Inferring domain-domain interactions from protein-protein interactions. - Minghua Deng; Shipra Mehta; Fengzhu Sun; Ting Chen 006 (RECOMB, 2002)

Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. - Kui Zhang; Ting Chen 006; Michael S. Waterman; Zhaohui S. Qin; Jun S. Liu; Fengzhu Sun (Computational Methods for SNPs and Haplotype Inference, 2002)

Assessment of the reliability of protein-protein interactions and protein function prediction. - Minghua Deng; Fengzhu Sun; Ting Chen 006 (Pacific Symposium on Biocomputing, 2003)

Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. - Kui Zhang; Fengzhu Sun; Michael S. Waterman; Ting Chen 006 (RECOMB, 2003)

Prediction of Protein Function Using Protein-Protein Interaction Data. - Minghua Deng; Kui Zhang; Shipra Mehta; Ting Chen 006; Fengzhu Sun (J. Comput. Biol., 2003)

Approximation Algorithms for the Selection of Robust Tag SNPs. - Yao-Ting Huang; Kui Zhang; Ting Chen 006; Kun-Mao Chao (WABI, 2004)

Mapping gene ontology to proteins based on protein-protein interaction data. - Minghua Deng; Zhidong Tu; Fengzhu Sun; Ting Chen 006 (Bioinform., 2004)

An Integrated Probabilistic Model for Functional Prediction of Proteins. - Minghua Deng; Ting Chen 006; Fengzhu Sun (J. Comput. Biol., 2004)

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. - Kui Zhang; Zhaohui S. Qin; Ting Chen 006; Jun S. Liu; Michael S. Waterman; Fengzhu Sun (Bioinform., 2005)

Selecting additional tag SNPs for tolerating missing data in genotyping. - Yao-Ting Huang; Kui Zhang; Ting Chen 006; Kun-Mao Chao (BMC Bioinform., 2005)

An Approximation Algorithm for Haplotype Inference by Maximum Parsimony. - Yao-Ting Huang; Kun-Mao Chao; Ting Chen 006 (J. Comput. Biol., 2005)

An integrative approach for causal gene identification and gene regulatory pathway inference. - Zhidong Tu; Li Wang; Michelle N. Arbeitman; Ting Chen 006; Fengzhu Sun (ISMB (Supplement of Bioinformatics), 2006)

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. - Rui Jiang 001; Hua Yang; Fengzhu Sun; Ting Chen 006 (BMC Bioinform., 2006)

An integrated approach to the prediction of domain-domain interactions. - Hyunju Lee; Minghua Deng; Fengzhu Sun; Ting Chen 006 (BMC Bioinform., 2006)

Approximation Algorithms for the Selection of Robust Tag SNPs. - Kui Zhang; Kun-Mao Chao; Yao-Ting Huang; Ting Chen 006 (Handbook of Approximation Algorithms and Metaheuristics, 2007)

Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks. - Ting Chen 006; Rui Jiang 001; Fengzhu Sun (Commun. Inf. Syst., 2009)

Preface: Special Issue. - Ting Chen 006; Paul Marjoram; Fengzhu Sun; Xianghong Jasmine Zhou (J. Comput. Biol., 2012)

Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. - Xiaotu Ma; Ting Chen 006; Fengzhu Sun (Briefings Bioinform., 2014)

Global optimization-based inference of chemogenomic features from drug-target interactions. - Songpeng Zu; Ting Chen 006; Shao Li (Bioinform., 2015)

Network-based method to infer the contributions of proteins to the etiology of drug side effects. - Rui Li; Ting Chen 006; Shao Li (Quant. Biol., 2015)

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach. - Muxuan Liang; Zhizhong Li; Ting Chen 006; Jianyang Zeng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

DeepEnhancer: Predicting enhancers by convolutional neural networks. - Xu Min; Ning Chen 002; Ting Chen 006; Rui Jiang 001 (BIBM, 2016)

mLDM: A New Hierarchical Bayesian Statistical Model for Sparse Microbial Association Discovery. - Yuqing Yang; Ning Chen 002; Ting Chen 006 (RECOMB, 2016)

Global inference of disease-causing single nucleotide variants from exome sequencing data. - Mengmeng Wu; Ting Chen 006; Rui Jiang 001 (BMC Bioinform., 2016)

TACO: Taxonomic prediction of unknown OTUs through OTU co-abundance networks. - Zohreh Baharvand Irannia; Ting Chen 006 (Quant. Biol., 2016)

Whole genome sequencing and its applications in medical genetics. - Jiaxin Wu 005; Mengmeng Wu; Ting Chen 006; Rui Jiang 001 (Quant. Biol., 2016)

Patient outcome prediction via convolutional neural networks based on multi-granularity medical concept embedding. - Yujuan Feng; Xu Min; Ning Chen 002; Hu Chen; Xiaolei Xie; Haibo Wang; Ting Chen 006 (BIBM, 2017)

Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes. - Mengmeng Wu; Wanwen Zeng; Wenqiang Liu; Yijia Zhang 001; Ting Chen 006; Rui Jiang 001 (BIBM, 2017)

DACE: a scalable DP-means algorithm for clustering extremely large sequence data. - Linhao Jiang; Yichao Dong; Ning Chen 002; Ting Chen 006 (Bioinform., 2017)

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. - Yang Young Lu; Ting Chen 006; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2017)

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding. - Xu Min; Wanwen Zeng; Ning Chen 002; Ting Chen 006; Rui Jiang 001 (Bioinform., 2017)

Predicting enhancers with deep convolutional neural networks. - Xu Min; Wanwen Zeng; Shengquan Chen; Ning Chen 002; Ting Chen 006; Rui Jiang 001 (BMC Bioinform., 2017)

Reading the Underlying Information From Massive Metagenomic Sequencing Data. - Xuegong Zhang; Shansong Liu; Hongfei Cui; Ting Chen 006 (Proc. IEEE, 2017)

Elastic restricted Boltzmann machines for cancer data analysis. - Sai Zhang; Muxuan Liang; Zhongjun Zhou; Chen Zhang; Ning Chen 002; Ting Chen 006; Jianyang Zeng 001 (Quant. Biol., 2017)

Approximation Algorithms for the Selection of Robust Tag SNPs. - Yao-Ting Huang; Kui Zhang; Ting Chen 006; Kun-Mao Chao (Handbook of Approximation Algorithms and Metaheuristics (2), 2018)

Ontology-based Venous Thromboembolism Risk Factors Mining and Model Developing from Medical Records. - Yuqing Yang; Xin Wang; Yu Huang; Ning Chen 002; Juhong Shi; Ting Chen 006 (BIBM, 2018)

Dropout training for SVMs with data augmentation. - Ning Chen 002; Jun Zhu 001; Jianfei Chen 001; Ting Chen 006 (Frontiers Comput. Sci., 2018)

Combo-Action: Training Agent For FPS Game with Auxiliary Tasks. - Shiyu Huang 001; Hang Su 006; Jun Zhu 001; Ting Chen 006 (AAAI, 2019)

Bone Age Assessment by Deep Convolutional Neural Networks Combined with Clinical TW3-RUS. - Xiaohong Liu 007; Guangyu Wang; Yiming Xu; Ning Chen 002; Ting Chen 006 (BIBM, 2019)

DeepTriager: A Neural Attention Model for Emergency Triage with Electronic Health Records. - Guangyu Wang; Xiaohong Liu 007; Ken Xie; Ning Chen 002; Ting Chen 006 (BIBM, 2019)

How Robust is Your Automatic Diagnosis Model? - Ke Wang; Guangyu Wang; Ning Chen 002; Ting Chen 006 (BIBM, 2019)

DCMN: Double Core Memory Network for Patient Outcome Prediction with Multimodal Data. - Yujuan Feng; Zhenxing Xu; Lin Gan; Ning Chen 002; Bin Yu; Ting Chen 006; Fei Wang 001 (ICDM, 2019)

Computer-aided Diagnosis of Ambulatory Electrocardiograms via ASRS: Active-Selection-Random-Selection. - Xuan Zhang; Guangyu Wang; Ning Chen 002; Ting Chen 006 (ICHI, 2019)

DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. - Hongfei Cui; Hailin Hu 002; Jianyang Zeng 001; Ting Chen 006 (BMC Bioinform., 2019)

Ontology-based venous thromboembolism risk assessment model developing from medical records. - Yuqing Yang; Xin Wang; Yu Huang; Ning Chen 002; Juhong Shi; Ting Chen 006 (BMC Medical Informatics Decis. Mak., 2019)

Attention U-net for Interpretable Classification on Chest X-ray Image. - Xuan Zhang; Ting Chen 006 (BIBM, 2020)

SVQN: Sequential Variational Soft Q-Learning Networks. - Shiyu Huang 001; Hang Su 006; Jun Zhu 001; Ting Chen 006 (ICLR, 2020)

Automatic Emergency Diagnosis with Knowledge-Based Tree Decoding. - Ke Wang; Xuyan Chen; Ning Chen 002; Ting Chen 006 (IJCAI, 2020)

Joint Medical Ontology Representation Learning for Healthcare Predictions. - Ke Wang; Ning Chen 002; Ting Chen 006 (IJCNN, 2020)

KISEG: A Three-Stage Segmentation Framework for Multi-level Acceleration of Chest CT Scans from COVID-19 Patients. - Xiaohong Liu 007; Kai Wang; Ke Wang; Ting Chen 006; Kang Zhang; Guangyu Wang (MICCAI (4), 2020)

Anterior Segment Eye Lesion Segmentation with Advanced Fusion Strategies and Auxiliary Tasks. - Ke Wang; Xiaohong Liu 007; Kang Zhang; Ting Chen 006; Guangyu Wang (MICCAI (5), 2020)

FIT: a Fast and Accurate Framework for Solving Medical Inquiring and Diagnosing Tasks. - Weijie He; Xiaohao Mao; Chao Ma 019; José Miguel Hernández-Lobato; Ting Chen 006 (CoRR, 2020)

Deep Active Learning For Fibrosis Segmentation Of Chest CT Scans From Covid-19 Patients. - Xiaohong Liu 007; Kai Wang; Ting Chen 006 (ICIP, 2021)

Off-Policy Training for Truncated TD(λ) Boosted Soft Actor-Critic. - Shiyu Huang 001; Bin Wang 034; Hang Su 006; Dong Li 016; Jianye Hao; Jun Zhu 001; Ting Chen 006 (PRICAI (3), 2021)

Ranking Cost: Building An Efficient and Scalable Circuit Routing Planner with Evolution-Based Optimization. - Shiyu Huang 001; Bin Wang 034; Dong Li 016; Jianye Hao; Ting Chen 006; Jun Zhu 001 (CoRR, 2021)

TiKick: Towards Playing Multi-agent Football Full Games from Single-agent Demonstrations. - Shiyu Huang 001; Wenze Chen; Longfei Zhang; Ziyang Li; Fengming Zhu; Deheng Ye; Ting Chen 006; Jun Zhu 001 (CoRR, 2021)

redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer. - Kaikun Xie; Zehua Liu; Ning Chen 002; Ting Chen 006 (Genom. Proteom. Bioinform., 2021)

kLDM: Inferring Multiple Metagenomic Association Networks Based on the Variation of Environmental Factors. - Yuqing Yang; Xin Wang; Kaikun Xie; Congmin Zhu; Ning Chen 002; Ting Chen 006 (Genom. Proteom. Bioinform., 2021)

VMAPD: Generate Diverse Solutions for Multi-Agent Games with Recurrent Trajectory Discriminators. - Shiyu Huang 001; Chao Yu 005; Bin Wang 034; Dong Li 016; Yu Wang 002; Ting Chen 006; Jun Zhu 001 (CoG, 2022)

Yolo-SG: Salience-Guided Detection Of Small Objects In Medical Images. - Rong Han; Xiaohong Liu 007; Ting Chen 006 (ICIP, 2022)

BSODA: A Bipartite Scalable Framework for Online Disease Diagnosis. - Weijie He; Xiaohao Mao; Chao Ma 019; Yu Huang; José Miguel Hernández-Lobato; Ting Chen 006 (WWW, 2022)

Robust Learning of Deep Time Series Anomaly Detection Models with Contaminated Training Data. - Wenkai Li; Cheng Feng 004; Ting Chen 006; Jun Zhu 001 (CoRR, 2022)

Explainable Dynamic Multimodal Variational Autoencoder for the Prediction of Patients With Suspected Central Precocious Puberty. - Yiming Xu; Xiaohong Liu 007; Liyan Pan; Xiaojian Mao; Huiying Liang; Guangyu Wang; Ting Chen 006 (IEEE J. Biomed. Health Informatics, 2022)

StackVAE-G: An efficient and interpretable model for time series anomaly detection. - Wenkai Li; Wenbo Hu 001; Ting Chen 006; Ning Chen 002; Cheng Feng 004 (AI Open, 2022)

DGPO: Discovering Multiple Strategies with Diversity-Guided Policy Optimization. - Wenze Chen; Shiyu Huang 001; Yuan Chiang; Ting Chen 006; Jun Zhu 001 (AAMAS, 2023)

Research on cooperative UAV countermeasure strategy based on interception triangle. - Shuyu Liu; Ting Chen 006; Tiantian Zhao; Shanshan Liu; Chao Ma 019 (ICMLCA, 2023)

Pre-trained Universal Medical Image Transformer. - Lingxiao Luo; Xuanzhong Chen; Bingda Tang; Xinsheng Chen; Chengpeng Hu; Yujiang Li; Rong Han; Ting Chen 006 (CoRR, 2023)

Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames. - Yiming Xu; Bowen Zheng; Xiaohong Liu 007; Tao Wu; Jinxiu Ju; Shi-jie Wang; Yufan Lian; Hongjun Zhang; Tong Liang; Ye Sang; Rui Jiang 001; Guangyu Wang; et al. (Briefings Bioinform., 2023)

DGPO: Discovering Multiple Strategies with Diversity-Guided Policy Optimization. - Wentse Chen; Shiyu Huang 001; Yuan Chiang; Tim Pearce; Wei-Wei Tu; Ting Chen 006; Jun Zhu 001 (AAAI, 2024)

RareBench: Can LLMs Serve as Rare Diseases Specialists? - Xuanzhong Chen; Xiaohao Mao; Qihan Guo; Lun Wang; Shuyang Zhang; Ting Chen 006 (KDD, 2024)

HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning. - Rong Han; Wenbing Huang 001; Lingxiao Luo; Xinyan Han; Jiaming Shen; Zhiqiang Zhang; Jun Zhou; Ting Chen 006 (CoRR, 2024)

RareAgents: Autonomous Multi-disciplinary Team for Rare Disease Diagnosis and Treatment. - Xuanzhong Chen; Ye Jin; Xiaohao Mao; Lun Wang; Shuyang Zhang; Ting Chen 006 (CoRR, 2024)

HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multi-task Learning. - Rong Han; Wenbing Huang 001; Lingxiao Luo; Xinyan Han; Jiaming Shen; Zhiqiang Zhang; Jun Zhou; Ting Chen 006 (AAAI, 2025)

CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. - Rong Han; Xiaohong Liu 007; Tong Pan; Jing Xu 008; Xiaoyu Wang 016; Wuyang Lan; Zhenyu Li; Zixuan Wang; Jiangning Song; Guangyu Wang; Ting Chen 006 (AAAI, 2025)

VividMed: Vision Language Model with Versatile Visual Grounding for Medicine. - Lingxiao Luo; Bingda Tang; Xuanzhong Chen; Rong Han; Ting Chen 006 (NAACL (Long Papers), 2025)

Rag2Mol: structure-based drug design based on retrieval augmented generation. - Peidong Zhang; Xingang Peng; Rong Han; Ting Chen 006; Jianzhu Ma (Briefings Bioinform., 2025)

A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs. - Xiaohao Mao; Yu Huang; Ye Jin; Lun Wang; Xuanzhong Chen; Honghong Liu; Xinglin Yang; Haopeng Xu; Xiaodong Luan; Ying Xiao; Siqin Feng; Jiahao Zhu; et al. (npj Digit. Medicine, 2025)