Reproducible evaluation of classification methods in Alzheimer's disease: framework and application to MRI and PET data. - Jorge Samper-González; Ninon Burgos; Simona Bottani; Sabrina Fontanella; Pascal Lu; Arnaud Marcoux; Alexandre Routier; Jérémy Guillon; Michael Bacci; Junhao Wen 002; Anne Bertrand; Hugo Bertin; et al. (CoRR, 2018)

Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimers disease. - Junhao Wen 002; Jorge Samper-González; Simona Bottani; Alexandre Routier; Ninon Burgos; Thomas Jacquemont; Sabrina Fontanella; Stanley Durrleman; Stéphane Epelbaum; Anne Bertrand; Olivier Colliot (CoRR, 2018)

An Automated Pipeline for the Analysis of PET Data on the Cortical Surface. - Arnaud Marcoux; Ninon Burgos; Anne Bertrand; Marc Teichmann; Alexandre Routier; Junhao Wen 002; Jorge Samper-González; Simona Bottani; Stanley Durrleman; Marie Odile Habert; Olivier Colliot (Frontiers Neuroinformatics, 2018)

Reproducible evaluation of classification methods in Alzheimer's disease: Framework and application to MRI and PET data. - Jorge Samper-González; Ninon Burgos; Simona Bottani; Sabrina Fontanella; Pascal Lu; Arnaud Marcoux; Alexandre Routier; Jérémy Guillon; Michael Bacci; Junhao Wen 002; Anne Bertrand; Hugo Bertin; et al. (NeuroImage, 2018)

Convolutional Neural Networks for Classification of Alzheimer's Disease: Overview and Reproducible Evaluation. - Junhao Wen 002; Elina Thibeau-Sutre; Jorge Samper-González; Alexandre Routier; Simona Bottani; Stanley Durrleman; Ninon Burgos; Olivier Colliot (CoRR, 2019)

nipy/nipype: 1.2.3. - Oscar Esteban; Christopher J. Markiewicz; Erik Ziegler; David Gage Ellis; Dorota Jarecka; Hans J. Johnson; Michael Philipp Notter; Christopher Burns 002; Alexandre Manhães-Savio; Carlo Hämäläinen; Benjamin Yvernault; Taylor Salo; et al. (Zenodo, 2019)

nipy/nipype: 1.3.0-rc1. - Oscar Esteban; Christopher J. Markiewicz; Dorota Jarecka; Erik Ziegler; Hans J. Johnson; Christopher Burns 002; Alexandre Manhães-Savio; Carlo Hämäläinen; Michael Philipp Notter; Benjamin Yvernault; David Gage Ellis; Taylor Salo; et al. (Zenodo, 2019)

nipy/nipype: 1.3.0. - Oscar Esteban; Christopher J. Markiewicz; Dorota Jarecka; Erik Ziegler; Hans J. Johnson; Christopher Burns 002; Alexandre Manhães-Savio; Carlo Hämäläinen; Michael Philipp Notter; Benjamin Yvernault; David Gage Ellis; Taylor Salo; et al. (Zenodo, 2019)

nipy/nipype: 1.4.0. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Hans J. Johnson; Erik Ziegler; Alexandre Manhães-Savio; Dorota Jarecka; David Gage Ellis; Benjamin Yvernault; Carlo Hämäläinen; Michael Philipp Notter; Taylor Salo; et al. (Zenodo, 2019)

MAGIC: Multi-scale Heterogeneity Analysis and Clustering for Brain Diseases. - Junhao Wen 002; Erdem Varol; Ganesh B. Chand; Aristeidis Sotiras; Christos Davatzikos (MICCAI (7), 2020)

Smile-GANs: Semi-supervised clustering via GANs for dissecting brain disease heterogeneity from medical images. - Zhijian Yang; Junhao Wen 002; Christos Davatzikos (CoRR, 2020)

Convolutional neural networks for classification of Alzheimer's disease: Overview and reproducible evaluation. - Junhao Wen 002; Elina Thibeau-Sutre; Mauricio Diaz-Melo; Jorge Samper-González; Alexandre Routier; Simona Bottani; Didier Dormont; Stanley Durrleman; Ninon Burgos; Olivier Colliot (Medical Image Anal., 2020)

nipy/nipype: 1.4.1. - Oscar Esteban; Christopher J. Markiewicz; Hans J. Johnson; Erik Ziegler; Alexandre Manhães-Savio; Dorota Jarecka; Christopher Burns 002; David Gage Ellis; Carlo Hämäläinen; Michael Philipp Notter; Benjamin Yvernault; Taylor Salo; et al. (Zenodo, 2020)

nipy/nipype: 1.4.2. - Oscar Esteban; Christopher J. Markiewicz; Hans J. Johnson; Erik Ziegler; Alexandre Manhães-Savio; Dorota Jarecka; Christopher Burns 002; David Gage Ellis; Carlo Hämäläinen; Michael Philipp Notter; Benjamin Yvernault; Taylor Salo; et al. (Zenodo, 2020)

nipy/nipype: 1.5.0. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2020)

nipy/nipype: 1.5.1. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2020)

Disentangling brain heterogeneity via semi-supervised deep-learning and MRI: dimensional representations of Alzheimer's Disease. - Zhijian Yang; Ilya M. Nasrallah; Haochang Shou; Junhao Wen 002; Jimit Doshi; Mohamad Habes; Güray Erus; Ahmed Abdulkadir; Susan M. Resnick; David A. Wolk; Christos Davatzikos (CoRR, 2021)

Multidimensional representations in late-life depression: convergence in neuroimaging, cognition, clinical symptomatology and genetics. - Junhao Wen 002; Cynthia H. Y. Fu; Duygu Tosun; Yogasudha Veturi; Zhijian Yang; Ahmed Abdulkadir; Elizabeth Mamourian; Dhivya Srinivasan; Jingxuan Bao; Güray Erus; Haochang Shou; Mohamad Habes; et al. (CoRR, 2021)

Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies. - Alexandre Routier; Ninon Burgos; Mauricio Diaz-Melo; Michael Bacci; Simona Bottani; Omar El-Rifai; Sabrina Fontanella; Pietro Gori; Jérémy Guillon; Alexis Guyot; Ravi Hassanaly; Thomas Jacquemont; et al. (Frontiers Neuroinformatics, 2021)

Predicting the progression of mild cognitive impairment using machine learning: A systematic, quantitative and critical review. - Manon Ansart; Stéphane Epelbaum; Giulia Bassignana; Alexandre Bône; Simona Bottani; Tiziana Cattai; Raphaël Couronné; Johann Faouzi; Igor Koval; Maxime Louis; Elina Thibeau-Sutre; Junhao Wen 002; et al. (Medical Image Anal., 2021)

Reproducible Evaluation of Diffusion MRI Features for Automatic Classification of Patients with Alzheimer's Disease. - Junhao Wen 002; Jorge Samper-González; Simona Bottani; Alexandre Routier; Ninon Burgos; Thomas Jacquemont; Sabrina Fontanella; Stanley Durrleman; Stéphane Epelbaum; Anne Bertrand; Olivier Colliot (Neuroinformatics, 2021)

nipy/nipype: 1.7.0. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2021)

Preference Matrix Guided Sparse Canonical Correlation Analysis for Genetic Study of Quantitative Traits in Alzheimer's Disease. - Jiahang Sha; Jingxuan Bao; Kefei Liu 001; Shu Yang 009; Zixuan Wen; Yuhan Cui; Junhao Wen 002; Christos Davatzikos; Jason H. Moore; Andrew J. Saykin; Qi Long; Li Shen 001 (BIBM, 2022)

Surreal-GAN: Semi-Supervised Representation Learning via GAN for uncovering heterogeneous disease-related imaging patterns. - Zhijian Yang; Junhao Wen 002; Christos Davatzikos (ICLR, 2022)

Subtyping brain diseases from imaging data. - Junhao Wen 002; Erdem Varol; Zhijian Yang; Gyujoon Hwang; Dominique Dwyer; Anahita Fathi Kazerooni; Paris Alexandros Lalousis; Christos Davatzikos (CoRR, 2022)

Multi-scale semi-supervised clustering of brain images: Deriving disease subtypes. - Junhao Wen 002; Erdem Varol; Aristeidis Sotiras; Zhijian Yang; Ganesh B. Chand; Güray Erus; Haochang Shou; Ahmed Abdulkadir; Gyujoon Hwang; Dominic B. Dwyer; Alessandro Pigoni; Paola Dazzan; et al. (Medical Image Anal., 2022)

nipy/nipype: 1.7.1. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2022)

nipy/nipype: 1.8.0. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2022)

nipy/nipype: 1.8.1. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2022)

nipy/nipype: 1.8.3. - Oscar Esteban; Christopher J. Markiewicz; Christopher Burns 002; Mathias Goncalves; Dorota Jarecka; Erik Ziegler; Shoshana Berleant; David Gage Ellis; Basile Pinsard; Cindee Madison; Michael Waskom; Michael Philipp Notter; et al. (Zenodo, 2022)

Shape analysis of amygdala atrophy using SPHARM-OT. - Zexuan Wang; Jiong Chen; Wenxi Yang; Sumita Garai; Frederick H. Xu; Junhao Wen 002; Christos Davatzikos; Li Shen 001 (Image Processing, 2023)

Gene-SGAN: a method for discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering. - Zhijian Yang; Junhao Wen 002; Ahmed Abdulkadir; Yuhan Cui; Güray Erus; Elizabeth Mamourian; Randa Melhem; Dhivya Srinivasan; Sindhuja T. Govindarajan; Jiong Chen; Mohamad Habes; Colin L. Masters; et al. (CoRR, 2023)

Applications of generative adversarial networks in neuroimaging and clinical neuroscience. - Rongguang Wang; Vishnu Bashyam; Zhijian Yang; Fanyang Yu; Vasiliki Tassopoulou; Sai Spandana Chintapalli; Ioanna Skampardoni; Lasya P. Sreepada; Dushyant Sahoo; Konstantina S. Nikita; Ahmed Abdulkadir; Junhao Wen 002; et al. (NeuroImage, 2023)

Multiscale functional connectivity patterns of the aging brain learned from harmonized rsfMRI data of the multi-cohort iSTAGING study. - Zhen Zhou 004; Hongming Li; Dhivya Srinivasan; Ahmed Abdulkadir; Ilya M. Nasrallah; Junhao Wen 002; Jimit Doshi; Güray Erus; Elizabeth Mamourian; R. Nick Bryan; David A. Wolk; Lori L. Beason-Held; et al. (NeuroImage, 2023)

Brain-wide genome-wide colocalization study for integrating genetics, transcriptomics and brain morphometry in Alzheimer's disease. - Jingxuan Bao; Junhao Wen 002; Zixuan Wen; Shu Yang 009; Yuhan Cui; Zhijian Yang; Güray Erus; Andrew J. Saykin; Qi Long; Christos Davatzikos; Li Shen 001 (NeuroImage, 2023)

Mutually-Constrained Cross-Sectional and Longitudinal Non-Negative Matrix Factorization: Application to Modeling Brain Aging Trajectories. - Ioanna Skampardoni; Junhao Wen 002; Güray Erus; Haochang Shou; Konstantina S. Nikita; Christos Davatzikos (ISBI, 2024)

Multiscale Estimation of Morphometricity for Revealing Neuroanatomical Basis of Cognitive Traits. - Zixuan Wen; Jingxuan Bao; Shu Yang 009; Junhao Wen 002; Qipeng Zhan; Yuhan Cui; Güray Erus; Zhijian Yang; Paul M. Thompson; Yize Zhao; Christos Davatzikos; Li Shen 001 (ISBI, 2024)

Dimensional Neuroimaging Endophenotypes: Neurobiological Representations of Disease Heterogeneity Through Machine Learning. - Junhao Wen 002; Mathilde Antoniades; Zhijian Yang; Gyujoon Hwang; Ioanna Skampardoni; Rongguang Wang; Christos Davatzikos (CoRR, 2024)

Interpretable deep clustering survival machines for Alzheimer's disease subtype discovery. - Bojian Hou; Zixuan Wen; Jingxuan Bao; Richard Zhang; Boning Tong; Shu Yang 009; Junhao Wen 002; Yuhan Cui; Jason H. Moore; Andrew J. Saykin; Heng Huang; Paul M. Thompson; et al. (Medical Image Anal., 2024)