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2020 – today
- 2024
[j20]Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji:
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies. Trans. Mach. Learn. Res. 2024 (2024)- 2023
- [j19]Victor Wang, Ardalan Naseri, Shaojie Zhang
, Degui Zhi:
Syllable-PBWT for space-efficient haplotype long-match query. Bioinform. 39(1) (2023) - [c18]Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu:
PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data. ICHI 2023: 268-275 - [c17]Bingyu Mao, Ziqian Xie, Laila Rasmy, Masayuki Nigo, Degui Zhi:
A Deep-Learning-based Two-Compartment Predictive Model (PKRNN-2CM) for Vancomycin Therapeutic Drug Monitoring. ICHI 2023: 484 - [c16]Laila Rasmy, Ziqian Xie, Degui Zhi:
Training Recurrent Neural Network-Based Model to Predict COVID-19 Patient Risk for PASC using Pytorch_EHR - Hands-on Tutorial on N3C. ICHI 2023: 529-530 - [i4]Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu:
PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data. CoRR abs/2303.10794 (2023) - [i3]Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji:
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies. CoRR abs/2309.15132 (2023) - 2022
- [j18]Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao:
Toward a standard formal semantic representation of the model card report. BMC Bioinform. 23(1): 281 (2022) - [j17]Masayuki Nigo, Hong Thoai Nga Tran, Ziqian Xie, Han Feng, Bingyu Mao, Laila Rasmy, Hongyu Miao, Degui Zhi:
PK-RNN-V E: A deep learning model approach to vancomycin therapeutic drug monitoring using electronic health record data. J. Biomed. Informatics 133: 104166 (2022) - [c15]Laila Rasmy, Peter Beshara, Bijun S. Kannadath, Degui Zhi:
Pancreatic cancer risk prediction using recurrent neural network models trained on electronic health records and claims data. AMIA 2022 - [c14]Angela Ross, Laila Rasmy, Degui Zhi, Kathleen McGrow:
Explainability versus Accuracy to Engender Trust. AMIA 2022 - [c13]Evan Yu, Cui Tao, Jingcheng Du, Degui Zhi, Yang Xiang, Kayo Fujimoto, Xi Luo, John A. Schneider:
Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction. AMIA 2022 - [c12]Ahsan Sanaullah, Degui Zhi, Shaoije Zhang:
Haplotype Threading Using the Positional Burrows-Wheeler Transform. WABI 2022: 4:1-4:14 - 2021
- [j16]Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
d-PBWT: dynamic positional Burrows-Wheeler transform. Bioinform. 37(16): 2390-2397 (2021) - [j15]Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi:
Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. npj Digit. Medicine 4 (2021) - [c11]Laila Rasmy, Bijun S. Kannadath, Masayuki Nigo, Ziqian Xie, Bingyu Mao, Khush A. Patel, Yujia Zhou, Xiao Dong, Hua Xu, Degui Zhi:
Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission. AMIA 2021 - [c10]Laila Rasmy, Masayuki Nigo, Bijun S. Kannadath, Ziqian Xie, Bingyu Mao, Khush A. Patel, Wanheng Zhang, Yujia Zhou, Angela Ross, Hua Xu, Degui Zhi:
CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing. AMIA 2021 - [c9]Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang:
mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching. ICCABS 2021: 115-130 - [c8]Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi:
Efficient Haplotype Block Matching in Bi-Directional PBWT. WABI 2021: 19:1-19:13 - [i2]Laila Rasmy, Jie Zhu, Zhiheng Li, Xin Hao, Hong Thoai Tran, Yujia Zhou, Firat Tiryaki, Yang Xiang, Hua Xu, Degui Zhi:
Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data. CoRR abs/2110.00998 (2021) - 2020
- [j14]Laila Rasmy, Firat Tiryaki, Yujia Zhou, Yang Xiang, Cui Tao, Hua Xu, Degui Zhi:
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J. Am. Medical Informatics Assoc. 27(10): 1593-1599 (2020) - [c7]Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
d-PBWT: Dynamic Positional Burrows-Wheeler Transform. RECOMB 2020: 269-270 - [i1]Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi:
Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction. CoRR abs/2005.12833 (2020)
2010 – 2019
- 2019
- [j13]Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang:
Efficient haplotype matching between a query and a panel for genealogical search. Bioinform. 35(14): i233-i241 (2019) - [j12]Ardalan Naseri, Degui Zhi, Shaojie Zhang:
Multi-allelic positional Burrows-Wheeler transform. BMC Bioinform. 20-S(11): 279:1-279:8 (2019) - [j11]Yang Xiang, Kayo Fujimoto, John A. Schneider, Yuxi Jia, Degui Zhi, Cui Tao:
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. J. Am. Medical Informatics Assoc. 26(11): 1263-1271 (2019) - [j10]Yang Xiang, Jun Xu, Yuqi Si, Zhiheng Li, Laila Rasmy, Yujia Zhou, Firat Tiryaki, Fang Li, Yaoyun Zhang, Yonghui Wu, Xiaoqian Jiang, W. Jim Zheng, Degui Zhi, Cui Tao, Hua Xu:
Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Medical Informatics Decis. Mak. 19-S(2): 139-148 (2019) - 2018
- [j9]Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC Bioinform. 19-S(17): 492:1-492:3 (2018) - [j8]Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi:
A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J. Biomed. Informatics 84: 11-16 (2018) - [c6]Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu:
Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. AMIA 2018 - [c5]Yang Xiang, Jun Xu, Jingcheng Du, Degui Zhi, Cui Tao:
Asthma Onset Prediction Using Structured EMR Data. AMIA 2018 - 2017
- [c4]Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu:
Clinical Named Entity Recognition Using Deep Learning Models. AMIA 2017 - [c3]Ardalan Naseri, Degui Zhi, Shaojie Zhang:
Multi-allelic positional burrows-wheeler transform. ICCABS 2017: 1 - [c2]Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi:
Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. RECOMB 2017: 387-388 - 2013
- [j7]Kui Zhang, Degui Zhi:
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads. Bioinform. 29(19): 2427-2434 (2013) - 2012
- [j6]Degui Zhi, Jihua Wu, Nianjun Liu, Kui Zhang:
Genotype calling from next-generation sequencing data using haplotype information of reads. Bioinform. 28(7): 938-946 (2012) - 2011
- [j5]Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui:
Length bias correction for RNA-seq data in gene set analyses. Bioinform. 27(5): 662-669 (2011) - 2010
- [j4]Degui Zhi, Maxim Shatsky, Steven E. Brenner:
Alignment-free local structural search by writhe decomposition. Bioinform. 26(9): 1176-1184 (2010)
2000 – 2009
- 2007
- [j3]Degui Zhi, Uri Keich, Pavel A. Pevzner, Steffen Heber, Haixu Tang:
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 4(1): 54-64 (2007) - [c1]Degui Zhi, Maxim Shatsky, Steven E. Brenner:
Alignment-Free Local Structural Search by Writhe Decomposition. WABI 2007: 194-195 - 2006
- [b1]Degui Zhi:
Discovery and analysis of mosaic arrangements in biological sequences and structures. University of California, San Diego, USA, 2006 - [j2]Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik:
Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinform. 7: 460 (2006) - [j1]Neil Christopher Jones, Degui Zhi, Benjamin J. Raphael:
AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Res. 34(Web-Server-Issue): 613-616 (2006)
Coauthor Index
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