Representing and comparing protein structures as paths in three-dimensional space. - Degui Zhi; S. Sri Krishna; Haibo Cao; Pavel A. Pevzner; Adam Godzik (BMC Bioinform., 2006)

AliWABA: alignment on the web through an A-Bruijn approach. - Neil Christopher Jones; Degui Zhi; Benjamin J. Raphael (Nucleic Acids Res., 2006)

Discovery and analysis of mosaic arrangements in biological sequences and structures. - Degui Zhi (2006)

Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly. - Degui Zhi; Uri Keich; Pavel A. Pevzner; Steffen Heber; Haixu Tang (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Alignment-free local structural search by writhe decomposition. - Degui Zhi; Maxim Shatsky; Steven E. Brenner (Bioinform., 2010)

Length bias correction for RNA-seq data in gene set analyses. - Liyan Gao; Zhide Fang; Kui Zhang; Degui Zhi; Xiangqin Cui (Bioinform., 2011)

Genotype calling from next-generation sequencing data using haplotype information of reads. - Degui Zhi; Jihua Wu; Nianjun Liu; Kui Zhang (Bioinform., 2012)

Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads. - Kui Zhang; Degui Zhi (Bioinform., 2013)

Clinical Named Entity Recognition Using Deep Learning Models. - Yonghui Wu; Min Jiang 007; Jun Xu 007; Degui Zhi; Hua Xu 001 (AMIA, 2017)

Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. - Ardalan Naseri; Xiaoming Liu; Shaojie Zhang 001; Degui Zhi (RECOMB, 2017)

Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. - Jing An; Mandana Salimi; Anupama E. Gururaj; Cui Tao; Degui Zhi; Hua Xu 001 (AMIA, 2018)

Asthma Onset Prediction Using Structured EMR Data. - Yang Xiang 003; Jun Xu 007; Jingcheng Du; Degui Zhi; Cui Tao (AMIA, 2018)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. - Xiaoming Liu; Lei Xie 006; Zhijin Wu; Kai Wang 063; Zhongming Zhao; Jianhua Ruan; Degui Zhi (BMC Bioinform., 2018)

A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. - Laila Rasmy; Yonghui Wu; Ningtao Wang; Xin Geng; W. Jim Zheng; Fei Wang 001; Hulin Wu; Hua Xu 001; Degui Zhi (J. Biomed. Informatics, 2018)

Efficient haplotype matching between a query and a panel for genealogical search. - Ardalan Naseri; Erwin Holzhauser; Degui Zhi; Shaojie Zhang 001 (Bioinform., 2019)

Multi-allelic positional Burrows-Wheeler transform. - Ardalan Naseri; Degui Zhi; Shaojie Zhang 001 (BMC Bioinform., 2019)

Network context matters: graph convolutional network model over social networks improves the detection of unknown HIV infections among young men who have sex with men. - Yang Xiang 003; Kayo Fujimoto; John A. Schneider; Yuxi Jia; Degui Zhi; Cui Tao (J. Am. Medical Informatics Assoc., 2019)

Time-sensitive clinical concept embeddings learned from large electronic health records. - Yang Xiang 003; Jun Xu 007; Yuqi Si; Zhiheng Li 004; Laila Rasmy; Yujia Zhou 003; Firat Tiryaki; Fang Li 011; Yaoyun Zhang; Yonghui Wu; Xiaoqian Jiang; W. Jim Zheng; et al. (BMC Medical Informatics Decis. Mak., 2019)

Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction. - Laila Rasmy; Yang Xiang 003; Ziqian Xie; Cui Tao; Degui Zhi (CoRR, 2020)

Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. - Laila Rasmy; Firat Tiryaki; Yujia Zhou 003; Yang Xiang 003; Cui Tao; Hua Xu 001; Degui Zhi (J. Am. Medical Informatics Assoc., 2020)

Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission. - Laila Rasmy; Bijun S. Kannadath; Masayuki Nigo; Ziqian Xie; Bingyu Mao; Khush A. Patel; Yujia Zhou 003; Xiao Dong; Hua Xu 001; Degui Zhi (AMIA, 2021)

CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing. - Laila Rasmy; Masayuki Nigo; Bijun S. Kannadath; Ziqian Xie; Bingyu Mao; Khush A. Patel; Wanheng Zhang; Yujia Zhou 003; Angela Ross; Hua Xu 001; Degui Zhi (AMIA, 2021)

mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching. - Pramesh Shakya; Ardalan Naseri; Degui Zhi; Shaojie Zhang 001 (ICCABS, 2021)

Efficient Haplotype Block Matching in Bi-Directional PBWT. - Ardalan Naseri; William Yue; Shaojie Zhang 001; Degui Zhi (WABI, 2021)

d-PBWT: dynamic positional Burrows-Wheeler transform. - Ahsan Sanaullah; Degui Zhi; Shaojie Zhang 001 (Bioinform., 2021)

Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data. - Laila Rasmy; Jie Zhu; Zhiheng Li 004; Xin Hao; Hong Thoai Tran; Yujia Zhou 003; Firat Tiryaki; Yang Xiang 003; Hua Xu 001; Degui Zhi (CoRR, 2021)

Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. - Laila Rasmy; Yang Xiang 003; Ziqian Xie; Cui Tao; Degui Zhi (npj Digit. Medicine, 2021)

Pancreatic cancer risk prediction using recurrent neural network models trained on electronic health records and claims data. - Laila Rasmy; Peter Beshara; Bijun S. Kannadath; Degui Zhi (AMIA, 2022)

Explainability versus Accuracy to Engender Trust. - Angela Ross; Laila Rasmy; Degui Zhi; Kathleen McGrow (AMIA, 2022)

Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction. - Evan Yu; Cui Tao; Jingcheng Du; Degui Zhi; Yang Xiang 003; Kayo Fujimoto; Xi Luo; John A. Schneider (AMIA, 2022)

Haplotype Threading Using the Positional Burrows-Wheeler Transform. - Ahsan Sanaullah; Degui Zhi; Shaoije Zhang (WABI, 2022)

Toward a standard formal semantic representation of the model card report. - Muhammad Tuan Amith; Licong Cui; Degui Zhi; Kirk Roberts; Xiaoqian Jiang; Fang Li 011; Evan Yu; Cui Tao (BMC Bioinform., 2022)

PK-RNN-V E: A deep learning model approach to vancomycin therapeutic drug monitoring using electronic health record data. - Masayuki Nigo; Hong Thoai Nga Tran; Ziqian Xie; Han Feng; Bingyu Mao; Laila Rasmy; Hongyu Miao 001; Degui Zhi (J. Biomed. Informatics, 2022)

A Deep-Learning-based Two-Compartment Predictive Model (PKRNN-2CM) for Vancomycin Therapeutic Drug Monitoring. - Bingyu Mao; Ziqian Xie; Laila Rasmy; Masayuki Nigo; Degui Zhi (ICHI, 2023)

Training Recurrent Neural Network-Based Model to Predict COVID-19 Patient Risk for PASC using Pytorch_EHR - Hands-on Tutorial on N3C. - Laila Rasmy; Ziqian Xie; Degui Zhi (ICHI, 2023)

PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data. - Shenghan Zhang; Haoxuan Li; Ruixiang Tang; Sirui Ding; Laila Rasmy; Degui Zhi; Na Zou 001; Xia Hu 001 (ICHI, 2023)

Syllable-PBWT for space-efficient haplotype long-match query. - Victor Wang; Ardalan Naseri; Shaojie Zhang 001; Degui Zhi (Bioinform., 2023)

Prompting Large Language Models for Clinical Temporal Relation Extraction. - Jianping He 002; Laila Rasmy; Haifang Li; Jianfu Li; Zenan Sun; Evan Yu; Degui Zhi; Cui Tao (CoRR, 2024)

Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies. - Yaochen Xie; Ziqian Xie; Sheikh Muhammad Saiful Islam; Degui Zhi; Shuiwang Ji (Trans. Mach. Learn. Res., 2024)

Learning to Discover Regulatory Elements for Gene Expression Prediction. - Xingyu Su; Haiyang Yu 005; Degui Zhi; Shuiwang Ji (ICLR, 2025)

Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. - Pramesh Shakya; Ahsan Sanaullah; Degui Zhi; Shaojie Zhang 001 (RECOMB, 2025)

An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. - Ahsan Sanaullah; Degui Zhi; Shaojie Zhang 001 (WABI, 2025)

iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics. - Kanglin Hsieh; Kai Zhang; Yan Chu 005; Lishan Yu; Xiaoyang Li; Nuo Hu; Isha Kawosa; Patrick G. Pilié; Pratip K. Bhattacharya; Degui Zhi; Xiaoqian Jiang; Zhongming Zhao; et al. (Briefings Bioinform., 2025)

Advancing Pancreatic Cancer Prediction with a Next Visit Token Prediction Head on top of Med-BERT. - Jianping He 002; Laila Rasmy; Degui Zhi; Cui Tao (CoRR, 2025)

Iterative Distillation for Reward-Guided Fine-Tuning of Diffusion Models in Biomolecular Design. - Xingyu Su; Xiner Li; Masatoshi Uehara; Sunwoo Kim; Yulai Zhao 002; Gabriele Scalia; Ehsan Hajiramezanali; Tommaso Biancalani; Degui Zhi; Shuiwang Ji (CoRR, 2025)

Language Models for Controllable DNA Sequence Design. - Xingyu Su; Xiner Li; Yuchao Lin; Ziqian Xie; Degui Zhi; Shuiwang Ji (CoRR, 2025)