URochester Medicine / Labs / Uddin Lab / Publications

Publications

1. Figley TD
2. Kornelsen J
3. Uddin MN
4. Wong K
5. Pirzada S
6. Carter S
7. Helmick CA
8. O'Grady CB
9. Mazerolle EL
10. Patel R
11. Bernstein CN
12. Fisk JD
13. Marrie RA
14. Figley CR
White matter damage in multiple sclerosis disproportionately targets default mode, executive control, and salience networks.; The Journal of neuroscience : the official journal of the Society for Neuroscience. 2026 Apr 10.
1. Uddin MN
2. Lande MB
3. Schifitto G
4. Adams H
5. Wu T
6. Xu H
7. Little E
8. Hooper SR
9. Tivarus ME
Prospective observational study of brain magnetic resonance imaging in adolescents with primary hypertension.; Pediatric nephrology (Berlin, Germany). 2025 Dec 18.
1. Mensah EA
2. Faiyaz A
3. Schifitto G
4. Uddin MN
Chemical Exchange Saturation Transfer Imaging in Neuroinflammation: Methods, Challenges, and Recommendations.; International journal of molecular sciences; Vol 26(22). 2025 Nov 15.
1. Faiyaz A
2. Hoang N
3. Schifitto G
4. Uddin MN
ArteryX: Advancing Brain Artery Feature Extraction with Vessel-Fused Networks and a Robust Validation Framework; arXiv preprint arXiv:2507.07920. 2025 Jan 01.
1. McIver TA
2. Bernstein CN
3. Marrie RA
4. Figley CR
5. Uddin MN
6. Fisk JD
7. Graff LA
8. Patel R
9. Mazerolle EL
10. Kornelsen J
Impact of fatigue in Crohn's disease is negatively related to resting state functional connectivity between the superior parietal lobule and parahippocampal gyrus/hippocampus.; Frontiers in human neuroscience; Vol 19, pp. 1561421. 2025 Apr 25.
1. Mišić M
2. Lee N
3. Zidda F
4. Sohn K
5. Usai K
6. Löffler M
7. Uddin MN
8. Farooqi A
9. Schifitto G
10. Zhang Z
11. Nees F
12. Geha P
13. Flor H
A multisite validation of brain white matter pathways of resilience to chronic back pain.; eLife; Vol 13. 2024 Dec 24.
1. Uddin MN
2. Singh MV
3. Faiyaz A
4. Szczepankiewicz F
5. Nilsson M
6. Boodoo ZD
7. Sutton KR
8. Tivarus ME
9. Zhong J
10. Wang L
11. Qiu X
12. Weber MT
13. Schifitto G
Tensor-valued diffusion MRI detects brain microstructural abnormalities in HIV infected individuals with cognitive impairment.; Scientific reports; Vol 14(1), pp. 28839. 2024 Nov 21.
1. Mišić M
2. Lee N
3. Zidda F
4. Sohn K
5. Usai K
6. Löffler M
7. Uddin MN
8. Farooqi A
9. Schifitto G
10. Zhang Z
11. Nees F
12. Geha P
13. Flor H
Brain white matter pathways of resilience to chronic back pain: a multisite validation.; bioRxiv : the preprint server for biology. 2024 Sep 02.
1. Parker KJ
2. Kabir IE
3. Doyley MM
4. Faiyaz A
5. Uddin MN
6. Flores G
7. Schifitto G
Brain elastography in aging relates to fluid/solid trendlines.; Physics in medicine and biology; Vol 69(11). 2024 May 29.
1. Carter SL
2. Patel R
3. Fisk JD
4. Figley CR
5. Marrie RA
6. Mazerolle EL
7. Uddin MN
8. Wong K
9. Graff LA
10. Bolton JA
11. Marriott JJ
Differences in resting state functional connectivity relative to multiple sclerosis and impaired information processing speed; Frontiers in Neurology; Vol 14. 2023 Jan 01.
1. Patel R
2. Marrie RA
3. Bernstein CN
4. Bolton JM
5. Graff LA
6. Marriott JJ
7. Figley CR
8. Kornelsen J
9. Mazerolle EL
10. Helmick C
11. Uddin MN
12. Fisk JD
Vascular Disease Is Associated With Differences in Brain Structure and Lower Cognitive Functioning in Inflammatory Bowel Disease: A Cross-Sectional Study.; Inflammatory bowel diseases. 2023 Sep 22.
1. Singh M
2. Uddin MN
3. Singh VB
4. Peterson AN
5. Murray KD
6. Zhuang Y
7. Tyrell A
8. Wang L
9. Tivarus ME
10. Zhong J
11. Qiu X
12. Schifitto G
Initiation of combined antiretroviral therapy confers suboptimal beneficial effects on neurovascular function in people with HIV; Frontiers in Neurology; Vol 14. 2023 Jan 01.
1. Aja-Fernández S
2. Martín-Martín C
3. Planchuelo-Gómez Á
4. Faiyaz A
5. Uddin MN
6. Schifitto G
7. Tiwari A
8. Shigwan SJ
9. Kumar Singh R
10. Zheng T
11. Cao Z
12. Wu D
13. Blumberg SB
14. Sen S
15. Goodwin-Allcock T
16. Slator PJ
17. Yigit Avci M
18. Li Z
19. Bilgic B
20. Tian Q
21. Wang X
22. Tang Z
23. Cabezas M
24. Rauland A
25. Merhof D
26. Manzano Maria R
27. Campos VP
28. Santini T
29. da Costa Vieira MA
30. HashemizadehKolowri S
31. DiBella E
32. Peng C
33. Shen Z
34. Chen Z
35. Ullah I
36. Mani M
37. Abdolmotalleby H
38. Eckstrom S
39. Baete SH
40. Filipiak P
41. Dong T
42. Fan Q
43. de Luis-García R
44. Tristán-Vega A
45. Pieciak T
Validation of deep learning techniques for quality augmentation in diffusion MRI for clinical studies.; NeuroImage. Clinical; Vol 39, pp. 103483. 2023 Jul 28.
1. Faiyaz A
2. Doyley M
3. Schifitto G
4. Uddin MN
Artificial intelligence for diffusion MRI-based tissue microstructure estimation in the human brain: an overview; Frontiers in Neurology; Vol 14(700), pp. 1-9. 2023 Jan 01.
1. Patel R
2. Marrie RA
3. Bernstein CN
4. Bolton JM
5. Graff LA
6. Marriott JJ
7. Figley CR
8. Kornelsen J
9. Mazerolle EL
10. Uddin MN
11. Fisk JD
Vascular comorbidity is associated with decreased cognitive functioning in inflammatory bowel disease.; Scientific reports; Vol 13(1), pp. 4317. 2023 Mar 15.
1. Singh MV
2. Uddin MN
3. Covacevich VM
4. Sutton KR
5. Boodoo ZD
6. Peterson A
7. Tyrell A
8. Brenner R
9. Tivarus ME
10. Wang HZ
11. Sahin B
12. Zhong J
13. Weber M
14. Wang L
15. Qiu X
16. Maggiwar SB
17. Schifitto G
Role of non-classical monocytes in HIV-associated vascular cognitive impairment; medRxiv. 2023 Jan 01.
1. Murray KD
2. Tivarus ME
3. Schifitto G
4. Uddin MN
5. Zhong J
Brain iron imaging markers in the presence of white matter hyperintensities.; Magnetic resonance imaging. 2023 Jan 19.
1. Kornelsen J
2. McIver T
3. Uddin MN
4. Figley CR
5. Marrie RA
6. Patel R
7. Fisk JD
8. Carter S
9. Graff L
10. Mazerolle EL
11. Bernstein CN
Altered voxel-based and surface-based morphometry in inflammatory bowel disease.; Brain research bulletin; Vol 203, pp. 110771. 2023 Jan 04.
1. Uddin MN
2. Tivarus ME
3. Schifitto G
4. Rudko DA
Neuroimaging of Neuroinflammation in Neurological Disorders; Frontiers in Neurology; Vol 14(1328511). 2023 Jan 01.
1. Patel R
2. Marrie RA
3. Bernstein CN
4. Bolton JM
5. Graff LA
6. Marriott JJ
7. Figley CR
8. Kornelsen J
9. Mazerolle EL
10. Uddin MN
11. Fisk JD
Vascular comorbidity is associated with decreased cognitive functioning in inflammatory bowel disease; . 2022 Jan 01.
1. Faiyaz A
2. Uddin MN
3. Schifitto G
Angular upsampling in diffusion MRI using contextual HemiHex sub-sampling in q-space; . 2022 Jan 01.
1. Uddin MN
2. Figley TD
3. Kornelsen J
4. Mazerolle EL
5. Helmick CA
6. O'Grady CB
7. Pirzada S
8. Patel R
9. Carter S
10. Wong K
11. Essig MR
12. Graff LA
13. Bolton JM
14. Marriott JJ
15. Bernstein CN
16. Fisk JD
17. Marrie RA
18. Figley CR
The Comorbidity and Cognition in Multiple Sclerosis (CCOMS) neuroimaging protocol: study rationale, MRI acquisition, and minimal image processing pipelines; Frontiers in Neuroimaging; Vol 1(970385). 2022 Jan 01.
1. Weber MT
2. Finkelstein A
3. Uddin MN
4. Reddy EA
5. Arduino RC
6. Wang L
7. Tivarus ME
8. Zhong J
9. Qui X
10. Schifitto G
Longitudinal Effects of Combination Antiretroviral Therapy on Cognition and Neuroimaging Biomarkers in Treatment-Naïve People with HIV.; Neurology. 2022 Jun 22.
1. Marrie RA
2. Patel R
3. Figley CR
4. Kornelsen J
5. Bolton JM
6. Graff LA
7. Mazerolle EL
8. Helmick C
9. Uddin MN
10. Figley TD
11. Marriott JJ
12. Bernstein CN
13. Fisk JD
Effects of Vascular Comorbidity on Cognition in Multiple Sclerosis Are Partially Mediated by Changes in Brain Structure.; Frontiers in neurology; Vol 13. 2022.
1. Faiyaz A
2. Doyley M
3. Schifitto G
4. Zhong J
5. Uddin MN
Single-shell NODDI using dictionary-learner-estimated isotropic volume fraction.; NMR in biomedicine. 2021 Oct 12.
1. Murray KD
2. Uddin MN
3. Tivarus ME
4. Sahin B
5. Wang HZ
6. Singh MV
7. Qiu X
8. Wang L
9. Spincemaille P
10. Wang Y
11. Maggirwar SB
12. Zhong J
13. Schifitto G
Increased risk for cerebral small vessel disease is associated with quantitative susceptibility mapping in HIV infected and uninfected individuals.; NeuroImage. Clinical; Vol 32. 2021 Aug 28.
1. Das S
2. Yasmin MR
3. Arefin M
4. Taher KA
5. Uddin MN
6. Rahman MA
Mixed Bangla-English Spoken Digit Classification Using Convolutional Neural Network; Applied Intelligence and Informatics pp 371–383; Vol 1435, pp. 371-383. 2021 Jan 01.
1. Marrie RA
2. Patel R
3. Figley CR
4. Kornelsen J
5. Bolton JM
6. Graff LA
7. Mazerolle EL
8. Helmick C
9. O'Grady C
10. Uddin MN
11. Marriott JJ
12. Bernstein CN
13. Fisk JD
Higher Framingham Risk Scores are associated with greater loss of brain volume over time in multiple sclerosis.; Multiple sclerosis and related disorders; Vol 54. 2021 Jun 17.
1. Uddin MN
2. Faiyaz A
3. Wang L
4. Zhuang Y
5. Murray KD
6. Descoteaux M
7. Tivarus ME
8. Weber MT
9. Zhong J
10. Qiu X
11. Schifitto G
A longitudinal analysis of brain extracellular free water in HIV infected individuals.; Scientific reports; Vol 11(1). 2021 Apr 15.
1. Uddin MN
2. Tivarus M
3. Adams H
4. Little E
5. Schifitto G
6. Lande MB
Magnetic Resonance Imaging in Childhood Primary Hypertension: Potential in the Study of Cognitive Outcomes.; Hypertension (Dallas, Tex. : 1979); Vol 77(3). 2021 Mar 03.
1. Murray KD
2. Tivarus MT
3. Schifitto G
4. Uddin MN
5. Zhong J
Brain Iron Imaging Markers in the Presence of White Matter Hyperintensities; bioRxiv. 2021 Jan 01.
1. Finkelstein A
2. Faiyaz A
3. Weber MT
4. Qiu X
5. Uddin MN
6. Zhong J
7. Schifitto G
Fixel-Based Analysis and Free Water Corrected DTI Evaluation of HIV-Associated Neurocognitive Disorders.; Frontiers in neurology; Vol 12. 2021.
1. Figley CR
2. Uddin MN
3. Wong K
4. Kornelsen J
5. Puig J
6. Figley TD
Potential Pitfalls of Using Fractional Anisotropy, Axial Diffusivity, and Radial Diffusivity as Biomarkers of Cerebral White Matter Microstructure.; Frontiers in neuroscience; Vol 15. 2021.
1. Uddin MN
2. Faiyaz A
3. Wang L
4. Zhuang Y
5. Murray KD
6. Descoteaux M
7. Tivarus ME
8. Weber MT
9. Zhong J
10. Qiu X
11. Schifitto G
Linking Neuroinflammation and Extracellular Free Water in HIV Infection: A Longitudinal Study; . 2020 Jan 01.
1. Puig J
2. Biarnes C
3. Pedraza S
4. Vilanova JC
5. Pamplona R
6. Fernández-Real JM
7. Brugada R
8. Ramos R
9. Coll-de-Tuero G
10. Calvo-Perxas L
11. Serena J
12. Ramió-Torrentà L
13. Gich J
14. Gallart L
15. Portero-Otin M
16. Alberich-Bayarri A
17. Jimenez-Pastor A
18. Camacho-Ramos E
19. Mayneris-Perxachs J
20. Pineda V
21. Font R
22. Prats-Puig A
23. Gacto ML
24. Deco G
25. Escrichs A
26. Clotet B
27. Paredes R
28. Negredo E
29. Triaire B
30. Rodríguez M
31. Heredia-Escámez A
32. Coronado R
33. de Graaf W
34. Prevost V
35. Mitulescu A
36. Daunis-I-Estadella P
37. Thió-Henestrosa S
38. Miralles F
39. Ribas-Ripoll V
40. Puig-Domingo M
41. Essig M
42. Figley CR
43. Figley TD
44. Albensi B
45. Ashraf A
46. Reiber JHC
47. Schifitto G
48. Md Nasir U
49. Leiva-Salinas C
50. Wintermark M
51. Nael K
52. Vilalta-Franch J
53. Barretina J
54. Garre-Olmo J
The Aging Imageomics Study: rationale, design and baseline characteristics of the study population.; Mechanisms of ageing and development; Vol 189. 2020 May 11.
1. Pirzada S
2. Uddin MN
3. Figley TD
4. Kornelsen J
5. Puig J
6. Marrie RA
7. Mazerolle EL
8. Fisk JD
9. Helmick CA
10. O'Grady CB
11. Patel R
12. Figley CR
Spatial normalization of multiple sclerosis brain MRI data depends on analysis method and software package.; Magnetic resonance imaging; Vol 68. 2020 May.
1. Murray KD
2. Singh MV
3. Zhuang Y
4. Uddin MN
5. Qiu X
6. Weber MT
7. Tivarus ME
8. Wang HZ
9. Sahin B
10. Zhong J
11. Maggirwar SB
12. Schifitto G
Pathomechanisms of HIV-Associated Cerebral Small Vessel Disease: A Comprehensive Clinical and Neuroimaging Protocol and Analysis Pipeline.; Frontiers in neurology; Vol 11. 2020.
1. Uddin MN
2. Figley TD
3. Solar KG
4. Shatil AS
5. Figley CR
Comparisons between multi-component myelin water fraction, T1w/T2w ratio, and diffusion tensor imaging measures in healthy human brain structures.; Scientific reports; Vol 9(1). 2019 Feb 21.
1. Uddin MN
2. Figley TD
3. Figley CR
Effect of echo time and T2-weighting on GRASE-based T1w/T2w ratio measurements at 3T.; Magnetic resonance imaging; Vol 51. 2018 Sep.
1. Uddin MN
2. Figley TD
3. Marrie RA
4. Figley CR
Can T1 w/T2 w ratio be used as a myelin-specific measure in subcortical structures? Comparisons between FSE-based T1 w/T2 w ratios, GRASE-based T1 w/T2 w ratios and multi-echo GRASE-based myelin water fractions.; NMR in biomedicine; Vol 31(3). 2018 Mar.
1. Shatil AS
2. Uddin MN
3. Matsuda KM
4. Figley CR
Quantitative Ex Vivo MRI Changes due to Progressive Formalin Fixation in Whole Human Brain Specimens: Longitudinal Characterization of Diffusion, Relaxometry, and Myelin Water Fraction Measurements at 3T.; Frontiers in medicine; Vol 5. 2018.
1. Uddin MN
2. Figley TD
3. Marie RA
4. Figley CR
Comparison of Multi-echo Gradient and Spin Echo (GRASE) and Fast Spin Echo (FSE) MRI Sequences for T1w/T2w Ratio Mapping; CMBES Proceedings; Vol 40. 2018 Jan 01.
1. Uddin MN
2. Figley TD
3. Marrie RA
4. Figley CR
Comparison of Multi-echo Gradient and Spin Echo (GRASE) and Fast Spin Echo (FSE) MRI Sequences for T1w/T2w Ratio Mapping; CMBES Proceedings; Vol 40. 2017 Jan 01.
1. Uddin MN
2. McPhee KC
3. Blevins G
4. Wilman AH
Recovery of accurate T2 from historical 1.5 tesla proton density and T2-weighted images: Application to 7-year T2 changes in multiple sclerosis brain.; Magnetic resonance imaging; Vol 37. 2017 Apr.
1. Uddin MN
2. Lebel RM
3. Seres P
4. Blevins G
5. Wilman AH
Spin echo transverse relaxation and atrophy in multiple sclerosis deep gray matter: A two-year longitudinal study.; Multiple sclerosis (Houndmills, Basingstoke, England); Vol 22(9). 2016 Aug.
1. Uddin MN
2. Lebel RM
3. Wilman AH
Value of transverse relaxometry difference methods for iron in human brain.; Magnetic resonance imaging; Vol 34(1). 2016 Jan.
1. Uddin MN
2. Marc Lebel R
3. Wilman AH
Transverse relaxometry with reduced echo train lengths via stimulated echo compensation.; Magnetic resonance in medicine; Vol 70(5). 2013 Nov.
1. Uddin MN
2. Morrow MR
Bicellar mixture phase behavior examined by variable-pressure deuterium NMR and ambient pressure DSC.; Langmuir : the ACS journal of surfaces and colloids; Vol 26(14). 2010 Jul 20.