Journal Publications

--- 2026 ---

1. Md Kaosar Uddina*, Nghi Nguyen*, Huajun Huang, Duy Duong-Tran, Ginny Zheng. "Divergence unveils Further Distinct Phenotypic Markers of Brain Fingerprinting Data" published iScience (Cell). [DOI]

--- 2025 ---

2. Dachuan Song, Li Shen, Duy Duong-Tran, Xuan Wang. "Reconstructing Brain Causal Dynamics for Subject and Task Fingerprints using fMRI Time-series Data" published  Journal of Health Information Science and Systems (HISS) [DOI Link]

3. Sumita Garai, Sandra Vo, Lucy Blank, Frederick Xu, Jiong Chen, Duy Duong-Tran, Yize Zhao, Li Shen (2025) "H-VIP: Quantifying regional topological contributions from the brain network towards cognition."  pubished Frontiers in Radiology. [Archived Link] [DOI Link]

4. Tianqi Shang, Shu Yang, Tianhua Zhai, Weiqing He, Elizabeth Mamourian, Jiayu Zhang, Bojian Hou, Joseph Lee, Peiming Li, Duy Duong-Tran, Jason H. Moore, Marylyn D. Ritchie, Li Shen. (2025) "A novel computational analysis integrating social determinants information from EHR and literature with Alzheimer’s disease biological knowledge through large language model and knowledge graphs." published, Innovation in Aging Journal (IF=4.7). [DOI]

5. Jiong Chen, Matei Ionita, Yanbo Feng, Yinfeng Lu, Patryk Orzechowski, Sumita Garai, Kenneth Hassinger, Jingxuan Bao, Junhao Wen, Duy Duong-Tran, Joost Wagenaar, Michelle L Mckeague, Mark M. Painter, Divij Mathew, Ajinkya Pattekar, Allison R. Greenplate, E. John Wherry, Li Shen. (2025) "Automated Cytometric Gating with Human-Level Performance Using Bivariate Segmentation." Nature Communication  16 (1), 1576 (Nature Portfolio Publisher, IF= 14.7 + Top 5 Publishing Journal, h-index=375). [Editor Choice] [DOI Link] [Archived Link] 

6. Jingxuan Bao, Junhao Wen, Changgee Chang, Shizhuo Mu, Jiong Chen, Manu Shivakumar, Yuhan Cui, Guray Erus, Zhijian Yang, Shu Yang, Zixuan Wen, for the Alzheimer’s Disease Neuroimaging Initiative, Yize Zhao, Dokyoon Kim, Duy Duong-Tran, Andrew J. Saykin, Bingxin Zhao, Christos Davatzikos, Qi Long, Li Shen. (2025) "GIANT: Genetically informed brain atlas for enhancing brain imaging genomics." Nature Communication 16 (1), 3524 (Nature Portfolio Publisher, IF= 14.7 + Top 5 Publishing Journal, h-index=375) [DOI Link]

--- 2024 ---

7. Duy Duong-Tran*, Ralph Kaufmann*, Jiong Chen*, Xuan Wang, Sumita Garai, Fredericks Xu, Jingxuan Bao, Enrico Amico, Alan D. Kaplan, Giovanni Petri, Joaquin Goni, Yize Zhao, and Li Shen. (2024) "Homological landscape of human brain functional sub-circuits." Published in Journal of Mathematics (IF=2.5, CiteScore=3.6, Q1 Journal [Source: WoS]), Special Issue "Computer Graphics, Visualization and Medical Imaging: Theory and Applications." [DOI Link]

8. Duy Duong-Tran*, Nghi Nguyen*, Shizhuo Mu, Jiong Chen, Jingxuan Bao, Frederick Xu, Sumita Garai, Jose Cadena-Pico, Alan David Kaplan, Tianlong Chen, Yize Zhao, Li Shen, Joaquín Goñi. (2024) "A principled framework to assess information-theoretic fitness of brain functional sub-circuits." Published in Journal of Mathematics (Computational and Applied Mathematics) (IF=2.3, CiteScore=4.0 - at time of publication). [Dept-of-Energy OSTI LINK] [DOI Link] [Archived Link]

--- <=2023 ---

9. Abbas, K., Liu, M., Duong-Tran, D., Tipnis, U., Amico, E., Kaplan, A., Dzemidzic, M., Kareken, D., Ances, B., Harezlak, J., Goñi, J. (2023). "Tangent functional connectomes uncover more unique phenotypic traits.. Published in iScience Journal (Cell Press), IF= 6.01. [DOI Link]

10. B Chiêm, K Abbas, E Amico, Duy Duong-Tran, F Crevecoeur, J Goñi. (2023) "Improving Functional Connectome Fingerprinting with Degree-Normalization". Published in Brain Connectivity Journal 12 (2), 180-192. IF=3.4 (Source: Clarivate)

11. Enrico Amico, Kausar Abbas, Duy Duong-Tran, Uttara Tipnis, Meenusree Rajapandian, Evgeny Chumin, Mario Ventresca, Jaroslaw Harezlak, Joaquín Goñi. (2023) "Toward an information theoretical description of communication in brain networks". Published in Network Neuroscience Journal (Methods Section) 5 (3), pg. 646-665. IF=4.7 (2023).

12. Duy Duong-Tran, Kausar Abbas, Enrico Amico, Bernat Corominas-Murtra, Mario Dzemidzic, David Kareken, Mario Ventresca, Joaquín Goñi. (2022) "A morphospace of functional configuration to assess configural breadth based on brain functional networks". Published in Network Neuroscience Journal (Methods Section) 5 (3), 666-688

13. Kausar Abbas, Enrico Amico, Diana Otero Svaldi, Uttara Tipnis, Duy Duong-Tran, Mintao Liu, Meenusree Rajapandian, Jaroslaw Harezlak, Beau M Ances, Joaquín Goñi. (2022) "Graph embedding for functional fingerprinting". Published in NeuroImage Journal 221, 117181. IF=7.4 (2023, Source: MIT Press)

14. D Duong-Tran, R Dastoorian, L Wells. (2021) "Revisiting the one-sided EWMA control chart". Published in Journal of applied research on industrial engineering 9 (2), 151-164.

[Under Review/Revisions]

15.  Jungyoun Janice Min, Jingxuan Bao, Jae Young Baik, Junhao Wen, Yize Zhao, Paul M. Thompson,  Li Shen, DuyDuong-Tran*. "Brain-Body Signatures of Trait Anxiety Uniquely Characterized by Functional Dynamics, Allostatic Load and Gene Expression." submitted, under-review: Nature Sub-journal. [Archived Link]

16. Xuan Wang, Duy Duong-Tran, Jorge Cortés. "Data-Driven Stabilization of Unknown Linear-Threshold Network Dynamics" submitted, under review - Journal of IEEE Transaction on Automatic Control (Impact Score of 4.6 and an SJR of 4.501)

17. Shu Yang*, Nhat Truong Pham*, Ziyang Li*, Jae Young Baik, Joseph Lee, Tianhua Zhai, Weicheng Yu, Bojian Hou, Tianqi Shang, Weiqing He, Duy Duong-Tran, Mayur Naik, Li Shen. (2025) "Advances in RNA secondary structure prediction and RNA modifications: Methods, tools, and applications" submitted, under review in Quantitative Biology Journal (Wiley Publisher - IF=1.0).  [Arvix Link]

[Manuscripts In Preparation]

18. Jiong Chen, Bojian Hou, Davoud D., Duy Duong-Tran, Li Shen. "Disentangling Homogeneous and Heterogeneous Representation of Human Functional Connectome via Graph Learning."