Shuaicheng Li

Nat. Comput. Sci., July, 2024

F<sup>2</sup>Key: Dynamically Converting Your Face into a Private Key Based on COTS Headphones for Reliable Voice Interaction.

[BibT_eX]

[DOI]

Proceedings of the 22nd Annual International Conference on Mobile Systems, 2024

2023

On triangle inequalities of correlation-based distances for gene expression profiles.

[BibT_eX]

[DOI]

BMC Bioinform., December, 2023

IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data.

[BibT_eX]

[DOI]

Briefings Bioinform., March, 2023

Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires.

[BibT_eX]

[DOI]

Yuepeng Jiang

Briefings Bioinform., March, 2023

TEINet: a deep learning framework for prediction of TCR-epitope binding specificity.

[BibT_eX]

[DOI]

Yuepeng Jiang

Miaozhe Huo

Briefings Bioinform., March, 2023

TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization.

[BibT_eX]

[DOI]

Nucleic Acids Res., January, 2023

2022

Correction: DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs.

[BibT_eX]

[DOI]

BMC Bioinform., December, 2022

Correction: On triangle inequalities of correlation-based distances for gene expression profiles.

[BibT_eX]

[DOI]

BMC Bioinform., March, 2022

Nucleophilicity Prediction Using Graph Neural Networks.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs.

[BibT_eX]

[DOI]

BMC Bioinform., 2022

DeepHost: phage host prediction with convolutional neural network.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Resolving single-cell copy number profiling for large datasets.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

2021

PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data.

[BibT_eX]

[DOI]

Shuai Wang

Yiqi Jiang

Bioinform., 2021

Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

Resolving complex structures at oncovirus integration loci with conjugate graph.

[BibT_eX]

[DOI]

Wenlong Jia

Chang Xu

Briefings Bioinform., 2021

2020

Oviz-Bio: a web-based platform for interactive cancer genomics data visualization.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2020

I-Impute: a self-consistent method to impute single cell RNA sequencing data.

[BibT_eX]

[DOI]

BMC Genom., 2020

LDscaff: LD-based scaffolding of de novo genome assemblies.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

2019

Large-scale 3D chromatin reconstruction from chromosomal contacts.

[BibT_eX]

[DOI]

BMC Genom., 2019

SpliceFinder: ab initio prediction of splice sites using convolutional neural network.

[BibT_eX]

[DOI]

BMC Bioinform., 2019

A unified STR profiling system across multiple species with whole genome sequencing data.

[BibT_eX]

[DOI]

BMC Bioinform., 2019

LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics.

[BibT_eX]

[DOI]

Chen Li

Yiqi Jiang

Shuaicheng Li

BMC Bioinform., 2019

MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals.

[BibT_eX]

[DOI]

BMC Bioinform., 2019

DeepMF: deciphering the latent patterns in omics profiles with a deep learning method.

[BibT_eX]

[DOI]

Lingxi Chen

Jiao Xu

BMC Bioinform., 2019

LysoPhD: predicting functional prophages in bacterial genomes from high-throughput sequencing.

[BibT_eX]

[DOI]

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

Guest Editorial for the 15th Asia Pacific Bioinformatics Conference.

[BibT_eX]

[DOI]

Lusheng Wang

Yi-Ping Phoebe Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

NGS-based likelihood ratio for identifying contributors in two- and three-person DNA mixtures.

[BibT_eX]

[DOI]

Comput. Biol. Chem., 2018

KDiamend: a package for detecting key drivers in a molecular ecological network of disease.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2018

In silico design of MHC class I high binding affinity peptides through motifs activation map.

[BibT_eX]

[DOI]

BMC Bioinform., 2018

Placing Segments on Parallel Arcs.

[BibT_eX]

[DOI]

Wenlong Jia

Proceedings of the Combinatorial Algorithms - 29th International Workshop, 2018

2017

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.

[BibT_eX]

[DOI]

Bioinform., 2017

2016

Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.

[BibT_eX]

[DOI]

CoRR, 2016

Protein-protein interface prediction based on hexagon structure similarity.

[BibT_eX]

[DOI]

Comput. Biol. Chem., 2016

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.

[BibT_eX]

[DOI]

Bioinform., 2016

Eliminating heterozygosity from reads through coverage normalization.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

More accurate models for detecting gene-gene interactions from public expression compendia.

[BibT_eX]

[DOI]

Lu Zhang

Jiaxing Chen

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Finding more effective microsatellite markers for forensics.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

Parameterized BLOSUM Matrices for Protein Alignment.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Finding All Longest Common Segments in Protein Structures Efficiently.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

On the Near-Linear Correlation of the Eigenvalues Across BLOSUM Matrices.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

Reconstructing directed gene regulatory network by only gene expression data.

[BibT_eX]

[DOI]

Lu Zhang

Shuaicheng Li

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Compare local pocket and global protein structure models by small structure patterns.

[BibT_eX]

[DOI]

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Quantifying Significance of MHC II Residues.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Probabilistic Models for Capturing More Physicochemical Properties on Protein-Protein Interface.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2014

Spectral probabilities of top-down tandem mass spectra.

[BibT_eX]

[DOI]

BMC Genom., 2014

Fingerprinting protein structures effectively and efficiently.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins.

[BibT_eX]

[DOI]

Daniel Holtby

J. Comput. Biol., 2013

Detecting Protein Conformational Changes in Interactions via Scaling Known Structures.

[BibT_eX]

[DOI]

J. Comput. Biol., 2013

The Difficulty Of Protein Structure Alignment Under The RMSD.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Towards Reliable Automatic Protein Structure Alignment.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012

Clustering 100, 000 Protein Structure Decoys in Minutes.

[BibT_eX]

[DOI]

Dongbo Bu

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations.

[BibT_eX]

[DOI]

Dongbo Bu

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Protein-protein binding site identification by enumerating the configurations.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

How Accurately Can We Model Protein Structures with Dihedral Angles?

[BibT_eX]

[DOI]

Xuefeng Cui

Dongbo Bu

Babak Alipanahi Ramandi

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

P-Binder: A System for the Protein-Protein Binding Sites Identification.

[BibT_eX]

[DOI]

Fei Guo

Lusheng Wang

Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

Finding Longest Common Segments in Protein Structures in Nearly Linear Time.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011

On protein structure alignment under distance constraint.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2011

Protein-Protein Binding Sites Prediction by 3D Structural Similarities.

[BibT_eX]

[DOI]

Fei Guo

Lusheng Wang

J. Chem. Inf. Model., 2011

Finding Nearly Optimal GDT Scores.

[BibT_eX]

[DOI]

J. Comput. Biol., 2011

Pedigree Reconstruction Using Identity by Descent.

[BibT_eX]

[DOI]

J. Comput. Biol., 2011

Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2011

2010

Protein Secondary Structure Prediction Using NMR Chemical Shift Data.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2010

Calibur: a tool for clustering large numbers of protein decoys.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

2009

On two open problems of 2-interval patterns.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2009

Finding compact structural motifs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2009

Predicting Local Quality of a Sequence-Structure Alignment.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2009

2008

A PTAS For The <i>k</i>-Consensus Structures Problem Under Squared Euclidean Distance.

[BibT_eX]

[DOI]

Louxin Zhang

Algorithms, 2008

Designing succinct structural alphabets.

[BibT_eX]

[DOI]

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance.

[BibT_eX]

[DOI]

Louxin Zhang

Proceedings of the Frontiers in Algorithmics, Second Annual International Workshop, 2008

Finding Largest Well-Predicted Subset of Protein Structure Models.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007

New Algorithms for the Spaced Seeds.

[BibT_eX]

[DOI]

Xin Gao

Shuaicheng Li

Yinan Lu

Proceedings of the Frontiers in Algorithmics, First Annual International Workshop, 2007

2006

On the Complexity of the Crossing Contact Map Pattern Matching Problem.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Faster Algorithms for Finding Missing Patterns.

[BibT_eX]

[DOI]

Proceedings of the Theory of Computing 2006, 2006

2005

Indexing DNA Sequences Using q-Grams.

[BibT_eX]

[DOI]

Xia Cao

Anthony K. H. Tung

Proceedings of the Database Systems for Advanced Applications, 2005

2004

Piers: An Efficient Model for Similarity Search in DNA Sequence Databases.

[BibT_eX]

[DOI]

SIGMOD Rec., 2004

String Join Using Precedence Count Matrix.

[BibT_eX]

[DOI]

Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM 2004), 2004

New Approximation Algorithms for Some Dynamic Storage Allocation Problems.

[BibT_eX]

[DOI]