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Md Nasir Uddin, Ph.D.

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Md Nasir Uddin, Ph.D.

About Me
Credentials
Research
Publications

About Me

Faculty Appointments

Assistant Professor - Department of Neurology, General Neurology (SMD)

Assistant Professor - Department of Biomedical Engineering (SMD) - Joint

Credentials

Education

PhD | University of Alberta. Biomedical Engineering. 2015

Awards

University Research Award. 2025

NIH Director's Pioneer Award (DP1). 2024

NIH OAR Innovation Award. 2023

Magna Cum Laude. 2014

Student Scholarship. 2010

SGS Merit Award. 2008

Research

Dr. Uddin is an Assistant Professor in the Departments of Neurology, Biomedical Engineering, and Electrical and Computer Engineering at the University of Rochester, New York, and an affiliated faculty member of the Goergen Institute for Data Science and Artificial Intelligence. He received his B.Sc. (Honours) and M.Sc. in Physics and Ph.D. in Biomedical Engineering.

His research focuses on the development and application of advanced quantitative MRI methods, computational imaging, and artificial intelligence to characterize tissue microstructure, metabolism, and vascular health in the brain and other organs. His work integrates MRI physics, pulse sequence development, image reconstruction, and multimodal data analysis to develop sensitive and biologically meaningful imaging biomarkers for neurological diseases.

His research program encompasses several complementary areas, including advanced diffusion MRI for assessing neuroinflammation and tissue microstructure; myelin- and iron-sensitive MRI using relaxometry and quantitative susceptibility mapping; accelerated chemical exchange saturation transfer (CEST) MRI for molecular and metabolic imaging; and AI-based analysis of cerebrovascular structure using time-of-flight MR angiography. These approaches are being applied to study cerebral small vessel disease (CSVD), HIV, multiple sclerosis, stroke, hypertension, Alzheimer’s disease, and healthy aging.

More recently, his research has expanded into two emerging directions: liver MRI, with a focus on fast and motion-robust quantitative CEST methods for investigating metabolic dysfunction and the brain–liver axis; and digital twin brain modeling for CSVD, integrating quantitative MRI, vascular imaging, blood biomarkers, cognitive measures, and clinical factors to characterize individual disease trajectories and predict disease progression.

These efforts establish a multidisciplinary research program at the intersection of quantitative MRI physics, computational imaging, artificial intelligence, and translational neuroscience, with the overarching goal of developing individualized imaging biomarkers to understand, monitor, and ultimately improve the diagnosis and management of neurological diseases.

Key Words: MRI, Brain, Neuroimaging, Iron, Myelin, Neuroinflammation, Diffusion MRI, Free Water, Multiple Sclerosis, HIV, CSVD, Machine Learning, Deep Learning, Artificial Intelligence.

Publications

Journal Articles

ArteryX: A Reliable End-To-End Toolbox for Standardized Intracranial Artery Feature Extraction From 3D TOF-MRA.

Faiyaz A, Hoang N, Schifitto G, Uddin MN

Magnetic resonance in medicine.. 2026 August 11 Epub 08/11/2026.

Brain MR Elastography Metrics Associated with Alterations in Learning and Memory in People with HIV.

Faiyaz A, Weber M, Singh MV, Kabir IE, Parker KJ, Sack I, Doyley MM, Uddin MN, Schifitto G

Research square.. 2026 June 15 Epub 06/15/2026.

Morphological feature remodeling of intracranial arteries in the context of inflammation and HIV-associated cognitive impairment.

Hoang N, Yang H, Uddin MN, Zhong J, Faiyaz A, Singh MV, Boodoo ZD, Sutton K, Wang HZ, Sahin B, Khan MW, Weber MT, Yuan C, Chen L, Schifitto G

medRxiv : the preprint server for health sciences.. 2026 May 27 Epub 05/27/2026.

White matter damage in multiple sclerosis disproportionately targets default mode, executive control, and salience networks.

Figley TD, Kornelsen J, Uddin MN, Wong K, Pirzada S, Carter S, Helmick CA, O'Grady CB, Mazerolle EL, Patel R, Bernstein CN, Fisk JD, Marrie RA, Figley CR,

The Journal of neuroscience : the official journal of the Society for Neuroscience.. 2026 April 10 Epub 04/10/2026.

HIV-Associated Microstructural Abnormalities in Default Mode, Executive Control, and Salience Networks: Insights from Tensor-Valued Diffusion Encoding.

Uddin MN, Faiyaz A, Figley CR, Qiu X, Weber MT, Schifitto G

Bioengineering.. 2026 April 113 (4)Epub 04/01/2026.

A multimodal imaging-based integrative framework for HIV-associated cognitive impairment and treatment response.

Qiu X, Uddin MN, Wang L, Tyrell A, Faiyaz A, Hoang N, Zhuang Y, Tivarus ME, Zhong J, Weber MT, Schifitto G

Frontiers in neuroscience.. 2026 20 :1775047. Epub 04/13/2026.

Prospective observational study of brain magnetic resonance imaging in adolescents with primary hypertension.

Uddin MN, Lande MB, Schifitto G, Adams H, Wu T, Xu H, Little E, Hooper SR, Tivarus ME

Pediatric nephrology : journal of the International Pediatric Nephrology Association.. 2025 December 18 Epub 12/18/2025.

Chemical Exchange Saturation Transfer Imaging in Neuroinflammation: Methods, Challenges, and Recommendations.

Mensah EA, Faiyaz A, Schifitto G, Uddin MN

International journal of molecular sciences.. 2025 November 1526 (22)Epub 11/15/2025.

ArteryX: Advancing Brain Artery Feature Extraction with Vessel-Fused Networks and a Robust Validation Framework

Faiyaz A; Hoang N; Schifitto G; Uddin MN.

arXiv preprint arXiv:2507.07920. 2025; .

Impact of fatigue in Crohn's disease is negatively related to resting state functional connectivity between the superior parietal lobule and parahippocampal gyrus/hippocampus.

McIver TA, Bernstein CN, Marrie RA, Figley CR, Uddin MN, Fisk JD, Graff LA, Patel R, Mazerolle EL, Kornelsen J

Frontiers in human neuroscience.. 2025 19 :1561421. Epub 04/25/2025.

A multisite validation of brain white matter pathways of resilience to chronic back pain.

Miši? M, Lee N, Zidda F, Sohn K, Usai K, Löffler M, Uddin MN, Farooqi A, Schifitto G, Zhang Z, Nees F, Geha P, Flor H

eLife.. 2024 December 2413 Epub 12/24/2024.

Tensor-valued diffusion MRI detects brain microstructural abnormalities in HIV infected individuals with cognitive impairment.

Uddin MN, Singh MV, Faiyaz A, Szczepankiewicz F, Nilsson M, Boodoo ZD, Sutton KR, Tivarus ME, Zhong J, Wang L, Qiu X, Weber MT, Schifitto G

Scientific reports.. 2024 November 2114 (1):28839. Epub 11/21/2024.

Brain white matter pathways of resilience to chronic back pain: a multisite validation.

Miši? M, Lee N, Zidda F, Sohn K, Usai K, Löffler M, Uddin MN, Farooqi A, Schifitto G, Zhang Z, Nees F, Geha P, Flor H

bioRxiv : the preprint server for biology.. 2024 September 2 Epub 09/02/2024.

Vascular Disease Is Associated With Differences in Brain Structure and Lower Cognitive Functioning in Inflammatory Bowel Disease: A Cross-Sectional Study.

Patel R, Marrie RA, Bernstein CN, Bolton JM, Graff LA, Marriott JJ, Figley CR, Kornelsen J, Mazerolle EL, Helmick C, Uddin MN, Fisk JD

Inflammatory bowel diseases.. 2024 August 130 (8):1309-1318. Epub 1900 01 01.

Brain elastography in aging relates to fluid/solid trendlines.

Parker KJ, Kabir IE, Doyley MM, Faiyaz A, Uddin MN, Flores G, Schifitto G

Physics in medicine and biology.. 2024 May 2969 (11)Epub 05/29/2024.

Altered voxel-based and surface-based morphometry in inflammatory bowel disease.

Kornelsen J, McIver T, Uddin MN, Figley CR, Marrie RA, Patel R, Fisk JD, Carter S, Graff L, Mazerolle EL, Bernstein CN,

Brain research bulletin.. 2023 October 15203 :110771. Epub 10/04/2023.

Brain iron imaging markers in the presence of white matter hyperintensities.

Murray KD, Tivarus ME, Schifitto G, Uddin MN, Zhong J

Magnetic resonance imaging.. 2023 May 98 :115-123. Epub 01/20/2023.

Vascular comorbidity is associated with decreased cognitive functioning in inflammatory bowel disease.

Patel R, Marrie RA, Bernstein CN, Bolton JM, Graff LA, Marriott JJ, Figley CR, Kornelsen J, Mazerolle EL, Uddin MN, Fisk JD,

Scientific reports.. 2023 March 1513 (1):4317. Epub 03/15/2023.

Role of non-classical monocytes in HIV-associated vascular cognitive impairment

Singh, MV; Uddin, MN; Covacevich, VM; Sutton, KR; Boodoo, ZD; Peterson, A; Tyrell, A; Brenner, R; Tivarus, ME; Wang, HZ; Sahin, B; Zhong, J; Weber, M; Wang, L; Qiu, X; Maggiwar, SB; Schifitto G.

medRxiv. 2023; : 2023-03.

Artificial intelligence for diffusion MRI-based tissue microstructure estimation in the human brain: an overview

Faiyaz, A; Doyley, M; Schifitto, G; Uddin, MN.

Frontiers in Neurology. 2023; 14(700): 1-9.

Periventricular and juxtacortical characterization of UManitoba-JHU functionally defined human white matter atlas networks

Figley, CR; Figley, TD; Wong, K; Uddin, MN; da Silva, RDC; and Kornelsen, J.

Front. Hum. Neurosci. 2023; 17: 1-8.

Initiation of combined antiretroviral therapy confers suboptimal beneficial effects on neurovascular function in people with HIV

Singh M, Uddin MN, Singh VB, Peterson AN, Murray KD, Zhuang Y, Tyrell A, Wang L, Tivarus ME, Zhong J, Qiu X, Schifitto G.

Frontiers in Neurology. 2023; 14: 1240300.

Differences in resting state functional connectivity relative to multiple sclerosis and impaired information processing speed

Carter SL, Patel R, Fisk JD, Figley CR, Marrie RA, Mazerolle EL, Uddin MN, Wong K, Graff LA, Bolton JM and Marriott JJ.

Frontiers in Neurology. 2023; 14: 1250894.

Neuroimaging of Neuroinflammation in Neurological Disorders

Uddin, MN; Tivarus, ME; Schifitto, G; & Rudko, DA.

Frontiers in Neurology. 2023; 14(1328511).

Validation of deep learning techniques for quality augmentation in diffusion MRI for clinical studies.

Aja-Fernández S, Martín-Martín C, Planchuelo-Gómez Á, Faiyaz A, Uddin MN, Schifitto G, Tiwari A, Shigwan SJ, Kumar Singh R, Zheng T, Cao Z, Wu D, Blumberg SB, Sen S, Goodwin-Allcock T, Slator PJ, Yigit Avci M, Li Z, Bilgic B, Tian Q, Wang X, Tang Z, Cabezas M, Rauland A, Merhof D, Manzano Maria R, Campos VP, Santini T, da Costa Vieira MA, HashemizadehKolowri S, DiBella E, Peng C, Shen Z, Chen Z, Ullah I, Mani M, Abdolmotalleby H, Eckstrom S, Baete SH, Filipiak P, Dong T, Fan Q, de Luis-García R, Tristán-Vega A, Pieciak T

NeuroImage. Clinical.. 2023 39 :103483. Epub 07/28/2023.

Longitudinal Effects of Combination Antiretroviral Therapy on Cognition and Neuroimaging Biomarkers in Treatment-Naïve People with HIV.

Weber MT, Finkelstein A, Uddin MN, Reddy EA, Arduino RC, Wang L, Tivarus ME, Zhong J, Qui X, Schifitto G

Neurology.. 2022 June 22 Epub 06/22/2022.

Single-shell NODDI using dictionary-learner-estimated isotropic volume fraction.

Faiyaz A, Doyley M, Schifitto G, Zhong J, Uddin MN

NMR in biomedicine.. 2022 February 35 (2):e4628. Epub 10/12/2021.

The Comorbidity and Cognition in Multiple Sclerosis (CCOMS) neuroimaging protocol: study rationale, MRI acquisition, and minimal image processing pipelines

Uddin, MN; Figley, TD; Kornelsen, J; Mazerolle, EL; Helmick, CA; O'Grady, CB; Pirzada, S; Patel, R; Carter, S; Wong, K; Essig, MR; Graff, LA; Bolton, JM; Marriott, JJ; Bernstein, CN; Fisk, JD; Marrie, RA; Figley CR.

Frontiers in Neuroimaging. 2022; 1(970385): 30.

Vascular comorbidity is associated with decreased cognitive functioning in inflammatory bowel disease

Patel, R; Marrie, RA; Bernstein, CN; Bolton, JM; Graff, LA; Marriott, JJ; Figley, CR; Kornelsen, J; Mazerolle, EL; Uddin, MN; Fisk, JD.

2022; .

Angular upsampling in diffusion MRI using contextual HemiHex sub-sampling in q-space (PDF)

Faiyaz, A; Uddin, MN; Schifitto, G.

2022; .

Effects of Vascular Comorbidity on Cognition in Multiple Sclerosis Are Partially Mediated by Changes in Brain Structure.

Marrie RA, Patel R, Figley CR, Kornelsen J, Bolton JM, Graff LA, Mazerolle EL, Helmick C, Uddin MN, Figley TD, Marriott JJ, Bernstein CN, Fisk JD

Frontiers in neurology. 2022 13 :910014. Epub 05/24/2022.

Higher Framingham Risk Scores are associated with greater loss of brain volume over time in multiple sclerosis.

Marrie RA, Patel R, Figley CR, Kornelsen J, Bolton JM, Graff LA, Mazerolle EL, Helmick C, O'Grady C, Uddin MN, Marriott JJ, Bernstein CN, Fisk JD,

Multiple sclerosis and related disorders.. 2021 September 54 :103088. Epub 06/17/2021.

A longitudinal analysis of brain extracellular free water in HIV infected individuals.

Uddin MN, Faiyaz A, Wang L, Zhuang Y, Murray KD, Descoteaux M, Tivarus ME, Weber MT, Zhong J, Qiu X, Schifitto G

Scientific reports.. 2021 April 1511 (1):8273. Epub 04/15/2021.

Magnetic Resonance Imaging in Childhood Primary Hypertension: Potential in the Study of Cognitive Outcomes.

Uddin MN, Tivarus M, Adams H, Little E, Schifitto G, Lande MB

Hypertension.. 2021 March 377 (3):751-758. Epub 02/10/2021.

Mixed Bangla-English Spoken Digit Classification Using Convolutional Neural Network

Das, S; Yasmin, MR; Arefin, M; Taher, KA; Uddin, MN; Rahman, MA.

Applied Intelligence and Informatics pp 371–383. 2021; 1435: 371–383.

Brain Iron Imaging Markers in the Presence of White Matter Hyperintensities

Murray, KD; Tivarus, MT; Schifitto, G; Uddin, MN; Zhong J.

bioRxiv. 2021; .

Increased risk for cerebral small vessel disease is associated with quantitative susceptibility mapping in HIV infected and uninfected individuals.

Murray KD, Uddin MN, Tivarus ME, Sahin B, Wang HZ, Singh MV, Qiu X, Wang L, Spincemaille P, Wang Y, Maggirwar SB, Zhong J, Schifitto G

NeuroImage. Clinical.. 2021 32 :102786. Epub 08/28/2021.

Fixel-Based Analysis and Free Water Corrected DTI Evaluation of HIV-Associated Neurocognitive Disorders.

Finkelstein A, Faiyaz A, Weber MT, Qiu X, Uddin MN, Zhong J, Schifitto G

Frontiers in neurology. 2021 12 :725059. Epub 11/04/2021.

Potential Pitfalls of Using Fractional Anisotropy, Axial Diffusivity, and Radial Diffusivity as Biomarkers of Cerebral White Matter Microstructure.

Figley CR, Uddin MN, Wong K, Kornelsen J, Puig J, Figley TD

Frontiers in neuroscience.. 2021 15 :799576. Epub 01/14/2022.

The Aging Imageomics Study: rationale, design and baseline characteristics of the study population.

Puig J, Biarnes C, Pedraza S, Vilanova JC, Pamplona R, Fernández-Real JM, Brugada R, Ramos R, Coll-de-Tuero G, Calvo-Perxas L, Serena J, Ramió-Torrentà L, Gich J, Gallart L, Portero-Otin M, Alberich-Bayarri A, Jimenez-Pastor A, Camacho-Ramos E, Mayneris-Perxachs J, Pineda V, Font R, Prats-Puig A, Gacto ML, Deco G, Escrichs A, Clotet B, Paredes R, Negredo E, Triaire B, Rodríguez M, Heredia-Escámez A, Coronado R, de Graaf W, Prevost V, Mitulescu A, Daunis-I-Estadella P, Thió-Henestrosa S, Miralles F, Ribas-Ripoll V, Puig-Domingo M, Essig M, Figley CR, Figley TD, Albensi B, Ashraf A, Reiber JHC, Schifitto G, Md Nasir U, Leiva-Salinas C, Wintermark M, Nael K, Vilalta-Franch J, Barretina J, Garre-Olmo J

Mechanisms of ageing and development.. 2020 July 189 :111257. Epub 05/11/2020.

Spatial normalization of multiple sclerosis brain MRI data depends on analysis method and software package.

Pirzada S, Uddin MN, Figley TD, Kornelsen J, Puig J, Marrie RA, Mazerolle EL, Fisk JD, Helmick CA, O'Grady CB, Patel R, Figley CR,

Magnetic resonance imaging.. 2020 May 68 :83-94. Epub 01/30/2020.

Linking Neuroinflammation and Extracellular Free Water in HIV Infection: A Longitudinal Study (PDF)

Uddin, MN; Faiyaz, A; Wang, L; Zhuang, Y; Murray, KD; Descoteaux, M; Tivarus, ME; Weber, MT; Zhong, J; Qiu, X; Schifitto, G.

2020; .

Pathomechanisms of HIV-Associated Cerebral Small Vessel Disease: A Comprehensive Clinical and Neuroimaging Protocol and Analysis Pipeline.

Murray KD, Singh MV, Zhuang Y, Uddin MN, Qiu X, Weber MT, Tivarus ME, Wang HZ, Sahin B, Zhong J, Maggirwar SB, Schifitto G

Frontiers in neurology. 2020 11 :595463. Epub 12/15/2020.

Comparisons between multi-component myelin water fraction, T1w/T2w ratio, and diffusion tensor imaging measures in healthy human brain structures.

Uddin MN, Figley TD, Solar KG, Shatil AS, Figley CR