Shuai Cheng Li

75 papers A 1B 9C 4Misc 2Journal 52Unranked 7
YearRankTypeTitle / Venue / Authors
2025 J jnl
A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Briefings Bioinform.
Xikang Feng, Miaozhe Huo, He Li, Yongze Yang, Yuepeng Jiang, Liang He, Shuai Cheng Li
2025 J jnl
AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.
Bioinform.
Jiaqi Luo, Yiping Zou, Shuai Cheng Li
2024 J jnl
Coding genomes with gapped pattern graph convolutional network.
Bioinform.
Ruohan Wang, Yen Kaow Ng, Xianglilan Zhang, Jianping Wang, Shuai Cheng Li
2024 J jnl
Elevated incidence of somatic mutations at prevalent genetic sites.
Briefings Bioinform.
Mengyao Wang, Shuai Cheng Li, Bairong Shen
2024 J jnl
SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization.
J. Comput. Biol.
Zhao Ling, Yuwei Zhang, Shuai Cheng Li
2024 J jnl
Unlocking T-cell receptor-epitope insights with structural analysis.
Nat. Comput. Sci.
Miaozhe Huo, Yuepeng Jiang, Shuai Cheng Li
2023 J jnl
Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires.
Briefings Bioinform.
Yuepeng Jiang, Shuai Cheng Li
2023 J jnl
TEINet: a deep learning framework for prediction of TCR-epitope binding specificity.
Briefings Bioinform.
Yuepeng Jiang, Miaozhe Huo, Shuai Cheng Li
2022 J jnl
DeepHost: phage host prediction with convolutional neural network.
Briefings Bioinform.
Ruohan Wang, Xiang-Li-Lan Zhang, Jianping Wang, Shuai Cheng Li
2022 J jnl
Resolving single-cell copy number profiling for large datasets.
Briefings Bioinform.
Ruohan Wang, Yuwei Zhang, Mengbo Wang, Xikang Feng, Jianping Wang, Shuai Cheng Li
2022 J jnl
Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics.
Briefings Bioinform.
Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li
2021 J jnl
Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5.
Briefings Bioinform.
Lu Liu, Xikang Feng, Haimei Li, Shuai Cheng Li, Qiujin Qian, Yufeng Wang
2021 J jnl
PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data.
Bioinform.
Shuai Wang, Yiqi Jiang, Shuai Cheng Li
2021 J jnl
Resolving complex structures at oncovirus integration loci with conjugate graph.
Briefings Bioinform.
Wenlong Jia, Chang Xu, Shuai Cheng Li
2020 J jnl
I-Impute: a self-consistent method to impute single cell RNA sequencing data.
BMC Genom.
Xikang Feng, Lingxi Chen, Zishuai Wang, Shuai Cheng Li
2020 J jnl
LDscaff: LD-based scaffolding of de novo genome assemblies.
BMC Bioinform.
Zicheng Zhao, Yingxiao Zhou, Shuai Wang, Xiuqing Zhang, Changfa Wang, Shuai Cheng Li
2020 J jnl
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization.
Nucleic Acids Res.
Wenlong Jia, Hechen Li, Shiying Li, Lingxi Chen, Shuai Cheng Li
2019 J jnl
A unified STR profiling system across multiple species with whole genome sequencing data.
BMC Bioinform.
Yilin Liu, Jiao Xu, Miaoxia Chen, Changfa Wang, Shuai Cheng Li
2019 J jnl
DeepMF: deciphering the latent patterns in omics profiles with a deep learning method.
BMC Bioinform.
Lingxi Chen, Jiao Xu, Shuai Cheng Li
2019 — conf
LysoPhD: predicting functional prophages in bacterial genomes from high-throughput sequencing.
BIBM
Qi Niu, Shaoliang Peng, Xiang-Li-Lan Zhang, Shuai Cheng Li, Ying Xu, Xiang-Cheng Xie, Yi-Gang Tong
2019 J jnl
MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals.
BMC Bioinform.
Xikang Feng, Zishuai Wang, Hechen Li, Shuai Cheng Li
2018 J jnl
Guest Editorial for the 15th Asia Pacific Bioinformatics Conference.
IEEE ACM Trans. Comput. Biol. Bioinform.
Lusheng Wang, Shuai Cheng Li, Yi-Ping Phoebe Chen
2018 J jnl
KDiamend: a package for detecting key drivers in a molecular ecological network of disease.
BMC Syst. Biol.
Mengxuan Lyu, Jiaxing Chen, Yiqi Jiang, Wei Dong, Zhou Fang, Shuai Cheng Li
2018 J jnl
NGS-based likelihood ratio for identifying contributors in two- and three-person DNA mixtures.
Comput. Biol. Chem.
Joshua Chan Mun Wei, Zicheng Zhao, Shuai Cheng Li, Yen Kaow Ng
2018 C conf
Placing Segments on Parallel Arcs.
IWOCA
Yen Kaow Ng, Wenlong Jia, Shuai Cheng Li
2017 J jnl
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.
Bioinform.
Jianwei Zhu, Haicang Zhang, Shuai Cheng Li, Chao Wang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu
2016 J jnl
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Bioinform.
Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, Dongbo Bu
2016 — conf
Finding more effective microsatellite markers for forensics.
BIBM
Bowen Tan, Zhe Zhang, Zicheng Zhao, Shengbin Li, Shuai Cheng Li
2016 — conf
More accurate models for detecting gene-gene interactions from public expression compendia.
BIBM
Lu Zhang, Jiaxing Chen, Shuai Cheng Li
2016 J jnl
Protein-protein interface prediction based on hexagon structure similarity.
Comput. Biol. Chem.
Fei Guo, Yijie Ding, Shuai Cheng Li, Chao Shen, Lusheng Wang
2015 — conf
Compare local pocket and global protein structure models by small structure patterns.
BCB
Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li, Xin Gao
2015 J jnl
Finding All Longest Common Segments in Protein Structures Efficiently.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yen Kaow Ng, Linzhi Yin, Hirotaka Ono, Shuai Cheng Li
2015 — conf
On the Near-Linear Correlation of the Eigenvalues Across BLOSUM Matrices.
ISBRA
Jin Li, Yen Kaow Ng, Xingwu Liu, Shuai Cheng Li
2015 J jnl
Parameterized BLOSUM Matrices for Protein Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform.
Dandan Song, Jiaxing Chen, Guang Chen, Ning Li, Jin Li, Jun Fan, Dongbo Bu, Shuai Cheng Li
2014 J jnl
Fingerprinting protein structures effectively and efficiently.
Bioinform.
Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li
2014 J jnl
Probabilistic Models for Capturing More Physicochemical Properties on Protein-Protein Interface.
J. Chem. Inf. Model.
Fei Guo, Shuai Cheng Li, Pufeng Du, Lusheng Wang
2014 J jnl
Quantifying Significance of MHC II Residues.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ying Fan, Ruoshui Lu, Lusheng Wang, Massimo Andreatta, Shuai Cheng Li
2014 J jnl
Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation.
IEEE ACM Trans. Comput. Biol. Bioinform.
Laleh Soltan Ghoraie, Forbes J. Burkowski, Shuai Cheng Li, Mu Zhu
2014 J jnl
Spectral probabilities of top-down tandem mass spectra.
BMC Genom.
Xiaowen Liu, Matthew W. Segar, Shuai Cheng Li, Sangtae Kim
2013 B conf
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures.
RECOMB
Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang
2013 J jnl
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures.
J. Comput. Biol.
Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang
2013 J jnl
LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins.
J. Comput. Biol.
Daniel Holtby, Shuai Cheng Li, Ming Li
2013 J jnl
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?
Algorithms Mol. Biol.
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi, Ming Li
2013 J jnl
The Difficulty Of Protein Structure Alignment Under The RMSD.
Algorithms Mol. Biol.
Shuai Cheng Li
2013 C conf
Towards Reliable Automatic Protein Structure Alignment.
WABI
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li
2012 J jnl
Clustering 100, 000 Protein Structure Decoys in Minutes.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuai Cheng Li, Dongbo Bu, Ming Li
2012 B conf
Finding Longest Common Segments in Protein Structures in Nearly Linear Time.
CPM
Yen Kaow Ng, Hirotaka Ono, Ling Ge, Shuai Cheng Li
2012 C conf
How Accurately Can We Model Protein Structures with Dihedral Angles?
WABI
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li
2012 B conf
LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins.
RECOMB
Daniel Holtby, Shuai Cheng Li, Ming Li
2012 — conf
P-Binder: A System for the Protein-Protein Binding Sites Identification.
ISBRA
Fei Guo, Shuai Cheng Li, Lusheng Wang
2012 J jnl
Protein-protein binding site identification by enumerating the configurations.
BMC Bioinform.
Fei Guo, Shuai Cheng Li, Lusheng Wang, Daming Zhu
2012 J jnl
Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuai Cheng Li, Dongbo Bu, Ming Li
2011 J jnl
Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation.
J. Bioinform. Comput. Biol.
Babak Alipanahi, Xin Gao, Emre Karakoç, Shuai Cheng Li, Frank J. Balbach, Guangyu Feng, Logan Donaldson, Ming Li
2011 J jnl
Finding Nearly Optimal GDT Scores.
J. Comput. Biol.
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
2011 J jnl
On protein structure alignment under distance constraint.
Theor. Comput. Sci.
Shuai Cheng Li, Yen Kaow Ng
2011 B conf
Pedigree Reconstruction Using Identity by Descent.
RECOMB
Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin
2011 J jnl
Pedigree Reconstruction Using Identity by Descent.
J. Comput. Biol.
Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin
2011 J jnl
Protein-Protein Binding Sites Prediction by 3D Structural Similarities.
J. Chem. Inf. Model.
Fei Guo, Shuai Cheng Li, Lusheng Wang
2010 J jnl
Calibur: a tool for clustering large numbers of protein decoys.
BMC Bioinform.
Shuai Cheng Li, Yen Kaow Ng
2010 J jnl
Protein Secondary Structure Prediction Using NMR Chemical Shift Data.
J. Bioinform. Comput. Biol.
Yuzhong Zhao, Babak Alipanahi, Shuai Cheng Li, Ming Li
2009 J jnl
Finding compact structural motifs.
Theor. Comput. Sci.
Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu
2009 B conf
On Protein Structure Alignment under Distance Constraint.
ISAAC
Shuai Cheng Li, Yen Kaow Ng
2009 J jnl
On two open problems of 2-interval patterns.
Theor. Comput. Sci.
Shuai Cheng Li, Ming Li
2009 J jnl
Predicting Local Quality of a Sequence-Structure Alignment.
J. Bioinform. Comput. Biol.
Xin Gao, Jinbo Xu, Shuai Cheng Li, Ming Li
2008 J jnl
A PTAS For The
Algorithms
Shuai Cheng Li, Yen Kaow Ng, Louxin Zhang
2008 Misc conf
A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance.
FAW
Shuai Cheng Li, Yen Kaow Ng, Louxin Zhang
2008 A conf
Designing succinct structural alphabets.
ISMB
Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li
2008 B conf
Finding Largest Well-Predicted Subset of Protein Structure Models.
CPM
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
2007 B conf
Finding Compact Structural Motifs.
CPM
Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu
2006 — conf
Faster Algorithms for Finding Missing Patterns.
CATS
Shuai Cheng Li
2006 C conf
On the Complexity of the Crossing Contact Map Pattern Matching Problem.
WABI
Shuai Cheng Li, Ming Li
2005 B conf
Indexing DNA Sequences Using q-Grams.
DASFAA
Xia Cao, Shuai Cheng Li, Anthony K. H. Tung
2004 Misc conf
New Approximation Algorithms for Some Dynamic Storage Allocation Problems.
COCOON
Shuai Cheng Li, Hon Wai Leong, Steven K. Quek
2004 J jnl
Piers: An Efficient Model for Similarity Search in DNA Sequence Databases.
SIGMOD Rec.
Xia Cao, Shuai Cheng Li, Beng Chin Ooi, Anthony K. H. Tung
2004 B conf
String Join Using Precedence Count Matrix.
SSDBM
Xia Cao, Anthony K. H. Tung, Beng Chin Ooi, Kian-Lee Tan, Shuai Cheng Li