Scientific publications on Web 3.0. - Mark Goetz; Tim Clark; Sudeshna Das 001; Lisa Girard (ELPUB, 2009)

Building biomedical web communities using a semantically aware content management system. - Sudeshna Das 001; Lisa Girard; Tom Green; Louis Weitzman; Alister Lewis-Bowen; Tim Clark (Briefings Bioinform., 2009)

An open annotation ontology for science on web 3.0. - Paolo Ciccarese; Marco Ocana; Leyla Jael García Castro; Sudeshna Das 001; Tim Clark (J. Biomed. Semant., 2011)

eXframe: reusable framework for storage, analysis and visualization of genomics experiments. - Amit U. Sinha; Emily Merrill; Scott A. Armstrong; Timothy W. Clark; Sudeshna Das 001 (BMC Bioinform., 2011)

Translating standards into practice - One Semantic Web API for Gene Expression. - Helena F. Deus; Eric Prud'hommeaux; Michael Miller 001; Jun Zhao 003; James Malone; Tomasz Adamusiak; Jamie P. McCusker; Sudeshna Das 001; Philippe Rocca-Serra; Ronan Fox; M. Scott Marshall (J. Biomed. Informatics, 2012)

Using eXframe to Build Semantic Web Genomics Repositories. - Emily Merrill; Shannan J. Ho Sui; Stephane Corlosquet; Tim Clark; Sudeshna Das 001 (SWAT4LS, 2014)

Semantic Web repositories for genomics data using the eXframe platform. - Emily Merrill; Stephane Corlosquet; Paolo Ciccarese; Tim Clark; Sudeshna Das 001 (J. Biomed. Semant., 2014)

Pain Research Forum: application of scientific social media frameworks in neuroscience. - Sudeshna Das 001; Patricia G. Mccaffrey; Megan Talkington; Neil Andrews; Stephane Corlosquet; Adrian Ivinson; Tim Clark (Frontiers Neuroinformatics, 2014)

Natural Language Processing to Detect Cognitive Concerns in Electronic Health Records Using Deep Learning. - Zhuoqiao Hong; Colin G. Magdamo; Yi-han Sheu; Prathamesh Mohite; Ayush Noori; Elissa M. Ye; Wendong Ge; Haoqi Sun; Laura Brenner; Gregory K. Robbins; Shibani Mukerji; Sahar Zafar; et al. (CoRR, 2020)

Using Deep Learning to Identify Patients with Cognitive Impairment in Electronic Health Records. - Tanish Tyagi; Colin G. Magdamo; Ayush Noori; Zhaozhi Li; Xiao Liu; Mayuresh Deodhar; Zhuoqiao Hong; Wendong Ge; Elissa M. Ye; Yi-han Sheu; Haitham Alabsi; Laura Brenner; et al. (CoRR, 2021)

Robust Segmentation of Brain MRI in the Wild with Hierarchical CNNs and No Retraining. - Benjamin Billot; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Juan Eugenio Iglesias (MICCAI (5), 2022)

Construction of a confounder-free clinical MRI dataset in the Mass General Brigham system for classification of Alzheimer's disease. - Matthew Leming; Sudeshna Das 001; Hyungsoon Im (Artif. Intell. Medicine, 2022)

Robust Segmentation of Brain MRI in the Wild with Hierarchical CNNs and no Retraining. - Benjamin Billot; Colin G. Magdamo; Sean E. Arnold; Sudeshna Das 001; Juan Eugenio Iglesias (CoRR, 2022)

Multi-confound regression adversarial network for deep learning-based diagnosis on highly heterogenous clinical data. - Matthew Leming; Sudeshna Das 001; Hyungsoon Im (CoRR, 2022)

Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets. - Benjamin Billot; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Juan Eugenio Iglesias (CoRR, 2022)

Cortical Analysis of Heterogeneous Clinical Brain MRI Scans for Large-Scale Neuroimaging Studies. - Karthik Gopinath; Douglas N. Greve; Sudeshna Das 001; Steven E. Arnold; Colin G. Magdamo; Juan Eugenio Iglesias (MICCAI (8), 2023)

Classification of neurologic outcomes from medical notes using natural language processing. - Marta B. Fernandes; Navid Valizadeh; Haitham Alabsi; Syed A. Quadri; Ryan A. Tesh; Abigail A. Bucklin; Haoqi Sun; Aayushee Jain; Laura Brenner; Elissa M. Ye; Wendong Ge; Sarah I. Collens; et al. (Expert Syst. Appl., 2023)

AI-assisted prediction of differential response to antidepressant classes using electronic health records. - Yi-han Sheu; Colin G. Magdamo; Matthew Miller; Sudeshna Das 001; Deborah Blacker; Jordan W. Smoller (npj Digit. Medicine, 2023)

causalCmprsk: An R package for nonparametric and Cox-based estimation of average treatment effects in competing risks data. - Bella Vakulenko-Lagun; Colin G. Magdamo; Marie-Laure Charpignon; Bang Zheng; Mark W. Albers; Sudeshna Das 001 (Comput. Methods Programs Biomed., 2023)

Leveraging Pre-trained and Transformer-derived Embeddings from EHRs to Characterize Heterogeneity Across Alzheimer's Disease and Related Dementias. - Matthew West 004; Colin G. Magdamo; Lily Cheng; Yingnan He; Sudeshna Das 001 (CoRR, 2024)

Multi Scale Graph Neural Network for Alzheimer's Disease. - Anya Chauhan; Ayush Noori; Zhaozhi Li; Yingnan He; Michelle M. Li; Marinka Zitnik; Sudeshna Das 001 (CoRR, 2024)

Automated phenotyping of mild cognitive impairment and Alzheimer's disease and related dementias using electronic health records. - Ruoqi Wei; Stephanie S. Buss; Rebecca Milde; Marta Fernandes; Daniel Sumsion; Elijah Davis; Wan-Yee Kong; Yiwen Xiong; Jet Veltink; Samvrit Rao; Tara M. Westover; Lydia Petersen; et al. (Int. J. Medical Informatics, 2025)

"Recon-all-clinical": Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI. - Karthik Gopinath; Douglas N. Greve; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Oula Puonti; Juan Eugenio Iglesias (Medical Image Anal., 2025)

A GPT-4o-powered framework for identifying cognitive impairment stages in electronic health records. - Yu Leng; Yingnan He; Samad Amini; Colin G. Magdamo; Ioannis Paschalidis; Shibani S. Mukerji; Lidia M. V. R. Moura; M. Brandon Westover; Ana-Maria Vranceanu; Christine S. Ritchie; Deborah Blacker; John R. Dickson; et al. (npj Digit. Medicine, 2025)

Evaluating GPT's Capability in Identifying Stages of Cognitive Impairment from Electronic Health Data. - Yu Leng; Yingnan He; Colin G. Magdamo; Ana-Maria Vranceanu; Christine S. Ritchie; Shibani S. Mukerji; Lidia M. V. R. Moura; John R. Dickson; Deborah Blacker; Sudeshna Das 001 (CoRR, 2025)

End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images. - Jesper Duemose Nielsen; Karthik Gopinath; Andrew Hoopes; Adrian V. Dalca; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Axel Thielscher; Juan Eugenio Iglesias; Oula Puonti (CoRR, 2025)