Shuaicheng Li

Orcid: 0000-0001-6246-6349

Affiliations:
  • City University of Hong Kong, Kowloon, Hong Kong
  • University of California, Berkeley, International Computer Science Institute, CA, USA
  • University of Waterloo, David R. Cheriton School of Computer Science, ON, Canada (PhD)
  • National University of Singapore, Department of Computer Science, Singapore


According to our database1, Shuaicheng Li authored at least 81 papers between 2004 and 2024.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Dataset
Other 

Links

Online presence:

On csauthors.net:

Bibliography

2024
Unlocking T-cell receptor-epitope insights with structural analysis.
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.
Proceedings of the 22nd Annual International Conference on Mobile Systems, 2024

2023
On triangle inequalities of correlation-based distances for gene expression profiles.
BMC Bioinform., December, 2023

IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data.
Briefings Bioinform., March, 2023

Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires.
Briefings Bioinform., March, 2023

TEINet: a deep learning framework for prediction of TCR-epitope binding specificity.
Briefings Bioinform., March, 2023

TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization.
Nucleic Acids Res., January, 2023

2022
Correction: DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs.
BMC Bioinform., December, 2022

Correction: On triangle inequalities of correlation-based distances for gene expression profiles.
BMC Bioinform., March, 2022

Nucleophilicity Prediction Using Graph Neural Networks.
J. Chem. Inf. Model., 2022

DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs.
BMC Bioinform., 2022

DeepHost: phage host prediction with convolutional neural network.
Briefings Bioinform., 2022

Resolving single-cell copy number profiling for large datasets.
Briefings Bioinform., 2022

Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics.
Briefings Bioinform., 2022

2021
PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data.
Bioinform., 2021

Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5.
Briefings Bioinform., 2021

Resolving complex structures at oncovirus integration loci with conjugate graph.
Briefings Bioinform., 2021

2020
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization.
Nucleic Acids Res., 2020

I-Impute: a self-consistent method to impute single cell RNA sequencing data.
BMC Genom., 2020

LDscaff: LD-based scaffolding of de novo genome assemblies.
BMC Bioinform., 2020

2019
Large-scale 3D chromatin reconstruction from chromosomal contacts.
BMC Genom., 2019

SpliceFinder: ab initio prediction of splice sites using convolutional neural network.
BMC Bioinform., 2019

A unified STR profiling system across multiple species with whole genome sequencing data.
BMC Bioinform., 2019

LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics.
BMC Bioinform., 2019

MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals.
BMC Bioinform., 2019

DeepMF: deciphering the latent patterns in omics profiles with a deep learning method.
BMC Bioinform., 2019

LysoPhD: predicting functional prophages in bacterial genomes from high-throughput sequencing.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018
Guest Editorial for the 15th Asia Pacific Bioinformatics Conference.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

NGS-based likelihood ratio for identifying contributors in two- and three-person DNA mixtures.
Comput. Biol. Chem., 2018

KDiamend: a package for detecting key drivers in a molecular ecological network of disease.
BMC Syst. Biol., 2018

In silico design of MHC class I high binding affinity peptides through motifs activation map.
BMC Bioinform., 2018

Placing Segments on Parallel Arcs.
Proceedings of the Combinatorial Algorithms - 29th International Workshop, 2018

2017
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.
Bioinform., 2017

2016
Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.
CoRR, 2016

Protein-protein interface prediction based on hexagon structure similarity.
Comput. Biol. Chem., 2016

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Bioinform., 2016

Eliminating heterozygosity from reads through coverage normalization.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

More accurate models for detecting gene-gene interactions from public expression compendia.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Finding more effective microsatellite markers for forensics.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
Parameterized BLOSUM Matrices for Protein Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Finding All Longest Common Segments in Protein Structures Efficiently.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

On the Near-Linear Correlation of the Eigenvalues Across BLOSUM Matrices.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

Reconstructing directed gene regulatory network by only gene expression data.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Compare local pocket and global protein structure models by small structure patterns.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014
Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Quantifying Significance of MHC II Residues.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Probabilistic Models for Capturing More Physicochemical Properties on Protein-Protein Interface.
J. Chem. Inf. Model., 2014

Spectral probabilities of top-down tandem mass spectra.
BMC Genom., 2014

Fingerprinting protein structures effectively and efficiently.
Bioinform., 2014

2013
LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins.
J. Comput. Biol., 2013

Detecting Protein Conformational Changes in Interactions via Scaling Known Structures.
J. Comput. Biol., 2013

The Difficulty Of Protein Structure Alignment Under The RMSD.
Algorithms Mol. Biol., 2013

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?
Algorithms Mol. Biol., 2013

Towards Reliable Automatic Protein Structure Alignment.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012
Clustering 100, 000 Protein Structure Decoys in Minutes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Protein-protein binding site identification by enumerating the configurations.
BMC Bioinform., 2012

How Accurately Can We Model Protein Structures with Dihedral Angles?
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

P-Binder: A System for the Protein-Protein Binding Sites Identification.
Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

Finding Longest Common Segments in Protein Structures in Nearly Linear Time.
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011
On protein structure alignment under distance constraint.
Theor. Comput. Sci., 2011

Protein-Protein Binding Sites Prediction by 3D Structural Similarities.
J. Chem. Inf. Model., 2011

Finding Nearly Optimal GDT Scores.
J. Comput. Biol., 2011

Pedigree Reconstruction Using Identity by Descent.
J. Comput. Biol., 2011

Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation.
J. Bioinform. Comput. Biol., 2011

2010
Protein Secondary Structure Prediction Using NMR Chemical Shift Data.
J. Bioinform. Comput. Biol., 2010

Calibur: a tool for clustering large numbers of protein decoys.
BMC Bioinform., 2010

2009
On two open problems of 2-interval patterns.
Theor. Comput. Sci., 2009

Finding compact structural motifs.
Theor. Comput. Sci., 2009

Predicting Local Quality of a Sequence-Structure Alignment.
J. Bioinform. Comput. Biol., 2009

2008
A PTAS For The <i>k</i>-Consensus Structures Problem Under Squared Euclidean Distance.
Algorithms, 2008

Designing succinct structural alphabets.
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.
Proceedings of the Frontiers in Algorithmics, Second Annual International Workshop, 2008

Finding Largest Well-Predicted Subset of Protein Structure Models.
Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007
New Algorithms for the Spaced Seeds.
Proceedings of the Frontiers in Algorithmics, First Annual International Workshop, 2007

2006
On the Complexity of the Crossing Contact Map Pattern Matching Problem.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Faster Algorithms for Finding Missing Patterns.
Proceedings of the Theory of Computing 2006, 2006

2005
Indexing DNA Sequences Using q-Grams.
Proceedings of the Database Systems for Advanced Applications, 2005

2004
Piers: An Efficient Model for Similarity Search in DNA Sequence Databases.
SIGMOD Rec., 2004

String Join Using Precedence Count Matrix.
Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM 2004), 2004

New Approximation Algorithms for Some Dynamic Storage Allocation Problems.
Proceedings of the Computing and Combinatorics, 10th Annual International Conference, 2004


  Loading...