Bin Ma

According to our database, Bin Ma authored at least 95 papers between 1998 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Novel Fine-Tuning Strategy on Pre-trained Protein Model Enhances ACP Functional Type Classification.

Shaokai Wang, Bin Ma

Proceedings of the Bioinformatics Research and Applications - 20th International Symposium, 2024

2023

NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry.

Shaokai Wang, Ming Zhu, Bin Ma

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

Deep learning boosted amyloidosis diagnosis.

Shaokai Wang, Bin Ma

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

SPEQ: quality assessment of peptide tandem mass spectra with deep learning.

Soroosh Gholamizoj, Bin Ma

Bioinform., 2022

2019

Designing and implementing algorithms for the closest string problem.

Shota Yuasa, Zhi-Zhong Chen, Bin Ma, Lusheng Wang

Theor. Comput. Sci., 2019

Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing.

Tiancong Wang, Bin Ma

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

An Improved Approach for N-Linked Glycan Structure Identification from HCD MS/MS Spectra.

Weiping Sun, Yi Liu, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

2017

An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra.

Yi Liu, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

2016

Closest String and Substring Problems.

Lusheng Wang, Ming Li, Bin Ma

Encyclopedia of Algorithms, 2016

Peptide De Novo Sequencing with MS/MS.

Bin Ma

Encyclopedia of Algorithms, 2016

Randomized Fixed-Parameter Algorithms for the Closest String Problem.

Zhi-Zhong Chen, Bin Ma, Lusheng Wang

Algorithmica, 2016

Chapter 2. De novo Peptide Sequencing.

Bin Ma

Proceedings of the Proteome Informatics, 2016

2015

A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry.

Weiping Sun, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang

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.

Yi Liu, Weiping Sun, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang

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

2014

Optimizing Spaced $k$-mer Neighbors for Efficient Filtration in Protein Similarity Search.

Weiming Li, Bin Ma, Kaizhong Zhang

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

Estimating feature ratings through an effective review selection approach.

Chong Long, Jie Zhang, Minlie Huang, Xiaoyan Zhu, Ming Li, Bin Ma

Knowl. Inf. Syst., 2014

An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra.

Yi Liu, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie

Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Randomized and Parameterized Algorithms for the Closest String Problem.

Zhi-Zhong Chen, Bin Ma, Lusheng Wang

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.

Lin He, Xi Han, Bin Ma

J. Bioinform. Comput. Biol., 2013

A combinatorial approach to the peptide feature matching problem for label-free quantification.

Hao Lin, Lin He, Bin Ma

Bioinform., 2013

Peptide Identification from Mass Spectrometry.

Bin Ma

Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

2012

A three-string approach to the closest string problem.

Zhi-Zhong Chen, Bin Ma, Lusheng Wang

J. Comput. Syst. Sci., 2012

Efficient filtration for similarity search with spaced k-mer neighbors.

Weiming Li, Bin Ma, Kaizhong Zhang

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.

Bin Ma, Louxin Zhang

J. Comb. Optim., 2011

Closest string with outliers.

Christina Boucher, Bin Ma

BMC Bioinform., 2011

2010

ZOOM Lite: next-generation sequencing data mapping and visualization software.

Zefeng Zhang, Hao Lin, Bin Ma

Nucleic Acids Res., 2010

Ancient Chinese zither (guqin) music recovery with support vector machine.

Qing Sun, Deyun Zhang, Yifeng Fan, Kaizhong Zhang, Bin Ma

ACM Journal on Computing and Cultural Heritage, 2010

Adepts: Advanced peptide <i>de novo</i> Sequencing with a Pair of Tandem Mass Spectra.

Lin He, Bin Ma

J. Bioinform. Comput. Biol., 2010

Better score function for peptide identification with ETD MS/MS spectra.

Xiaowen Liu, Baozhen Shan, Lei Xin, Bin Ma

BMC Bioinform., 2010

On the Longest Common Rigid Subsequence Problem.

Nikhil Bansal, Moshe Lewenstein, Bin Ma, Kaizhong Zhang

Algorithmica, 2010

De Novo Sequencing Methods in Proteomics.

Christopher Hughes, Bin Ma, Gilles A. Lajoie

Proceedings of the Proteome Bioinformatics, 2010

2009

Why greed works for shortest common superstring problem.

Bin Ma

Theor. Comput. Sci., 2009

On the similarity metric and the distance metric.

Shihyen Chen, Bin Ma, Kaizhong Zhang

Theor. Comput. Sci., 2009

More Efficient Algorithms for Closest String and Substring Problems.

Bin Ma, Xiaoming Sun

SIAM J. Comput., 2009

Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics.

Bin Ma

J. Comput. Sci. Technol., 2009

Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design.

Bin Ma, Hongyi Yao

Inf. Process. Lett., 2009

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.

Xiaowen Liu, Yonghua Han, Denis Yuen, Bin Ma

Bioinform., 2009

Specialized Review Selection for Feature Rating Estimation.

Chong Long, Jie Zhang, Minlie Huang, Xiaoyan Zhu, Ming Li, Bin Ma

Proceedings of the 2009 IEEE/WIC/ACM International Conference on Web Intelligence, 2009

Amino Acid Classification and Hash Seeds for Homology Search.

Weiming Li, Bin Ma, Kaizhong Zhang

Proceedings of the Bioinformatics and Computational Biology, 2009

2008

Peptide De Novo Sequencing with MS/MS.

Bin Ma

Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Rainbow Network Flow of Multiple Description Codes.

Xiaolin Wu, Bin Ma, Nima Sarshar

IEEE Trans. Inf. Theory, 2008

A new quartet approach for reconstructing phylogenetic trees: quartet joining method.

Bin Ma, Lei Xin, Kaizhong Zhang

J. Comb. Optim., 2008

Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry.

Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie

J. Bioinform. Comput. Biol., 2008

ZOOM! Zillions of oligos mapped.

Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li

Bioinform., 2008

Information shared by many objects.

Chong Long, Xiaoyan Zhu, Ming Li, Bin Ma

Proceedings of the 17th ACM Conference on Information and Knowledge Management, 2008

Seed Optimization Is No Easier than Optimal Golomb Ruler Design.

Bin Ma, Hongyi Yao

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

PAS: Predicate-Based Authentication Services Against Powerful Passive Adversaries.

Xiaole Bai, Wenjun Gu, Sriram Chellappan, Xun Wang, Dong Xuan, Bin Ma

Proceedings of the Twenty-Fourth Annual Computer Security Applications Conference, 2008

2007

Mobility Limited Flip-Based Sensor Networks Deployment.

Sriram Chellappan, Xiaole Bai, Bin Ma, Dong Xuan, Changqing Xu

IEEE Trans. Parallel Distributed Syst., 2007

Deploying Wireless Sensor Networks under Limited Mobility Constraints.

Sriram Chellappan, Wenjun Gu, Xiaole Bai, Dong Xuan, Bin Ma, Kaizhong Zhang

IEEE Trans. Mob. Comput., 2007

Near optimal multiple alignment within a band in polynomial time.

Bin Ma, Lusheng Wang, Ming Li

J. Comput. Syst. Sci., 2007

On the complexity of the spaced seeds.

Bin Ma, Ming Li

J. Comput. Syst. Sci., 2007

Rapid Homology Search with Neighbor Seeds.

Miklós Csürös, Bin Ma

Algorithmica, 2007

The Normalized Similarity Metric and Its Applications.

Shihyen Chen, Bin Ma, Kaizhong Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007

Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry.

Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie

Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006

Optimizing Multiple Spaced Seeds for Homology Search.

Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma

J. Comput. Biol., 2006

Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures.

Bin Ma, Lieyu Wu, Kaizhong Zhang

J. Bioinform. Comput. Biol., 2006

Prima: Peptide Robust Identification from Ms/ms Spectra.

Jian Liu, Bin Ma, Ming Li

J. Bioinform. Comput. Biol., 2006

Superiority and complexity of the spaced seeds.

Ming Li, Bin Ma, Louxin Zhang

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.

Bin Ma, Kaizhong Zhang, Chengzhi Liang

J. Comput. Syst. Sci., 2005

Spider: Software for Protein Identification from Sequence Tags with <i>de Novo</i> Sequencing Error.

Yonghua Han, Bin Ma, Kaizhong Zhang

J. Bioinform. Comput. Biol., 2005

An automata approach to match gapped sequence tags against protein database.

Yonghua Han, Bin Ma, Kaizhong Zhang

Int. J. Found. Comput. Sci., 2005

tPatternHunter: gapped, fast and sensitive translated homology search .

Derek Kisman, Ming Li, Bin Ma, Li Wang

Bioinform., 2005

Sensor networks deployment using flip-based sensors.

Sriram Chellappan, Xiaole Bai, Bin Ma, Dong Xuan

Proceedings of the IEEE 2nd International Conference on Mobile Adhoc and Sensor Systems, 2005

Rainbow network problems and multiple description coding.

Xiaolin Wu, Bin Ma, Nima Sarshar

Proceedings of the 2005 IEEE International Symposium on Information Theory, 2005

On the Longest Common Rigid Subsequence Problem.

Bin Ma, Kaizhong Zhang

Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005

Rapid Homology Search with Two-Stage Extension and Daughter Seeds.

Miklós Csürös, Bin Ma

Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

PRIME: Peptide robust identification from MS/MS spectra.

Jian Liu, Bin Ma, Ming Li

Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2004

The similarity metric.

Ming Li, Xin Chen, Xin Li, Bin Ma, Paul M. B. Vitányi

IEEE Trans. Inf. Theory, 2004

The longest common subsequence problem for arc-annotated sequences.

Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang

J. Discrete Algorithms, 2004

Patternhunter Ii: Highly Sensitive and Fast Homology Search.

Ming Li, Bin Ma, Derek Kisman, John Tromp

J. Bioinform. Comput. Biol., 2004

A Tutorial of Recent Developments in the Seeding of Local Alignment.

Daniel G. Brown, Ming Li, Bin Ma

J. Bioinform. Comput. Biol., 2004

On spaced seeds for similarity search.

Uri Keich, Ming Li, Bin Ma, John Tromp

Discret. Appl. Math., 2004

SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error.

Yonghua Han, Bin Ma, Kaizhong Zhang

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003

Genetic Design of Drugs Without Side-Effects.

Xiaotie Deng, Guojun Li, Zimao Li, Bin Ma, Lusheng Wang

SIAM J. Comput., 2003

Distinguishing string selection problems.

J. Kevin Lanctôt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang

Inf. Comput., 2003

Greedy method for inferring tandem duplication history.

Louxin Zhang, Bin Ma, Lusheng Wang, Ying Xu

Bioinform., 2003

An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.

Bin Ma, Kaizhong Zhang, Chengzhi Liang

Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003

Alignment between Two Multiple Alignments.

Bin Ma, Zhuozhi Wang, Kaizhong Zhang

Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003

2002

Computing similarity between RNA structures.

Bin Ma, Lusheng Wang, Kaizhong Zhang

Theor. Comput. Sci., 2002

Finding Similar Regions in Many Sequences.

Ming Li, Bin Ma, Lusheng Wang

J. Comput. Syst. Sci., 2002

Methods for reconstructing the history of tandem repeats and their application to the human genome.

Deep Jaitly, Paul E. Kearney, Guo-Hui Lin, Bin Ma

J. Comput. Syst. Sci., 2002

A General Edit Distance between RNA Structures.

Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang

J. Comput. Biol., 2002

On the closest string and substring problems.

Ming Li, Bin Ma, Lusheng Wang

J. ACM, 2002

PatternHunter: faster and more sensitive homology search.

Bin Ma, John Tromp, Ming Li

Bioinform., 2002

DNACompress: fast and effective DNA sequence compression.

Xin Chen, Ming Li, Bin Ma, John Tromp

Bioinform., 2002

Efficient Methods for Inferring Tandem Duplication History.

Louxin Zhang, Bin Ma, Lusheng Wang

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

A PTAS for Distinguishing (Sub)string Selection.

Xiaotie Deng, Guojun Li, Zimao Li, Bin Ma, Lusheng Wang

Proceedings of the Automata, Languages and Programming, 29th International Colloquium, 2002

2001

Edit distance between two RNA structures.

Guohui Lin, Bin Ma, Kaizhong Zhang

Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

2000

From Gene Trees to Species Trees.

Bin Ma, Ming Li, Louxin Zhang

SIAM J. Comput., 2000

On the Inapproximability of Disjoint Paths and Minimum Steiner Forest with Bandwidth Constraints.

Bin Ma, Lusheng Wang

J. Comput. Syst. Sci., 2000

Fixed topology alignment with recombination.

Lusheng Wang, Bin Ma, Ming Li

Discret. Appl. Math., 2000

A Polynominal Time Approximation Scheme for the Closest Substring Problem.

Bin Ma

Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1999

Fitting Distances by Tree Metrics with Increment Error.

Bin Ma, Lusheng Wang, Louxin Zhang

J. Comb. Optim., 1999

Finding Similar Regions in Many Strings.

Ming Li, Bin Ma, Lusheng Wang

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.

Bin Ma, Ming Li, Louxin Zhang

Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998