A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. - Abhishek Biswas; Dong Si; Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Jing He 002 (BIBM, 2011)

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. - Kamal Al-Nasr; Lin Chen 007; Dong Si; Desh Ranjan; Mohammad Zubair; Jing He 002 (BCB, 2012)

CryoEM skeleton length estimation using a decimated curve. - Andrew McKnight; Kamal Al-Nasr; Dong Si; Andrey N. Chernikov; Nikos Chrisochoides; Jing He 002 (BIBM Workshops, 2012)

Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. - Abhishek Biswas; Dong Si; Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Jing He 002 (J. Bioinform. Comput. Biol., 2012)

A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. - Kamal Al-Nasr; Lin Chen 007; Desh Ranjan; Mohammad Zubair; Dong Si; Jing He 002 (BCB, 2013)

Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. - Dong Si; Jing He 002 (BCB, 2013)

Orientations of beta-strand traces and near maximum twist. - Dong Si; Jing He 002 (BCB, 2014)

Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. - Dong Si; Jing He 002 (EMBC, 2014)

Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. - Jing He 002; Dong Si; Maryam Arab (ICIG (2), 2015)

Automatic Detection of Beta-barrel from Medium Resolution Cryo-EM Density Maps. - Dong Si (BCB, 2016)

Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy. - Rongjian Li; Dong Si; Tao Zeng; Shuiwang Ji; Jing He 002 (BIBM, 2016)

A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps. - Peter Collins; Dong Si (BCB, 2017)

Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool. - Michael Nissenson; Dong Si (BCB, 2017)

Comparison of Feature Reduction Methods and Machine Learning Models for Breast Cancer Diagnosis. - Todor K. Avramov; Dong Si (ICCDA, 2017)

Prediction of Injuries and Fatalities in Aviation Accidents through Machine Learning. - R. Alan Burnett; Dong Si (ICCDA, 2017)

Analyze NYC Transportation to Mitigate Speeding and Explore New Business Models Using Machine Learning. - Joe Ma; Dong Si (ICCDA, 2017)

Addressing Forest Management Challenges by Refining Tree Cover Type Classification with Machine Learning Models. - Duncan Macmichael; Dong Si (IRI, 2017)

Genetic Algorithm Based Beta-Barrel Detection for Medium Resolution Cryo-EM Density Maps. - Albert Ng; Dong Si (ISBRA, 2017)

Classification of Brain Activity Using Brainwaves Recorded by Consumer-grade EEG Devices. - Elizaveta Kosiachenko; Dong Si (MDA, 2017)

Anomaly Detection from Kepler Satellite Time-Series Data. - Nathaniel Grabaskas; Dong Si (MLDM, 2017)

Prediction of Insurance Claim Severity Loss Using Regression Models. - Ruth M. Ogunnaike; Dong Si (MLDM, 2017)

Deep Learning for Resolution Validation of Three Dimensional Cryo-Electron Microscopy Density Maps. - Todor K. Avramov; Dong Si (BCB, 2018)

EMNets: A Convolutional Autoencoder for Protein Surface Retrieval Based on Cryo-Electron Microscopy Imaging. - Jingjing Yang; Renzhi Cao; Dong Si (BCB, 2018)

Who's Next: Evaluating Attrition with Machine Learning Algorithms and Survival Analysis. - Jessica Frierson; Dong Si (BigData Congress, 2018)

Cancer Type Prediction and Classification Based on RNA-sequencing Data. - Yi-Hsin Hsu; Dong Si (EMBC, 2018)

Machine Learning of Spatiotemporal Bursting Behavior in Developing Neural Networks. - Jewel Yun-Hsuan Lee; Michael Stiber; Dong Si (EMBC, 2018)

Parkinson's Disease Classification of mPower Walking Activity Participants. - Benjamin Pittman; Reza Hosseini Ghomi; Dong Si (EMBC, 2018)

GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM Maps. - Albert Ng; Adedayo Odesile; Dong Si (ISBRA, 2018)

Machine Learning Classification of Tree Cover Type and Application to Forest Management. - Duncan Macmichael; Dong Si (Int. J. Multim. Data Eng. Manag., 2018)

Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing. - Albert Ng; Dong Si (J. Comput. Biol., 2018)

Automated Threshold Selection for Cryo-EM Density Maps. - Jonas Pfab; Dong Si (BCB, 2019)

Traveler's Next Activity Predication with Location-Based Social Network Data. - Diem To; Dong Si; Ying Chen (PredictGIS@SIGSPATIAL, 2019)

Scaling up Prediction of Psychosis by Natural Language Processing. - Dong Si; Sunny Chieh Cheng; Ruiwen Xing; Chang Liu; Hoi Yan Wu (ICTAI, 2019)

A Wizard-of-Oz Interface and Persona-based Methodology for Collecting Health Counseling Dialog. - William R. Kearns; Neha Kaura; Myra Divina; Cuong Vo; Dong Si; Teresa Ward; Weichao Yuwen (CHI Extended Abstracts, 2020)

TopQA: a topological representation for single-model protein quality assessment with machine learning. - John Smith; Matthew Conover; Natalie Stephenson; Jesse Eickholt; Dong Si; Miao Sun; Renzhi Cao (Int. J. Comput. Biol. Drug Des., 2020)

Dementia Detection using Transformer-Based Deep Learning and Natural Language Processing Models. - Ploypaphat Saltz; Shih Yin Lin; Sunny Chieh Cheng; Dong Si (ICHI, 2021)

Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM. - Dong Si; Andrew Nakamura; Runbang Tang; Haowen Guan; Jie Hou 001; Ammaar Firozi; Renzhi Cao; Kyle Hippe; Minglei Zhao (CoRR, 2021)

Self-Attention Generative Adversarial Network for Iterative Reconstruction of CT Images. - Ruiwen Xing; Thomas Humphries; Dong Si (CoRR, 2021)

A Raspberry Pi-Based Traumatic Brain Injury Detection System for Single-Channel Electroencephalogram. - Navjodh Singh Dhillon; Agustinus Sutandi; Manoj Vishwanath; Miranda M. Lim; Hung Cao; Dong Si (Sensors, 2021)

Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignments. - Mahdi Rahbar; Rahul Kumar Chauhan; Pankil Nimeshbhai Shah; Renzhi Cao; Dong Si; Jie Hou 001 (BCB, 2022)

DeepTracer-Denoising: Deep Learning for 3D Electron Density Map Denoising. - Haowen Guan; Dong Si (BIBM, 2022)

Psychosis iREACH: Reach for Psychosis Treatment using Artificial Intelligence. - Jonathan Lee; Sarah Kopelovich; Sunny Chieh Cheng; Dong Si (BIBM, 2022)

ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features. - Kyle Hippe; Cade Lilley; Joshua William Berkenpas; Ciri Chandana Pocha; Kiyomi Kishaba; Hui Ding; Jie Hou 001; Dong Si; Renzhi Cao (Briefings Bioinform., 2022)

Neural representations of cryo-EM maps and a graph-based interpretation. - Nathan Ranno; Dong Si (BMC Bioinform., 2022)

Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps. - Andrew Nakamura; Hanze Meng; Minglei Zhao; Fengbin Wang; Jie Hou 001; Renzhi Cao; Dong Si (Briefings Bioinform., 2023)

ComplexQA: a deep graph learning approach for protein complex structure assessment. - Lei Zhang; Sheng Wang; Jie Hou 001; Dong Si; Junyong Zhu; Renzhi Cao (Briefings Bioinform., 2023)

Building Personality-Adaptive Conversational AI for Mental Health Therapy. - Sugam Jaiswal; Joyce Lee; Joe Berria; Raviteja Tanikella; Annuska Zolyomi; Muhammad Aurangzeb Ahmad; Dong Si (BCB, 2024)

iCare - An AI - Powered Virtual Assistant for Mental Health. - Remya Mavila; Sugam Jaiswal; Raghav Naswa; Weichao Yuwen; Bill Erdly; Dong Si (ICHI, 2024)

Assessing Empathy in Mental Health Caregivers using Conversational AI. - Raghav Naswa; Sugam Jaiswal; Remya Mavila; Weichao Yuwen; Bill Erdly; Dong Si (ICHI, 2024)

Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration. - Jason Chen; Ayisha Zia; Albert Luo; Hanze Meng; Fengbin Wang; Jie Hou 001; Renzhi Cao; Dong Si (Briefings Bioinform., 2024)

Advancing Protein-Ligand Binding Site Prediction with 3D Instance Segmentation Techniques. - Esha Rajesh Gavali; Jie Hou 001; Renzhi Cao; Dong Si (CAI, 2025)

Geometric Deep Learning for Multiple Conformation Generation from Electron Density Images. - Saurav Jayakumar; Jie Hou 001; Renzhi Cao; Dong Si (CAI, 2025)

Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps. - Xin Ma; Dong Si (Comput. Biol. Chem., 2025)