2024
Novel Fine-Tuning Strategy on Pre-trained Protein Model Enhances ACP Functional Type Classification.
Proceedings of the Bioinformatics Research and Applications - 20th International Symposium, 2024
2023
NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023
Deep learning boosted amyloidosis diagnosis.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023
2022
SPEQ: quality assessment of peptide tandem mass spectra with deep learning.
Bioinform., 2022
2019
Designing and implementing algorithms for the closest string problem.
Theor. Comput. Sci., 2019
Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
An Improved Approach for N-Linked Glycan Structure Identification from HCD MS/MS Spectra.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
2017
An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
2016
Closest String and Substring Problems.
Encyclopedia of Algorithms, 2016
Peptide De Novo Sequencing with MS/MS.
Encyclopedia of Algorithms, 2016
Randomized Fixed-Parameter Algorithms for the Closest String Problem.
Algorithmica, 2016
Chapter 2. De novo Peptide Sequencing.
Proceedings of the Proteome Informatics, 2016
2015
A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015
An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015
2014
Optimizing Spaced $k$-mer Neighbors for Efficient Filtration in Protein Similarity Search.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
Estimating feature ratings through an effective review selection approach.
Knowl. Inf. Syst., 2014
An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra.
Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014
Randomized and Parameterized Algorithms for the Closest String Problem.
Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014
2013
<i>De novo</i> sequencing with Limited Number of Post-Translational Modifications per peptide.
J. Bioinform. Comput. Biol., 2013
A combinatorial approach to the peptide feature matching problem for label-free quantification.
Bioinform., 2013
Peptide Identification from Mass Spectrometry.
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013
2012
A three-string approach to the closest string problem.
J. Comput. Syst. Sci., 2012
Efficient filtration for similarity search with spaced k-mer neighbors.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012
2011
Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction.
J. Comb. Optim., 2011
Closest string with outliers.
BMC Bioinform., 2011
2010
ZOOM Lite: next-generation sequencing data mapping and visualization software.
Nucleic Acids Res., 2010
Ancient Chinese zither (guqin) music recovery with support vector machine.
ACM Journal on Computing and Cultural Heritage, 2010
Adepts: Advanced peptide <i>de novo</i> Sequencing with a Pair of Tandem Mass Spectra.
J. Bioinform. Comput. Biol., 2010
Better score function for peptide identification with ETD MS/MS spectra.
BMC Bioinform., 2010
On the Longest Common Rigid Subsequence Problem.
Algorithmica, 2010
De Novo Sequencing Methods in Proteomics.
Proceedings of the Proteome Bioinformatics, 2010
2009
Why greed works for shortest common superstring problem.
Theor. Comput. Sci., 2009
On the similarity metric and the distance metric.
Theor. Comput. Sci., 2009
More Efficient Algorithms for Closest String and Substring Problems.
SIAM J. Comput., 2009
Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics.
J. Comput. Sci. Technol., 2009
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design.
Inf. Process. Lett., 2009
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.
Bioinform., 2009
Specialized Review Selection for Feature Rating Estimation.
Proceedings of the 2009 IEEE/WIC/ACM International Conference on Web Intelligence, 2009
Amino Acid Classification and Hash Seeds for Homology Search.
Proceedings of the Bioinformatics and Computational Biology, 2009
2008
Peptide De Novo Sequencing with MS/MS.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008
Rainbow Network Flow of Multiple Description Codes.
IEEE Trans. Inf. Theory, 2008
A new quartet approach for reconstructing phylogenetic trees: quartet joining method.
J. Comb. Optim., 2008
Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol., 2008
ZOOM! Zillions of oligos mapped.
Bioinform., 2008
Information shared by many objects.
Proceedings of the 17th ACM Conference on Information and Knowledge Management, 2008
Seed Optimization Is No Easier than Optimal Golomb Ruler Design.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008
PAS: Predicate-Based Authentication Services Against Powerful Passive Adversaries.
Proceedings of the Twenty-Fourth Annual Computer Security Applications Conference, 2008
2007
Mobility Limited Flip-Based Sensor Networks Deployment.
IEEE Trans. Parallel Distributed Syst., 2007
Deploying Wireless Sensor Networks under Limited Mobility Constraints.
IEEE Trans. Mob. Comput., 2007
Near optimal multiple alignment within a band in polynomial time.
J. Comput. Syst. Sci., 2007
On the complexity of the spaced seeds.
J. Comput. Syst. Sci., 2007
Rapid Homology Search with Neighbor Seeds.
Algorithmica, 2007
The Normalized Similarity Metric and Its Applications.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007
Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007
2006
Optimizing Multiple Spaced Seeds for Homology Search.
J. Comput. Biol., 2006
Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures.
J. Bioinform. Comput. Biol., 2006
Prima: Peptide Robust Identification from Ms/ms Spectra.
J. Bioinform. Comput. Biol., 2006
Superiority and complexity of the spaced seeds.
Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2006
2005
An effective algorithm for peptide de novo sequencing from MS/MS spectra.
J. Comput. Syst. Sci., 2005
Spider: Software for Protein Identification from Sequence Tags with <i>de Novo</i> Sequencing Error.
J. Bioinform. Comput. Biol., 2005
An automata approach to match gapped sequence tags against protein database.
Int. J. Found. Comput. Sci., 2005
tPatternHunter: gapped, fast and sensitive translated homology search .
Bioinform., 2005
Sensor networks deployment using flip-based sensors.
Proceedings of the IEEE 2nd International Conference on Mobile Adhoc and Sensor Systems, 2005
Rainbow network problems and multiple description coding.
Proceedings of the 2005 IEEE International Symposium on Information Theory, 2005
On the Longest Common Rigid Subsequence Problem.
Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005
Rapid Homology Search with Two-Stage Extension and Daughter Seeds.
Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005
PRIME: Peptide robust identification from MS/MS spectra.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
IEEE Trans. Inf. Theory, 2004
The longest common subsequence problem for arc-annotated sequences.
J. Discrete Algorithms, 2004
Patternhunter Ii: Highly Sensitive and Fast Homology Search.
J. Bioinform. Comput. Biol., 2004
A Tutorial of Recent Developments in the Seeding of Local Alignment.
J. Bioinform. Comput. Biol., 2004
On spaced seeds for similarity search.
Discret. Appl. Math., 2004
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
2003
Genetic Design of Drugs Without Side-Effects.
SIAM J. Comput., 2003
Distinguishing string selection problems.
Inf. Comput., 2003
Greedy method for inferring tandem duplication history.
Bioinform., 2003
An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.
Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003
Alignment between Two Multiple Alignments.
Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003
2002
Computing similarity between RNA structures.
Theor. Comput. Sci., 2002
Finding Similar Regions in Many Sequences.
J. Comput. Syst. Sci., 2002
Methods for reconstructing the history of tandem repeats and their application to the human genome.
J. Comput. Syst. Sci., 2002
A General Edit Distance between RNA Structures.
J. Comput. Biol., 2002
On the closest string and substring problems.
J. ACM, 2002
PatternHunter: faster and more sensitive homology search.
Bioinform., 2002
DNACompress: fast and effective DNA sequence compression.
Bioinform., 2002
Efficient Methods for Inferring Tandem Duplication History.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
A PTAS for Distinguishing (Sub)string Selection.
Proceedings of the Automata, Languages and Programming, 29th International Colloquium, 2002
2001
Edit distance between two RNA structures.
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001
2000
From Gene Trees to Species Trees.
SIAM J. Comput., 2000
On the Inapproximability of Disjoint Paths and Minimum Steiner Forest with Bandwidth Constraints.
J. Comput. Syst. Sci., 2000
Fixed topology alignment with recombination.
Discret. Appl. Math., 2000
A Polynominal Time Approximation Scheme for the Closest Substring Problem.
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000
1999
Fitting Distances by Tree Metrics with Increment Error.
J. Comb. Optim., 1999
Finding Similar Regions in Many Strings.
Proceedings of the Thirty-First Annual ACM Symposium on Theory of Computing, 1999
1998
On reconstructing species trees from gene trees in term of duplications and losses.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998