New Approximation Algorithms for Some Dynamic Storage Allocation Problems. - Shuai Cheng Li 001; Hon Wai Leong; Steven K. Quek (COCOON, 2004)

String Join Using Precedence Count Matrix. - Xia Cao; Anthony K. H. Tung; Beng Chin Ooi; Kian-Lee Tan; Shuai Cheng Li 001 (SSDBM, 2004)

Piers: An Efficient Model for Similarity Search in DNA Sequence Databases. - Xia Cao; Shuai Cheng Li 001; Beng Chin Ooi; Anthony K. H. Tung (SIGMOD Rec., 2004)

Indexing DNA Sequences Using q-Grams. - Xia Cao; Shuai Cheng Li 001; Anthony K. H. Tung (DASFAA, 2005)

Faster Algorithms for Finding Missing Patterns. - Shuai Cheng Li 001 (CATS, 2006)

On the Complexity of the Crossing Contact Map Pattern Matching Problem. - Shuai Cheng Li 001; Ming Li 001 (WABI, 2006)

New Algorithms for the Spaced Seeds. - Xin Gao 001; Shuaicheng Li 001; Yinan Lu (FAW, 2007)

Finding Largest Well-Predicted Subset of Protein Structure Models. - Shuai Cheng Li 001; Dongbo Bu; Jinbo Xu; Ming Li 001 (CPM, 2008)

A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance. - Shuai Cheng Li 001; Yen Kaow Ng; Louxin Zhang (FAW, 2008)

Designing succinct structural alphabets. - Shuai Cheng Li 001; Dongbo Bu; Xin Gao 001; Jinbo Xu; Ming Li 001 (ISMB, 2008)

A PTAS For The k-Consensus Structures Problem Under Squared Euclidean Distance. - Shuai Cheng Li 001; Yen Kaow Ng; Louxin Zhang (Algorithms, 2008)

Predicting Local Quality of a Sequence-Structure Alignment. - Xin Gao 001; Jinbo Xu; Shuai Cheng Li 001; Ming Li 001 (J. Bioinform. Comput. Biol., 2009)

Finding compact structural motifs. - Dongbo Bu; Ming Li 001; Shuai Cheng Li 001; Jianbo Qian; Jinbo Xu (Theor. Comput. Sci., 2009)

On two open problems of 2-interval patterns. - Shuai Cheng Li 001; Ming Li 001 (Theor. Comput. Sci., 2009)

Calibur: a tool for clustering large numbers of protein decoys. - Shuai Cheng Li 001; Yen Kaow Ng (BMC Bioinform., 2010)

Protein Secondary Structure Prediction Using NMR Chemical Shift Data. - Yuzhong Zhao; Babak Alipanahi; Shuai Cheng Li 001; Ming Li 001 (J. Bioinform. Comput. Biol., 2010)

Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation. - Babak Alipanahi; Xin Gao 001; Emre Karakoç; Shuai Cheng Li 001; Frank J. Balbach; Guangyu Feng; Logan Donaldson; Ming Li 001 (J. Bioinform. Comput. Biol., 2011)

Pedigree Reconstruction Using Identity by Descent. - Bonnie Kirkpatrick; Shuai Cheng Li 001; Richard M. Karp; Eran Halperin (J. Comput. Biol., 2011)

Finding Nearly Optimal GDT Scores. - Shuai Cheng Li 001; Dongbo Bu; Jinbo Xu; Ming Li 001 (J. Comput. Biol., 2011)

Protein-Protein Binding Sites Prediction by 3D Structural Similarities. - Fei Guo 001; Shuai Cheng Li 001; Lusheng Wang 001 (J. Chem. Inf. Model., 2011)

On protein structure alignment under distance constraint. - Shuai Cheng Li 001; Yen Kaow Ng (Theor. Comput. Sci., 2011)

Finding Longest Common Segments in Protein Structures in Nearly Linear Time. - Yen Kaow Ng; Hirotaka Ono 001; Ling Ge; Shuai Cheng Li 001 (CPM, 2012)

P-Binder: A System for the Protein-Protein Binding Sites Identification. - Fei Guo 001; Shuai Cheng Li 001; Lusheng Wang 001 (ISBRA, 2012)

How Accurately Can We Model Protein Structures with Dihedral Angles? - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Babak Alipanahi Ramandi; Ming Li 001 (WABI, 2012)

Protein-protein binding site identification by enumerating the configurations. - Fei Guo 001; Shuai Cheng Li 001; Lusheng Wang 001; Daming Zhu (BMC Bioinform., 2012)

Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations. - Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Clustering 100, 000 Protein Structure Decoys in Minutes. - Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Towards Reliable Automatic Protein Structure Alignment. - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (WABI, 2013)

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Babak Alipanahi; Ming Li 001 (Algorithms Mol. Biol., 2013)

The Difficulty Of Protein Structure Alignment Under The RMSD. - Shuai Cheng Li 001 (Algorithms Mol. Biol., 2013)

Detecting Protein Conformational Changes in Interactions via Scaling Known Structures. - Fei Guo 001; Shuai Cheng Li 001; Wenji Ma; Lusheng Wang 001 (J. Comput. Biol., 2013)

LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins. - Daniel Holtby; Shuai Cheng Li 001; Ming Li 001 (J. Comput. Biol., 2013)

Fingerprinting protein structures effectively and efficiently. - Xuefeng Cui; Shuai Cheng Li 001; Lin He 002; Ming Li 001 (Bioinform., 2014)

Spectral probabilities of top-down tandem mass spectra. - Xiaowen Liu; Matthew W. Segar; Shuai Cheng Li 001; Sangtae Kim (BMC Genom., 2014)

Probabilistic Models for Capturing More Physicochemical Properties on Protein-Protein Interface. - Fei Guo 001; Shuai Cheng Li 001; Pufeng Du; Lusheng Wang 001 (J. Chem. Inf. Model., 2014)

Quantifying Significance of MHC II Residues. - Ying Fan; Ruoshui Lu; Lusheng Wang 001; Massimo Andreatta; Shuai Cheng Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation. - Laleh Soltan Ghoraie; Forbes J. Burkowski; Shuai Cheng Li 001; Mu Zhu (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Compare local pocket and global protein structure models by small structure patterns. - Xuefeng Cui; Hiroyuki Kuwahara; Shuai Cheng Li 001; Xin Gao 001 (BCB, 2015)

Reconstructing directed gene regulatory network by only gene expression data. - Lu Zhang 061; Yen Kaow Ng; Shuaicheng Li 001 (BIBM, 2015)

On the Near-Linear Correlation of the Eigenvalues Across BLOSUM Matrices. - Jin Li; Yen Kaow Ng; Xingwu Liu; Shuai Cheng Li 001 (ISBRA, 2015)

Finding All Longest Common Segments in Protein Structures Efficiently. - Yen Kaow Ng; Linzhi Yin; Hirotaka Ono 001; Shuai Cheng Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Parameterized BLOSUM Matrices for Protein Alignment. - Dandan Song; Jiaxing Chen; Guang Chen; Ning Li; Jin Li; Jun Fan; Dongbo Bu; Shuai Cheng Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Finding more effective microsatellite markers for forensics. - Bowen Tan; Zhe Zhang; Zicheng Zhao; Shengbin Li; Shuai Cheng Li 001 (BIBM, 2016)

More accurate models for detecting gene-gene interactions from public expression compendia. - Lu Zhang 061; Jiaxing Chen; Shuai Cheng Li 001 (BIBM, 2016)

Eliminating heterozygosity from reads through coverage normalization. - Zicheng Zhao; Yen Kaow Ng; Xiaodong Fang; Shuaicheng Li 001 (BIBM, 2016)

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. - Chao Wang; Haicang Zhang; Wei-Mou Zheng; Dong Xu 002; Jianwei Zhu; Bing Wang; Kang Ning 001; Shiwei Sun; Shuai Cheng Li 001; Dongbo Bu (Bioinform., 2016)

Protein-protein interface prediction based on hexagon structure similarity. - Fei Guo 001; Yijie Ding; Shuai Cheng Li 001; Chao Shen; Lusheng Wang 001 (Comput. Biol. Chem., 2016)

Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats. - Dan Wang; Shuaicheng Li 001; Fei Guo 001; Lusheng Wang 001 (CoRR, 2016)

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. - Jianwei Zhu; Haicang Zhang; Shuai Cheng Li 001; Chao Wang; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (Bioinform., 2017)

Placing Segments on Parallel Arcs. - Yen Kaow Ng; Wenlong Jia; Shuai Cheng Li 001 (IWOCA, 2018)

In silico design of MHC class I high binding affinity peptides through motifs activation map. - Zhoujian Xiao; Yuwei Zhang 005; Runsheng Yu; Yin Chen; Xiaosen Jiang; Ziwei Wang; Shuaicheng Li 001 (BMC Bioinform., 2018)

KDiamend: a package for detecting key drivers in a molecular ecological network of disease. - Mengxuan Lyu; Jiaxing Chen; Yiqi Jiang; Wei Dong; Zhou Fang; Shuai Cheng Li 001 (BMC Syst. Biol., 2018)

NGS-based likelihood ratio for identifying contributors in two- and three-person DNA mixtures. - Joshua Chan Mun Wei; Zicheng Zhao; Shuai Cheng Li 001; Yen Kaow Ng (Comput. Biol. Chem., 2018)

Guest Editorial for the 15th Asia Pacific Bioinformatics Conference. - Lusheng Wang 001; Shuai Cheng Li 001; Yi-Ping Phoebe Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

LysoPhD: predicting functional prophages in bacterial genomes from high-throughput sequencing. - Qi Niu; Shaoliang Peng; Xiang-Li-Lan Zhang; Shuai Cheng Li 001; Ying Xu; Xiang-Cheng Xie; Yi-Gang Tong (BIBM, 2019)

DeepMF: deciphering the latent patterns in omics profiles with a deep learning method. - Lingxi Chen; Jiao Xu; Shuai Cheng Li 001 (BMC Bioinform., 2019)

MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals. - Xikang Feng; Zishuai Wang; Hechen Li; Shuai Cheng Li 001 (BMC Bioinform., 2019)

LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics. - Chen Li 023; Yiqi Jiang; Shuaicheng Li 001 (BMC Bioinform., 2019)

A unified STR profiling system across multiple species with whole genome sequencing data. - Yilin Liu; Jiao Xu; Miaoxia Chen; Changfa Wang; Shuai Cheng Li 001 (BMC Bioinform., 2019)

SpliceFinder: ab initio prediction of splice sites using convolutional neural network. - Ruohan Wang; Zishuai Wang; Jianping Wang 001; Shuaicheng Li 001 (BMC Bioinform., 2019)

Large-scale 3D chromatin reconstruction from chromosomal contacts. - Yanlin Zhang; Weiwei Liu 008; Yu Lin 001; Yen Kaow Ng; Shuaicheng Li 001 (BMC Genom., 2019)

LDscaff: LD-based scaffolding of de novo genome assemblies. - Zicheng Zhao; Yingxiao Zhou; Shuai Wang 036; Xiuqing Zhang; Changfa Wang; Shuai Cheng Li 001 (BMC Bioinform., 2020)

I-Impute: a self-consistent method to impute single cell RNA sequencing data. - Xikang Feng; Lingxi Chen; Zishuai Wang; Shuai Cheng Li 001 (BMC Genom., 2020)

Oviz-Bio: a web-based platform for interactive cancer genomics data visualization. - Wenlong Jia; Hechen Li; Shiying Li; Lingxi Chen; Shuai Cheng Li 001 (Nucleic Acids Res., 2020)

Resolving complex structures at oncovirus integration loci with conjugate graph. - Wenlong Jia; Chang Xu; Shuai Cheng Li 001 (Briefings Bioinform., 2021)

Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5. - Lu Liu; Xikang Feng; Haimei Li; Shuai Cheng Li 001; Qiujin Qian; Yufeng Wang (Briefings Bioinform., 2021)

PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data. - Shuai Wang 036; Yiqi Jiang; Shuai Cheng Li 001 (Bioinform., 2021)

Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics. - Lingxi Chen; Yuhao Qing; Ruikang Li; Chaohui Li; Hechen Li; Xikang Feng; Shuai Cheng Li 001 (Briefings Bioinform., 2022)

Resolving single-cell copy number profiling for large datasets. - Ruohan Wang; Yuwei Zhang 005; Mengbo Wang 001; Xikang Feng; Jianping Wang 001; Shuai Cheng Li 001 (Briefings Bioinform., 2022)

DeepHost: phage host prediction with convolutional neural network. - Ruohan Wang; Xiang-Li-Lan Zhang; Jianping Wang 001; Shuai Cheng Li 001 (Briefings Bioinform., 2022)

DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs. - Xuedong Wang; Yanle Liu; Xinyao Miao; Yin Chen; Xiao Cao; Yuchen Zhang; Shuaicheng Li 001; Qin Zhou (BMC Bioinform., 2022)

Nucleophilicity Prediction Using Graph Neural Networks. - Wan Nie; Deguang Liu; Shuaicheng Li 001; Haizhu Yu; Yao Fu (J. Chem. Inf. Model., 2022)

Correction: On triangle inequalities of correlation-based distances for gene expression profiles. - Jiaxing Chen; Yen Kaow Ng; Lu Lin; Xianglilan Zhang; Shuaicheng Li 001 (BMC Bioinform., 2022)

Correction: DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs. - Xuedong Wang; Yanle Liu; Xinyao Miao; Yin Chen; Xiao Cao; Yuchen Zhang; Shuaicheng Li 001; Qin Zhou (BMC Bioinform., 2022)

TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization. - Xueying Wang; Lingxi Chen; Wei Liu; Yuanzheng Zhang; Dawei Liu; Chenxin Zhou; Shuai Shi; Jiajie Dong; Zhengtao Lai; Bingran Zhao; Wenjingyu Zhang; Haoyue Cheng; et al. (Nucleic Acids Res., 2023)

TEINet: a deep learning framework for prediction of TCR-epitope binding specificity. - Yuepeng Jiang; Miaozhe Huo; Shuai Cheng Li 001 (Briefings Bioinform., 2023)

Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires. - Yuepeng Jiang; Shuai Cheng Li 001 (Briefings Bioinform., 2023)

IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data. - Wei Zhang 178; Jia Ju; Yong Zhou; Teng Xiong; Mengyao Wang; Chaohui Li; Shixin Lu; Zefeng Lu; Liya Lin; Xiao Liu; Shuaicheng Li 001 (Briefings Bioinform., 2023)

On triangle inequalities of correlation-based distances for gene expression profiles. - Jiaxing Chen; Yen Kaow Ng; Lu Lin; Xianglilan Zhang; Shuaicheng Li 001 (BMC Bioinform., 2023)

F2Key: Dynamically Converting Your Face into a Private Key Based on COTS Headphones for Reliable Voice Interaction. - Di Duan; Zehua Sun; Tao Ni 003; Shuaicheng Li 001; Xiaohua Jia; Weitao Xu; Tianxing Li 001 (MobiSys, 2024)

Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome. - Yinhu Li; Guangze Pan; Shuai Wang 036; Zhengtu Li; Ru Yang; Yiqi Jiang; Yu Chen; Shuaicheng Li 001; Bairong Shen (Briefings Bioinform., 2024)

SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization. - Zhao Ling; Yu Wei Zhang; Shuai Cheng Li 001 (J. Comput. Biol., 2024)

Unlocking T-cell receptor-epitope insights with structural analysis. - Miaozhe Huo; Yuepeng Jiang; Shuai Cheng Li 001 (Nat. Comput. Sci., 2024)

Automated Prediction of Protein Pair Distances Based on Deep Learning: A Novel Approach to Protein Structure Prediction in SCOP. - Duo Feng; Shuaicheng Li 001; Yue Zhang (ISBRA (2), 2025)