Dish_Master: an Intelligent and Adaptive Manager for a Web-based Recipe Database System. - Liping Wang 002; Qing Li 001; Yu Li 006; Xiaofeng Meng 001 (SKG, 2006)

RecipeCrawler: Collecting Recipe Data from WWW Incrementally. - Yu Li 006; Xiaofeng Meng 001; Liping Wang 002; Qing Li 001 (WAIM, 2006)

Hybrid Method for Automated News Content Extraction from the Web. - Yu Li 006; Xiaofeng Meng 001; Qing Li 001; Liping Wang 002 (WISE, 2006)

Semantic knowledge facilities for a web-based recipe database system supporting personalization. - Liping Wang 002; Qing Li 001; Guozhu Dong; Yu Li 006 (Concurr. Comput. Pract. Exp., 2008)

Event Recognition from News Webpages through Latent Ingredients Extraction. - Rui Yan 001; Yu Li 006; Yan Zhang 004; Xiaoming Li 001 (AIRS, 2010)

Dynamic memory paravirtualization transparent to guest OS. - Xiaolin Wang 001; Yifeng Sun; Yingwei Luo; Zhenlin Wang; Yu Li 006; Binbin Zhang; Haogang Chen 002; Xiaoming Li 001 (Sci. China Inf. Sci., 2010)

A finegrained digestion of news webpages through Event Snippet Extraction. - Rui Yan 001; Liang Kong 001; Yu Li 006; Yan Zhang 004; Xiaoming Li 001 (WWW (Companion Volume), 2011)

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. - Hanjun Dai; Ramzan Umarov; Hiroyuki Kuwahara; Yu Li 006; Le Song; Xin Gao 001 (Bioinform., 2017)

An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. - Renmin Han; Yu Li 006; Xin Gao 001; Sheng Wang 001 (Bioinform., 2018)

DeepSimulator: a deep simulator for Nanopore sequencing. - Yu Li 006; Renmin Han; Chongwei Bi; Mo Li 005; Sheng Wang 001; Xin Gao 001 (Bioinform., 2018)

DEEPre: sequence-based enzyme EC number prediction by deep learning. - Yu Li 006; Sheng Wang 001; Ramzan Umarov; Bingqing Xie; Ming Fan 003; Lihua Li 002; Xin Gao 001 (Bioinform., 2018)

DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. - Yu Li 006; Fan Xu; Fa Zhang 001; Pingyong Xu; Mingshu Zhang; Ming Fan 003; Lihua Li 002; Xin Gao 001; Renmin Han (Bioinform., 2018)

SupportNet: solving catastrophic forgetting in class incremental learning with support data. - Yu Li 006; Zhongxiao Li; Lizhong Ding 001; Peng Yang 010; Yuhui Hu; Wei Chen 029; Xin Gao 001 (CoRR, 2018)

On the Decision Boundary of Deep Neural Networks. - Yu Li 006; Lizhong Ding 001; Xin Gao 001 (CoRR, 2018)

PromID: human promoter prediction by deep learning. - Ramzan Umarov; Hiroyuki Kuwahara; Yu Li 006; Xin Gao 001; Victor V. Solovyev (CoRR, 2018)

Linear Kernel Tests via Empirical Likelihood for High-Dimensional Data. - Lizhong Ding 001; Zhi Liu; Yu Li 006; Shizhong Liao; Yong Liu 018; Peng Yang 010; Ge Yu; Ling Shao 001; Xin Gao 001 (AAAI, 2019)

Approximate Kernel Selection with Strong Approximate Consistency. - Lizhong Ding 001; Yong Liu 018; Shizhong Liao; Yu Li 006; Peng Yang 010; Yijie Pan; Chao Huang; Ling Shao 001; Xin Gao 001 (AAAI, 2019)

Two Generator Game: Learning to Sample via Linear Goodness-of-Fit Test. - Lizhong Ding 001; Mengyang Yu; Li Liu 004; Fan Zhu 001; Yong Liu 018; Yu Li 006; Ling Shao 001 (NeurIPS, 2019)

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. - Renmin Han; Xiaohua Wan; Lun Li; Albert F. Lawrence; Peng Yang 010; Yu Li 006; Sheng Wang 001; Fei Sun; Zhiyong Liu 002; Xin Gao 001; Fa Zhang 001 (Bioinform., 2019)

Promoter analysis and prediction in the human genome using sequence-based deep learning models. - Ramzan Umarov; Hiroyuki Kuwahara; Yu Li 006; Xin Gao 001; Victor V. Solovyev (Bioinform., 2019)

PredMP: a web server for de novo prediction and visualization of membrane proteins. - Sheng Wang 001; Shiyang Fei; Zongan Wang; Yu Li 006; Jinbo Xu; Feng Zhao; Xin Gao 001 (Bioinform., 2019)

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification. - Zhihao Xia; Yu Li 006; Bin Zhang 042; Zhongxiao Li; Yuhui Hu; Wei Chen 029; Xin Gao 001 (Bioinform., 2019)

Deep learning in bioinformatics: introduction, application, and perspective in big data era. - Yu Li 006; Chao Huang; Lizhong Ding 001; Zhongxiao Li; Yijie Pan; Xin Gao 001 (CoRR, 2019)

Accelerating flash calculation through deep learning methods. - Yu Li 006; Tao Zhang 026; Shuyu Sun 001; Xin Gao 001 (J. Comput. Phys., 2019)

RNA Secondary Structure Prediction By Learning Unrolled Algorithms. - Xinshi Chen; Yu Li 006; Ramzan Umarov; Xin Gao 001; Le Song (ICLR, 2020)

Learning To Stop While Learning To Predict. - Xinshi Chen; Hanjun Dai; Yu Li 006; Xin Gao 001; Le Song (ICML, 2020)

DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing. - Yu Li 006; Sheng Wang 001; Chongwei Bi; Zhaowen Qiu; Mo Li 005; Xin Gao 001 (Bioinform., 2020)

Towards Structured Prediction in Bioinformatics with Deep Learning. - Yu Li 006 (CoRR, 2020)

Towards Structured Prediction in Bioinformatics with Deep Learning. - Yu Li 006 (2020)

DeepCURATER: Deep Learning for CoURse And Teaching Evaluation and Review. - Zhihang Hu; Bhaavanaa Thumu; Yuren Qin; ZhiSheng Tao; Yijian Lu; Omar Kan; Yu Li 006; Irwin King (TALE, 2021)

Disease gene prediction with privileged information and heteroscedastic dropout. - Juan Shu; Yu Li 006; Sheng Wang 012; Bowei Xi; Jianzhu Ma (Bioinform., 2021)

HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial Peptides. - Qinze Yu; Zhihang Dong; Xingyu Fan; Licheng Zong; Yu Li 006 (CoRR, 2021)

Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration. - Xuesong Wang; Zhihang Hu; Tingyang Yu; Ruijie Wang; Yumeng Wei; Juan Shu; Jianzhu Ma; Yu Li 006 (CoRR, 2021)

DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment. - Ramzan Umarov; Yu Li 006; Erik Arner (PLoS Comput. Biol., 2021)

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. - Ramzan Umarov; Yu Li 006; Takahiro Arakawa; Satoshi Takizawa; Xin Gao 001; Erik Arner (PLoS Comput. Biol., 2021)

Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation. - Qin Wang 011; Jiayang Chen; Yuzhe Zhou; Yu Li 006; Liangzhen Zheng; Sheng Wang 001; Zhen Li 026; Shuguang Cui (AAAI, 2022)

CLMB: Deep Contrastive Learning for Robust Metagenomic Binning. - Pengfei Zhang; Zhengyuan Jiang; Yixuan Wang; Yu Li 006 (RECOMB, 2022)

Understanding Dropout for Graph Neural Networks. - Juan Shu; Bowei Xi; Yu Li 006; Fan Wu; Charles A. Kamhoua; Jianzhu Ma (WWW (Companion Volume), 2022)

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis. - Wenkai Han; Yuqi Cheng; Jiayang Chen; Huawen Zhong; Zhihang Hu; Siyuan Chen; Licheng Zong; Liang Hong; Ting-Fung Chan; Irwin King; Xin Gao 001; Yu Li 006 (Briefings Bioinform., 2022)

Protein-RNA interaction prediction with deep learning: structure matters. - Junkang Wei; Siyuan Chen; Licheng Zong; Xin Gao 001; Yu Li 006 (Briefings Bioinform., 2022)

Deep learning identifies and quantifies recombination hotspot determinants. - Yu Li 006; Siyuan Chen; Trisevgeni Rapakoulia; Hiroyuki Kuwahara; Kevin Y. Yip; Xin Gao 001 (Bioinform., 2022)

E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction. - Tao Shen; Zhihang Hu; Zhangzhi Peng; Jiayang Chen; Peng Xiong; Liang Hong; Liangzhen Zheng; Yixuan Wang; Irwin King; Sheng Wang; Siqi Sun; Yu Li 006 (CoRR, 2022)

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. - Zhongxiao Li; Yisheng Li; Bin Zhang 042; Yu Li 006; Yongkang Long; Juexiao Zhou; Xudong Zou; Min Zhang; Yuhui Hu; Wei Chen 029; Xin Gao 001 (Genom. Proteom. Bioinform., 2022)

Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning. - Zhihang Hu; Qinze Yu; Yucheng Guo; Taifeng Wang; Irwin King; Xin Gao 001; Le Song; Yu Li 006 (CoRR, 2023)

Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation. - Le Zhang; Jiayang Chen; Tao Shen; Yu Li 006; Siqi Sun (CoRR, 2023)

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. - Junbo Shen; Qinze Yu; Shenyang Chen; Qingxiong Tan; Jingcheng Li; Yu Li 006 (CoRR, 2023)

The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. - Gengjie Jia; Yu Li 006; Xue Zhong; Kanix Wang; Milton Pividori; Rabab Alomairy; Aniello Esposito; Hatem Ltaief; Chikashi Terao; Masato Akiyama; Koichi Matsuda; David E. Keyes; et al. (Nat. Comput. Sci., 2023)

Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. - Gengjie Jia; Yu Li 006; Xue Zhong; Kanix Wang; Milton Pividori; Rabab Alomairy; Aniello Esposito; Hatem Ltaief; Chikashi Terao; Masato Akiyama; Koichi Matsuda; David E. Keyes; et al. (Nat. Comput. Sci., 2023)

Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. - Xuesong Wang; Zhihang Hu; Tingyang Yu; Yixuan Wang; Ruijie Wang; Yumeng Wei; Juan Shu; Jianzhu Ma; Yu Li 006 (Bioinform., 2023)

AcrNET: predicting anti-CRISPR with deep learning. - Yunxiang Li; Yumeng Wei; Sheng Xu; Qingxiong Tan; Licheng Zong; Jiuming Wang; Yixuan Wang; Jiayang Chen; Liang Hong; Yu Li 006 (Bioinform., 2023)

Enhancing Biomedical Question Answering with Parameter-Efficient Fine-Tuning and Hierarchical Retrieval Augmented Generation. - Yichen Gao; Licheng Zong; Yu Li 006 (CLEF (Working Notes), 2024)

SeRTS: Self-Rewarding Tree Search for Biomedical Retrieval-Augmented Generation. - Minda Hu; Licheng Zong; Hongru Wang 003; Jingyan Zhou; Jingjing Li 007; Yichen Gao; Kam-Fai Wong; Yu Li 006; Irwin King (EMNLP (Findings), 2024)

Task Groupings Regularization: Data-Free Meta-Learning with Heterogeneous Pre-trained Models. - Yongxian Wei; Zixuan Hu; Li Shen 008; Zhenyi Wang 001; Yu Li 006; Chun Yuan; Dacheng Tao (ICML, 2024)

MSA Generation with Seqs2Seqs Pretraining: Advancing Protein Structure Predictions. - Le Zhang; Jiayang Chen; Tao Shen; Yu Li 006; Siqi Sun (NeurIPS, 2024)

GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. - Yimin Fan; Yu Li 006; Jun Ding; Yue Li (RECOMB, 2024)

Progress and opportunities of foundation models in bioinformatics. - Qing Li 075; Zhihang Hu; Yixuan Wang; Lei Li 051; Yimin Fan; Irwin King; Gengjie Jia; Sheng Wang; Le Song; Yu Li 006 (Briefings Bioinform., 2024)

ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers. - Qingxiong Tan; Jin Xiao; Jiayang Chen; Yixuan Wang; Zeliang Zhang; Tiancheng Zhao; Yu Li 006 (Briefings Bioinform., 2024)

scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics. - Chuanyang Zheng; Yixuan Wang; Yuqi Cheng; Xuesong Wang; Hongxin Wei; Irwin King; Yu Li 006 (Briefings Bioinform., 2024)

Learning meaningful representation of single-neuron morphology via large-scale pre-training. - Yimin Fan; Yaxuan Li 002; Yunhua Zhong; Liang Hong; Lei Li 051; Yu Li 006 (Bioinform., 2024)

RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. - Han Huang; Ziqian Lin; Dongchen He; Liang Hong; Yu Li 006 (Bioinform., 2024)

Developing ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering. - Qing Li; Lei Li 051; Yu Li 006 (CoRR, 2024)

Progress and Opportunities of Foundation Models in Bioinformatics. - Qing Li 001; Zhihang Hu; Yixuan Wang; Lei Li 051; Yimin Fan; Irwin King; Le Song; Yu Li 006 (CoRR, 2024)

Enhancing Biomedical Knowledge Retrieval-Augmented Generation with Self-Rewarding Tree Search and Proximal Policy Optimization. - Minda Hu; Licheng Zong; Hongru Wang 003; Jingyan Zhou; Jingjing Li 007; Yichen Gao; Kam-Fai Wong; Yu Li 006; Irwin King (CoRR, 2024)

Data Augmentation of Multi-turn Psychological Dialogue via Knowledge-driven Progressive Thought Prompting. - Jiyue Jiang; Liheng Chen; Sheng Wang; Lingpeng Kong; Yu Li 006; Chuan Wu (CoRR, 2024)

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. - Junbo Shen; Qinze Yu; Shenyang Chen; Qingxiong Tan; Jingchen Li; Yu Li 006 (Nat. Comput. Sci., 2024)

Lyra: Orchestrating Dual Correction in Automated Theorem Proving. - Chuanyang Zheng; Haiming Wang; Enze Xie; Zhengying Liu; Jiankai Sun; Huajian Xin; Jianhao Shen; Zhenguo Li; Yu Li 006 (Trans. Mach. Learn. Res., 2024)

ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles. - Junkang Wei; Jin Xiao; Siyuan Chen; Licheng Zong; Xin Gao 001; Yu Li 006 (Database J. Biol. Databases Curation, 2024)

Deep generative design of RNA aptamers using structural predictions. - Felix Wong; Dongchen He; Aarti Krishnan; Liang Hong; Alexander Z. Wang; Jiuming Wang; Zhihang Hu; Satotaka Omori; Alicia Li; Jiahua Rao; Qinze Yu; Wengong Jin; et al. (Nat. Comput. Sci., 2024)

Meta-Learning Without Data via Unconditional Diffusion Models. - Yongxian Wei; Zixuan Hu; Li Shen 008; Zhenyi Wang 001; Lei Li 051; Yu Li 006; Chun Yuan (IEEE Trans. Circuits Syst. Video Technol., 2024)

CipherBank: Exploring the Boundary of LLM Reasoning Capabilities through Cryptography Challenge. - Yu Li 006; Qizhi Pei; Mengyuan Sun; Honglin Lin; Chenlin Ming; Xin Gao 001; Jiang Wu; Conghui He; Lijun Wu 003 (ACL (Findings), 2025)

MathFusion: Enhancing Mathematical Problem-solving of LLM through Instruction Fusion. - Qizhi Pei; Lijun Wu 003; Zhuoshi Pan; Yu Li 006; Honglin Lin; Chenlin Ming; Xin Gao 001; Conghui He; Rui Yan 001 (ACL (1), 2025)

Large Language Models in Bioinformatics: A Survey. - Zhenyu Wang; Zikang Wang; Jiyue Jiang; Pengan Chen; Xiangyu Shi; Yu Li 006 (ACL (Findings), 2025)

cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNA. - Yixuan Wang; Jiayi Li; Jingqi Li; Shen Yang; Yuhan Huang; Xinyuan Liu; Yimin Fan; Irwin King; Yumei Li 019; Yu Li 006 (RECOMB, 2025)

An effective encoding of human medical conditions in disease space provides a versatile framework for deciphering disease associations. - Tianxin Xu; Yu Li 006; Xin Gao 001; Andrey Rzhetsky; Gengjie Jia (Quant. Biol., 2025)

Developing and Utilizing a Large-Scale Cantonese Dataset for Multi-Tasking in Large Language Models. - Jiyue Jiang; Alfred Kar Yin Truong; Yanyu Chen; Qinghang Bao; Sheng Wang; Pengan Chen; Jiuming Wang; Lingpeng Kong; Yu Li 006; Chuan Wu (CoRR, 2025)

Benchmarking Large Language Models on Multiple Tasks in Bioinformatics NLP with Prompting. - Jiyue Jiang; Pengan Chen; Jiuming Wang; Dongchen He; Ziqin Wei; Liang Hong; Licheng Zong; Sheng Wang; Qinze Yu; Zixian Ma; Yanyu Chen; Yimin Fan; et al. (CoRR, 2025)

MathFusion: Enhancing Mathematic Problem-solving of LLM through Instruction Fusion. - Qizhi Pei; Lijun Wu 003; Zhuoshi Pan; Yu Li 006; Honglin Lin; Chenlin Ming; Xin Gao 001; Conghui He; Rui Yan 001 (CoRR, 2025)

Can One Domain Help Others? A Data-Centric Study on Multi-Domain Reasoning via Reinforcement Learning. - Yu Li 006; Zhuoshi Pan; Honglin Lin; Mengyuan Sun; Conghui He; Lijun Wu 003 (CoRR, 2025)