*: Equal First-Author Contributions; **: Corresponding/Supervising Author
IF=Impact Factor and Journal Ranking/Quantiles
h-index=Google Scholar Index
[J] = Journal; [C] = Conference Proceedings
Disclaimer: In Computer Science and Bioinformatics, Conference Proceedings are considered esteemed research outputs. For more information on Conference Ranking, please visit: https://csrankings.org/
--- 2026 ---
[J] 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 Press). [DOI]
[C] Duy Minh Ho Nguyen, Trung Quoc Nguyen, Ha Thi Hong Le, Mai Thanh Nhat Truong, TrungTin Nguyen, Nhat Ho, Khoa D Doan, Duy Duong-Tran, Li Shen, Daniel Sonntag, James Zou, Mathias Niepert, Hyojin Kim, Jonathan E Allen. "FACET: A Fragment-Aware Conformer Ensemble Transformer." accepted, in-press International Conference in Learning Representation (ICLR, Rank A+ in Comp. Sci)
[C] Chen J*, Xu C*, Yu H*, Shen K*, Carroll A*, Wu N*, Mercado MF, Bao J, Yang S, Duong-Tran D, Garai S, Li M, Luo W^, Xu M^, Shen L^. "MSCA-Net: Multi-Modal Cell Segmentation for Spatial Transcriptomics." accepted, in-press AMIA-IS’26: AMIA 2026 Amplify - Informatics Summit, May 18-21, 2026, Denver, CO. *co-first authors, ^co-corresponding authors.
Garai S, Chen H, Xu F, Duong-Tran D, Chaudhari P, Davatzikos C, Brown BC, Shen L. "Robust FDR Control for Neuroimaging-based Classification via Knockoffs." accepted, in-press AMIA-IS’26: AMIA 2026 Amplify - Informatics Summit, May 18-21, 2026, Denver, CO
[C] Farica Zhuang, Shu Yang, Zixuan Wen, Duy Duong-Tran, Li Shen. "Interpretable Alzheimer’s Diagnosis via Multimodal Fusion of Regional Brain Experts" under-review in 2026 IEEE International Conference on Health and Informatics (IEEE ICHI). [Arxiv Link]
[J] 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." under consideration Nature Sub-journal. [Archived Link]
[J] Xuan Wang, Duy Duong-Tran, Jorge Cortés. "Data-Driven Stabilization of Unknown Linear-Threshold Network Dynamics" under review - Journal of IEEE Transaction on Automatic Control (Impact Score of 4.6 and an SJR of 4.501)
[J] Sophie Kearney∗ and Shu Yang∗, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, Jason H. Moore, Marylyn D. Ritchie, and Li Shen. "Interpretable Few-Shot Alzheimer’s Disease Prediction on Multimodal Biomedical Data with Tabular LLMs." under review - Journal of Biomedical and Health Informatics (JBHI)
[J] Frederick Xu, Duy Duong-Tran, Heng Huang, Andrew Saykin, Paul Thompson, Christos Davatzikos, Yize Zhao, Li Shen. "Characterizing Amyloid Pathogenic Spread in Alzheimer’s Disease Through A Network Diffusion Model." under review - IEEE Transactions on Computational Biology and Bioinformatics (TCBB) Journal
[C] Wu R*, Shukla R*, Chen H, Duong-Tran D, Nguyen DMH, Niepert M, Beeche C, Gee J, Duda J, Sharma R, Davaztikos C, Witschey W, Hou B^, Shen L^. "Volumetric-to-Text: Native 3D Vision–Language Modeling for Automated CT Report Generation." under review - 29th International conference on medical image computing and computer assisted intervention (MICCAI, Rank A*)
[J] Jiong Chen, Duy Duong-Tran, Davoud Ataee Tarzanagh, Bojian Hou, Jingxuan Bao, Nghi Nguyen, Chentianye Xu, Min Xu, Li Shen. "Disentangling Homogeneous and Heterogeneous Representation of Human Functional Connectome via Graph Learning." under consideration Nature Sub-journal.
[J] Shu Yang*, Nhat Truong Pham*, Jae Young Baik, Joseph Lee, Tianhua Zhai, Weicheng Yu, Bojian Hou, Tianqi Shang, Weiqing He, Duy Duong-Tran, Li Shen. (2025) "Advances in RNA secondary structure prediction and RNA modifications: Methods, tools, and applications" in-preparation-to submit Wiley WIRE Journal (IF=11). [Arvix Link]
[J] Boning Tong, Trang Cao, Duy Duong-Tran, Andrew Saykin, Alex Fornito, Li Shen. "Mode-based Decomposition of Multimodality Reveals Relationships across Spatial Scales in Alzheimer’s Disease." in-preparation-to submit Nature Aging.
--- 2025 ---
[J] 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]
[J] 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." published Frontiers in Radiology. [Archived Link] [DOI Link]
[J] 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]
[J] 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]
[J] 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]
[C] Jungyoun Janice Min, Jiong Chen, Jingxuan Bao, Shu Yang, Yize Zhao, Li Shen, Duy Duong-Tran*. "Integrating Slow Neural Oscillations and Physiological Burden for Train Anxiety Prediction." accepted, in-press in 2025 NeurIPS Workshop Time-Series for Health (TS4H) [Thirty-Ninth Annual Conference on Neural Information Processing Systems, Rank A++].
[C] Frederick Xu, Duy Duong-Tran, Heng Huang, Andrew Saykin, Paul Thompson, Christos Davatzikos, Yize Zhao, Li Shen. "Quantifying Amyloid Spread in Alzheimer’s Disease Through A Network Diffusion Model." accepted, in-press in 2025 Association for Computing Machinery on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Philadelphia, PA.
Sophie Kearney, Shu Yang, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, Jason Moore, Marylyn Ritchie, Li Shen. "Few-Shot Alzheimer’s Disease Diagnosis on Tabular Biomarker Data with Large Language Models." accepted, in-press in 2025 Association for Computing Machinery on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Philadelphia, PA.
[C] Chen H, Shukla R, Wu R, Yang S, Duong-Tran D, Nguyen DMH, Niepert M, Beeche C, Gee J, Duda J, Sharma R, Davaztikos C, Witschey W, Hou B, Shen L. (2025) "Adapting Vision-Language Models for 3D CT/MRI Understanding on PMBB via Slice Selection and Explanation Analysis." ICCV-VADH’25: ICCV Workshop on Vision-Based AI for Digital Health: From Pixels to Practice, Oct 19-20, 2025, in press
[C] Duy Minh Ho Nguyen, Trung Quoc Nguyen, Ha Thi Hong Le, Mai Thanh Nhat Truong, TrungTin Nguyen, Nhat Ho, Khoa D Doan, Duy Duong-Tran, Li Shen, Daniel Sonntag, James Zou, Mathias Niepert, Hyojin Kim, Jonathan E Allen. "From Fragments to Geometry : A Unified Graph Transformer for Molecular Representation from Conformer Ensembles." accepted in the 2025 International Conference on Machine Learning (ICML) 2nd Workshop on Generative AI and Biology (GenBIO)
[C] Bach Viet Nguyen, Tianlong Chen, Shu Yang, Bojian Hou, Li Shen, Duy Duong-Tran. "Evaluating topological fitness of human brain-inspired sub-circuits in Echo State Networks". (2025) in-press Proceedings of Machine Learning Research (PMLR) - 2025 Association for the Advancement of Artificial Intelligence (AAAI): Bridge Program's AI for Medical Health (AIMedHealth), Philadelphia, Pennsylvania, February, 2025. [Archived] [Honor: Runner-up paper Award!]
[C] Joseph Lee, Shu Yang, Jae Young Baik, Xiaoxi Liu, Zhen Tan, Dawei Li, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, and Li Shen. "Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models." (2025) in-press 2025 American Medical Informatics Association Informatics Summit (AMIA-IS), Pittsburgh, PA. [Honor: Marco Ramoni Distinguished Paper Award for Translational Bioinformatics]
--- 2024 ---
[J] 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]
[J] 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]
[C] Dawei Li, Shu Yang, Zhen Tan, Jae Young Baik, Sukwon Yun, Joseph Lee, Aaron Chacko, Bojian Hou, Duy Duong-Tran, Ying Ding, Huan Liu, Li Shen, Tianlong Chen "DALK: Dynamic Co-Augmentation of Large Language Models and Knowledge Graph to answer Alzheimer’s Disease Questions with Scientific Literature." (2024) published in the 62nd Annual Meeting - Empirical Methods on Natural Language Processing (EMNLP 2024, Rank A++ in CSRanking). [DOI Link] [Archived Link]
[C] Duy Nguyen, An T. Le, Nghiem Diep, Trung Nguyen, Duy Duong-Tran, Binh T. Nguyen, Jan Peters, Li Shen, Mathias Niepert, Daniel Sonntag. "Dude: Dual Distribution-Aware Context Prompt Learning For Large Vision-Language Model." (2024) published in the 16th Asian Conference on Machine Learning (ACML; Rank: A) [Published Link] [Archived Link]
[C] Nghi Nguyen, Tao Hou, Enrico Amico, Jinny Zheng, Huajun Huang, Alan D. Kaplan, Giovanni Petri, Joaquin Goni, Ralph Kaufmann, Yize Zhao, Li Shen, Duy Duong-Tran**. "Volume-optimal persistence homological scaffolds of hemodynamic networks covary with MEG theta-alpha aperiodic dynamics." (2024) Conference Paper published in the 2024 Medical Image Computing and Computer Assisted Intervention (MICCAI - Rank: A1). [Publication Link] [top 11% out of 2869 submissions]
[C] Duy Duong-Tran*, Mark Magsino*, Joaquin Goni, and Li Shen. "PRESERVING HUMAN LARGE-SCALE BRAIN CONNECTIVITY FINGERPRINT IDENTIFIABILITY WITH RANDOM PROJECTIONS." (2024) published in the 21st IEEE International Symposium on Biomedical Imaging (ISBI), IEEE Xplore Index, 2024. [DOI Link]
[C] Frederick H. Xu, Michael Gao, Jiong Chen, Sumita Garai, Duy Duong-Tran, Yize Zhao, Li Shen. (2024) "Topology-based Clustering of Functional Brain Networks in an Alzheimer’s Disease Cohort." (2024) Conference paper published in AMIA-IS’24: AMIA Informatics Summit. [Publication Link]
[C] Duong-Tran, D., Siqing Wei, Li Shen. "Theorizing neuro-induced relationships between cognitive diversity, motivation, grit and academic performance in multidisciplinary engineering education context." (2024) Conference Paper published in 2024 American Society of Engineering Education Conference, Portland, Oregon. [Publication Link]
[C] Frederick Xu, Duy Duong-Tran, Yize Zhao, Li Shen. "Caudal and Thalamic Segregation in White Matter Brain Network Communities in Alzheimer's Disease Population." (2024) published in IEEE-EMBS International Conference on Biomedical and Health Informatics (IEEE BHI). [Publication Link]
[C] Dachuan Song, Li Shen, Duy Duong-Tran, Xuan Wang. "Subject and Task Fingerprint using Dynamics Reconstruction from fMRI Time-series Data." (2024) accepted with oral presentation category (top 38 out of 204 submissions) in the 15th Association for Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). [2024] ACM-BCB has h5-index=28 and h5-median=50. [DOI Link]
--- 2023 ---
[J] 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]
[J] 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)
[J] 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).
[C] S Garai, F Xu, D Duong-Tran, Y Zhao, L Shen. "Mining Correlation between Fluid Intelligence and Whole-brain Large Scale Structural Connectivity". (2023) Published in AMIA Summits on Translational Science Proceedings, 225
[C] F Xu, S Garai, D Duong-Tran, AJ Saykin, Y Zhao, L Shen. "Consistency of Graph Theoretical Measurements of Alzheimer’s Disease Fiber Density Connectomes Across Multiple Parcellation Scales". (2022) pg 1323-1328. published in 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Acceptance Rate=19.65%.
--- Before 2022 ---
[J] 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
[J] 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)
[J] 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.
