wang Y, Gauthier SA. PMID: 26331978.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    34. Exploring the brain's structural connectome: A quantitative stroke lesion-dysfunction mapping study. Hum Brain Mapp. 2015 Jun; 36(6):2147-60. Kuceyeski A, Navi BB, Kamel H, Relkin N, Villanueva M, Raj A, Toglia J, O'Dell M, Iadecola C. PMID: 25655204.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    35. 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. Raj A, LoCastro E, Kuceyeski A, Tosun D, Relkin N, Weiner M. PMID: 25600871.
      View in: PubMed   Mentions: 38     Fields:    
    36. 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. Dong J, Liu T, Chen F, Zhou D, Dimov A, Raj A, Cheng Q, Spincemaille P, Wang Y. PMID: 25312917.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    37. Widespread white matter degeneration preceding the onset of dementia. Alzheimers Dement. 2015 May; 11(5):485-493.e2. Maier-Hein KH, Westin CF, Shenton ME, Weiner MW, Raj A, Thomann P, Kikinis R, Stieltjes B, Pasternak O. PMID: 25035154.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    38. Multi-compartment T2 relaxometry using a spatially constrained multi-Gaussian model. PLoS One. 2014; 9(6):e98391. Raj A, Pandya S, Shen X, LoCastro E, Nguyen TD, Gauthier SA. PMID: 24896833.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    39. 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. Goel P, Kuceyeski A, LoCastro E, Raj A. PMID: 24677576.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    40. Predicting future brain tissue loss from white matter connectivity disruption in ischemic stroke. Stroke. 2014 Mar; 45(3):717-22. Kuceyeski A, Kamel H, Navi BB, Raj A, Iadecola C. PMID: 24523041.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    41. Network diffusion accurately models the relationship between structural and functional brain connectivity networks. Neuroimage. 2014 Apr 15; 90:335-47. Abdelnour F, Voss HU, Raj A. PMID: 24384152.
      View in: PubMed   Mentions: 36     Fields:    Translation:Humans
    42. Discriminative random field segmentation of lung nodules in CT studies. Comput Math Methods Med. 2013; 2013:683216. Liu B, Raj A. PMID: 24592283.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    43. 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, Maruta J, Relkin N, Raj A. PMID: 23855491.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    44. 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. Shen X, Nguyen TD, Gauthier SA, Raj A. PMID: 24505719.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    45. Loss in connectivity among regions of the brain reward system in alcohol dependence. Hum Brain Mapp. 2013 Dec; 34(12):3129-42. Kuceyeski A, Meyerhoff DJ, Durazzo TC, Raj A. PMID: 22815206.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    46. Statistics of weighted brain networks reveal hierarchical organization and Gaussian degree distribution. PLoS One. 2012; 7(6):e35029. Ivkovic M, Kuceyeski A, Raj A. PMID: 22761649.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    47. A network diffusion model of disease progression in dementia. Neuron. 2012 Mar 22; 73(6):1204-15. Raj A, Kuceyeski A, Weiner M. PMID: 22445347.
      View in: PubMed   Mentions: 176     Fields:    Translation:Humans
    48. 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. Kuceyeski A, Zhang Y, Raj A. PMID: 22484307.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    49. Bayesian algorithm using spatial priors for multiexponential T2 relaxometry from multiecho spin echo MRI. Magn Reson Med. 2012 Nov; 68(5):1536-43. Kumar D, Nguyen TD, Gauthier SA, Raj A. PMID: 22266707.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    50. 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. Nguyen TD, Wisnieff C, Cooper MA, Kumar D, Raj A, Spincemaille P, Wang Y, Vartanian T, Gauthier SA. PMID: 22344579.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    51. The wiring economy principle: connectivity determines anatomy in the human brain. PLoS One. 2011; 6(9):e14832. Raj A, Chen YH. PMID: 21915250.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    52. 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. Moore DW, Kovanlikaya I, Heier LA, Raj A, Huang C, Chu KW, Relkin NR. PMID: 21860791.
      View in: PubMed   Mentions:
    53. The generation and validation of white matter connectivity importance maps. Neuroimage. 2011 Sep 01; 58(1):109-21. Kuceyeski A, Maruta J, Niogi SN, Ghajar J, Raj A. PMID: 21722739.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    54. A fast Edge-preserving Bayesian reconstruction method for Parallel Imaging applications in cardiac MRI. Magn Reson Med. 2011 Jan; 65(1):184-9. Singh G, Raj A, Kressler B, Nguyen TD, Spincemaille P, Zabih R, Wang Y. PMID: 20939095.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    55. Spatial HARDI: improved visualization of complex white matter architecture with Bayesian spatial regularization. Neuroimage. 2011 Jan 01; 54(1):396-409. Raj A, Hess C, Mukherjee P. PMID: 20670684.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    56. Visualization and segmentation of liver tumors using dynamic contrast MRI. Annu Int Conf IEEE Eng Med Biol Soc. 2009; 2009:6985-9. Raj A, Juluru K. PMID: 19964723.
      View in: PubMed   Mentions:
    57. A maximum likelihood approach to parallel imaging with coil sensitivity noise. IEEE Trans Med Imaging. 2007 Aug; 26(8):1046-57. Raj A, Wang Y, Zabih R. PMID: 17695125.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    58. Fast and stable bayesian image expansion using sparse edge priors. IEEE Trans Image Process. 2007 Apr; 16(4):1073-84. Raj A, Thakur K. PMID: 17405438.
      View in: PubMed   Mentions:    Fields:    
    59. Bayesian parallel imaging with edge-preserving priors. Magn Reson Med. 2007 Jan; 57(1):8-21. Raj A, Singh G, Zabih R, Kressler B, Wang Y, Schuff N, Weiner M. PMID: 17195165.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    60. 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. Raj A, Zhang H, Prince MR, Wang Y, Zabih R. PMID: 16463347.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    61. Statistical aspects of parallel imaging reconstruction. Conf Proc IEEE Eng Med Biol Soc. 2006; 2006:377-80. Raj A, Kressler B, Singh G, Zabih R, Wang Y. PMID: 17946826.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    62. 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. Singh G, Nguyen T, Kressler B, Spincemaille P, Raj A, Zabih R, Wang Y. PMID: 17946852.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
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