Ashish Raj, PhD

InstitutionUniversity of California San Francisco
Address185 Berry Street Bldg B
San Francisco CA 94158
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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
    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

    Collapse ORNG Applications 
    Collapse Websites

    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.
    List All   |   Timeline
    1. Barry E, Cerda-Gonzalez S, Luh W, Daws RE, Raj A, Johnson PJ. Normal Diffusivity of the Domestic Feline Brain. J Comp Neurol. 2018 Oct 09. PMID: 30298687.
      View in: PubMed
    2. Raj A, Powell F. Models of Network Spread and Network Degeneration in Brain Disorders. Biol Psychiatry Cogn Neurosci Neuroimaging. 2018 Sep; 3(9):788-797. PMID: 30170711.
      View in: PubMed
    3. Powell F, Tosun D, Sadeghi R, Weiner M, Raj A. Preserved Structural Network Organization Mediates Pathology Spread in Alzheimer's Disease Spectrum Despite Loss of White Matter Tract Integrity. J Alzheimers Dis. 2018 Mar 23. PMID: 29578480.
      View in: PubMed
    4. Abdelnour F, Dayan M, Devinsky O, Thesen T, Raj A. Functional brain connectivity is predictable from anatomic network's Laplacian eigen-structure. Neuroimage. 2018 Feb 14; 172:728-739. PMID: 29454104.
      View in: PubMed
    5. Torok J, Maia PD, Powell F, Pandya S, Raj A. A method for inferring regional origins of neurodegeneration. Brain. 2018 02 02. PMID: 29409009.
      View in: PubMed
    6. 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. PMID: 29868450.
      View in: PubMed
    7. Acosta D, Powell F, Zhao Y, Raj A. Regional vulnerability in Alzheimer's: The role of cell-autonomous and transneuronal processes. Alzheimers Dement. 2018 Jan 04. PMID: 29306583.
      View in: PubMed
    8. Pandya S, Mezias C, Raj A. Predictive Model of Spread of Progressive Supranuclear Palsy Using Directional Network Diffusion. Front Neurol. 2017; 8:692. PMID: 29312121.
      View in: PubMed
    9. Mezias C, Raj A. Analysis of Amyloid-ß Pathology Spread in Mouse Models Suggests Spread Is Driven by Spatial Proximity, Not Connectivity. Front Neurol. 2017; 8:653. PMID: 29326640.
      View in: PubMed
    10. 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 Nov; 7(9):574-589. PMID: 28946750.
      View in: PubMed
    11. 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. 2017 Sep 23. PMID: 29150182.
      View in: PubMed
    12. 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 Aug 14; 5(1):61. PMID: 28807028.
      View in: PubMed
    13. 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. PMID: 28640803.
      View in: PubMed
    14. 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. PMID: 28603479.
      View in: PubMed
    15. Pandya S, Kuceyeski A, Raj A. The Brain's Structural Connectome Mediates the Relationship between Regional Neuroimaging Biomarkers in Alzheimer's Disease. J Alzheimers Dis. 2017; 55(4):1639-1657. PMID: 27911289.
      View in: PubMed
    16. 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 Sep 07. PMID: 27405726.
      View in: PubMed
    17. 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. PMID: 27484739; PMCID: PMC4971748.
    18. 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. PMID: 27016287.
      View in: PubMed
    19. 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. PMID: 26667008.
      View in: PubMed
    20. 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. PMID: 26513579; PMCID: PMC4626097.
    21. 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. PMID: 26594620.
      View in: PubMed
    22. 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. PMID: 26331978.
      View in: PubMed
    23. 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. PMID: 25655204; PMCID: PMC4414746.
    24. Raj A, LoCastro E, Kuceyeski A, Tosun D, Relkin N, Weiner M. Network Diffusion Model of Progression Predicts Longitudinal Patterns of Atrophy and Metabolism in Alzheimer's Disease. Cell Rep. 2015 Jan 14. PMID: 25600871.
      View in: PubMed
    25. 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. PMID: 25312917.
      View in: PubMed
    26. 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. PMID: 25035154; PMCID: PMC4295016.
    27. 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. PMID: 24896833; PMCID: PMC4045663.
    28. 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. PMID: 24677576; PMCID: PMC4283562.
    29. 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. PMID: 24523041; PMCID: PMC3943489.
    30. 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. PMID: 24384152; PMCID: PMC3951650.
    31. Liu B, Raj A. Discriminative random field segmentation of lung nodules in CT studies. Comput Math Methods Med. 2013; 2013:683216. PMID: 24592283; PMCID: PMC3925502.
    32. 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. PMID: 23855491; PMCID: PMC3796322.
    33. 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. PMID: 24505719.
      View in: PubMed
    34. 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. PMID: 22815206; PMCID: PMC3931305.
    35. Ivkovic M, Kuceyeski A, Raj A. Statistics of weighted brain networks reveal hierarchical organization and Gaussian degree distribution. PLoS One. 2012; 7(6):e35029. PMID: 22761649; PMCID: PMC3382201.
    36. Raj A, Kuceyeski A, Weiner M. A network diffusion model of disease progression in dementia. Neuron. 2012 Mar 22; 73(6):1204-15. PMID: 22445347; PMCID: PMC3623298.
    37. 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. PMID: 22484307; PMCID: PMC3376902.
    38. 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. PMID: 22266707.
      View in: PubMed
    39. 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. PMID: 22344579.
      View in: PubMed
    40. Raj A, Chen YH. The wiring economy principle: connectivity determines anatomy in the human brain. PLoS One. 2011; 6(9):e14832. PMID: 21915250; PMCID: PMC3168442.
    41. 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. PMID: 21860791; PMCID: PMC3154385.
    42. 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. PMID: 21722739; PMCID: PMC3144270.
    43. 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. PMID: 20939095; PMCID: PMC3005027.
    44. 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. PMID: 20670684; PMCID: PMC2962674.
    45. Raj A, Juluru K. Visualization and segmentation of liver tumors using dynamic contrast MRI. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:6985-9. PMID: 19964723.
      View in: PubMed
    46. 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. PMID: 17695125.
      View in: PubMed
    47. Raj A, Thakur K. Fast and stable bayesian image expansion using sparse edge priors. IEEE Trans Image Process. 2007 Apr; 16(4):1073-84. PMID: 17405438.
      View in: PubMed
    48. 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. PMID: 17195165; PMCID: PMC2291515.
    49. 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. PMID: 16463347.
      View in: PubMed
    50. 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; 1:703-6. PMID: 17946852.
      View in: PubMed
    51. Raj A, Kressler B, Singh G, Zabih R, Wang Y. Statistical aspects of parallel imaging reconstruction. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:377-80. PMID: 17946826.
      View in: PubMed