On reconstructing species trees from gene trees in term of duplications and losses. - Bin Ma 002; Ming Li 001; Louxin Zhang (RECOMB, 1998)

Finding Similar Regions in Many Strings. - Ming Li 001; Bin Ma 002; Lusheng Wang 001 (STOC, 1999)

Fitting Distances by Tree Metrics with Increment Error. - Bin Ma 002; Lusheng Wang 001; Louxin Zhang (J. Comb. Optim., 1999)

A Polynominal Time Approximation Scheme for the Closest Substring Problem. - Bin Ma 002 (CPM, 2000)

Fixed topology alignment with recombination. - Lusheng Wang 001; Bin Ma 002; Ming Li 001 (Discret. Appl. Math., 2000)

On the Inapproximability of Disjoint Paths and Minimum Steiner Forest with Bandwidth Constraints. - Bin Ma 002; Lusheng Wang 001 (J. Comput. Syst. Sci., 2000)

From Gene Trees to Species Trees. - Bin Ma 002; Ming Li 001; Louxin Zhang (SIAM J. Comput., 2000)

Edit distance between two RNA structures. - Guohui Lin; Bin Ma 002; Kaizhong Zhang (RECOMB, 2001)

A PTAS for Distinguishing (Sub)string Selection. - Xiaotie Deng; Guojun Li; Zimao Li; Bin Ma 002; Lusheng Wang 001 (ICALP, 2002)

Efficient Methods for Inferring Tandem Duplication History. - Louxin Zhang; Bin Ma 002; Lusheng Wang 001 (WABI, 2002)

DNACompress: fast and effective DNA sequence compression. - Xin Chen; Ming Li 001; Bin Ma 002; John Tromp (Bioinform., 2002)

PatternHunter: faster and more sensitive homology search. - Bin Ma 002; John Tromp; Ming Li 001 (Bioinform., 2002)

On the closest string and substring problems. - Ming Li 001; Bin Ma 002; Lusheng Wang 001 (J. ACM, 2002)

A General Edit Distance between RNA Structures. - Tao Jiang 001; Guohui Lin; Bin Ma 002; Kaizhong Zhang (J. Comput. Biol., 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 002 (J. Comput. Syst. Sci., 2002)

Finding Similar Regions in Many Sequences. - Ming Li 001; Bin Ma 002; Lusheng Wang 001 (J. Comput. Syst. Sci., 2002)

Computing similarity between RNA structures. - Bin Ma 002; Lusheng Wang 001; Kaizhong Zhang (Theor. Comput. Sci., 2002)

Alignment between Two Multiple Alignments. - Bin Ma 002; Zhuozhi Wang; Kaizhong Zhang (CPM, 2003)

An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum. - Bin Ma 002; Kaizhong Zhang; Chengzhi Liang (CPM, 2003)

Greedy method for inferring tandem duplication history. - Louxin Zhang; Bin Ma 002; Lusheng Wang 001; Ying Xu 002 (Bioinform., 2003)

Distinguishing string selection problems. - J. Kevin Lanctôt; Ming Li 001; Bin Ma 002; Shaojiu Wang; Louxin Zhang (Inf. Comput., 2003)

Genetic Design of Drugs Without Side-Effects. - Xiaotie Deng; Guojun Li; Zimao Li; Bin Ma 002; Lusheng Wang 001 (SIAM J. Comput., 2003)

SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error. - Yonghua Han; Bin Ma 002; Kaizhong Zhang (CSB, 2004)

On spaced seeds for similarity search. - Uri Keich; Ming Li 001; Bin Ma 002; John Tromp (Discret. Appl. Math., 2004)

A Tutorial of Recent Developments in the Seeding of Local Alignment. - Daniel G. Brown 001; Ming Li 001; Bin Ma 002 (J. Bioinform. Comput. Biol., 2004)

Patternhunter Ii: Highly Sensitive and Fast Homology Search. - Ming Li 001; Bin Ma 002; Derek Kisman; John Tromp (J. Bioinform. Comput. Biol., 2004)

The longest common subsequence problem for arc-annotated sequences. - Tao Jiang 001; Guohui Lin; Bin Ma 002; Kaizhong Zhang (J. Discrete Algorithms, 2004)

The similarity metric. - Ming Li 001; Xin Chen; Xin Li; Bin Ma 002; Paul M. B. Vitányi (IEEE Trans. Inf. Theory, 2004)

PRIME: Peptide robust identification from MS/MS spectra. - Jian Liu; Bin Ma 002; Ming Li 001 (APBC, 2005)

Rapid Homology Search with Two-Stage Extension and Daughter Seeds. - Miklós Csürös; Bin Ma 002 (COCOON, 2005)

On the Longest Common Rigid Subsequence Problem. - Bin Ma 002; Kaizhong Zhang (CPM, 2005)

Rainbow network problems and multiple description coding. - Xiaolin Wu 001; Bin Ma 002; Nima Sarshar (ISIT, 2005)

Sensor networks deployment using flip-based sensors. - Sriram Chellappan; Xiaole Bai; Bin Ma 002; Dong Xuan (MASS, 2005)

tPatternHunter: gapped, fast and sensitive translated homology search . - Derek Kisman; Ming Li 001; Bin Ma 002; Li Wang (Bioinform., 2005)

An automata approach to match gapped sequence tags against protein database. - Yonghua Han; Bin Ma 002; Kaizhong Zhang (Int. J. Found. Comput. Sci., 2005)

Spider: Software for Protein Identification from Sequence Tags with de Novo Sequencing Error. - Yonghua Han; Bin Ma 002; Kaizhong Zhang (J. Bioinform. Comput. Biol., 2005)

An effective algorithm for peptide de novo sequencing from MS/MS spectra. - Bin Ma 002; Kaizhong Zhang; Chengzhi Liang (J. Comput. Syst. Sci., 2005)

Superiority and complexity of the spaced seeds. - Ming Li 001; Bin Ma 002; Louxin Zhang (SODA, 2006)

Prima: Peptide Robust Identification from Ms/ms Spectra. - Jian Liu; Bin Ma 002; Ming Li 001 (J. Bioinform. Comput. Biol., 2006)

Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures. - Bin Ma 002; Lieyu Wu; Kaizhong Zhang (J. Bioinform. Comput. Biol., 2006)

Optimizing Multiple Spaced Seeds for Homology Search. - Jinbo Xu; Daniel G. Brown 001; Ming Li 001; Bin Ma 002 (J. Comput. Biol., 2006)

Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry. - Baozhen Shan; Bin Ma 002; Kaizhong Zhang; Gilles A. Lajoie (APBC, 2007)

The Normalized Similarity Metric and Its Applications. - Shihyen Chen; Bin Ma 002; Kaizhong Zhang (BIBM, 2007)

Rapid Homology Search with Neighbor Seeds. - Miklós Csürös; Bin Ma 002 (Algorithmica, 2007)

On the complexity of the spaced seeds. - Bin Ma 002; Ming Li 001 (J. Comput. Syst. Sci., 2007)

Near optimal multiple alignment within a band in polynomial time. - Bin Ma 002; Lusheng Wang 001; Ming Li 001 (J. Comput. Syst. Sci., 2007)

Deploying Wireless Sensor Networks under Limited Mobility Constraints. - Sriram Chellappan; Wenjun Gu; Xiaole Bai; Dong Xuan; Bin Ma 002; Kaizhong Zhang (IEEE Trans. Mob. Comput., 2007)

Mobility Limited Flip-Based Sensor Networks Deployment. - Sriram Chellappan; Xiaole Bai; Bin Ma 002; Dong Xuan; Changqing Xu (IEEE Trans. Parallel Distributed Syst., 2007)

PAS: Predicate-Based Authentication Services Against Powerful Passive Adversaries. - Xiaole Bai; Wenjun Gu; Sriram Chellappan; Xun Wang 009; Dong Xuan; Bin Ma 002 (ACSAC, 2008)

Seed Optimization Is No Easier than Optimal Golomb Ruler Design. - Bin Ma 002; Hongyi Yao (APBC, 2008)

Information shared by many objects. - Chong Long; Xiaoyan Zhu 001; Ming Li 001; Bin Ma 002 (CIKM, 2008)

ZOOM! Zillions of oligos mapped. - Hao Lin; Zefeng Zhang; Michael Q. Zhang; Bin Ma 002; Ming Li 001 (Bioinform., 2008)

Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry. - Baozhen Shan; Bin Ma 002; Kaizhong Zhang; Gilles A. Lajoie (J. Bioinform. Comput. Biol., 2008)

A new quartet approach for reconstructing phylogenetic trees: quartet joining method. - Bin Ma 002; Lei Xin; Kaizhong Zhang (J. Comb. Optim., 2008)

Rainbow Network Flow of Multiple Description Codes. - Xiaolin Wu 001; Bin Ma 002; Nima Sarshar (IEEE Trans. Inf. Theory, 2008)

Peptide De Novo Sequencing with MS/MS. - Bin Ma 002 (Encyclopedia of Algorithms, 2008)

Amino Acid Classification and Hash Seeds for Homology Search. - Weiming Li; Bin Ma 002; Kaizhong Zhang (BICoB, 2009)

Specialized Review Selection for Feature Rating Estimation. - Chong Long; Jie Zhang 002; Minlie Huang; Xiaoyan Zhu 001; Ming Li 001; Bin Ma 002 (Web Intelligence, 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 002 (Bioinform., 2009)

Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design. - Bin Ma 002; Hongyi Yao (Inf. Process. Lett., 2009)

Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics. - Bin Ma 002 (J. Comput. Sci. Technol., 2009)

More Efficient Algorithms for Closest String and Substring Problems. - Bin Ma 002; Xiaoming Sun 001 (SIAM J. Comput., 2009)

On the similarity metric and the distance metric. - Shihyen Chen; Bin Ma 002; Kaizhong Zhang (Theor. Comput. Sci., 2009)

Why greed works for shortest common superstring problem. - Bin Ma 002 (Theor. Comput. Sci., 2009)

De Novo Sequencing Methods in Proteomics. - Christopher Hughes; Bin Ma 002; Gilles A. Lajoie (Proteome Bioinformatics, 2010)

On the Longest Common Rigid Subsequence Problem. - Nikhil Bansal 001; Moshe Lewenstein; Bin Ma 002; Kaizhong Zhang (Algorithmica, 2010)

Better score function for peptide identification with ETD MS/MS spectra. - Xiaowen Liu; Baozhen Shan; Lei Xin; Bin Ma 002 (BMC Bioinform., 2010)

Adepts: Advanced peptide de novo Sequencing with a Pair of Tandem Mass Spectra. - Lin He 002; Bin Ma 002 (J. Bioinform. Comput. Biol., 2010)

Ancient Chinese zither (guqin) music recovery with support vector machine. - Qing Sun; Deyun Zhang; Yifeng Fan; Kaizhong Zhang; Bin Ma 002 (ACM Journal on Computing and Cultural Heritage, 2010)

ZOOM Lite: next-generation sequencing data mapping and visualization software. - Zefeng Zhang; Hao Lin; Bin Ma 002 (Nucleic Acids Res., 2010)

Closest string with outliers. - Christina Boucher 001; Bin Ma 002 (BMC Bioinform., 2011)

Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction. - Bin Ma 002; Louxin Zhang (J. Comb. Optim., 2011)

Efficient filtration for similarity search with spaced k-mer neighbors. - Weiming Li; Bin Ma 002; Kaizhong Zhang (BIBM, 2012)

A three-string approach to the closest string problem. - Zhi-Zhong Chen; Bin Ma 002; Lusheng Wang 001 (J. Comput. Syst. Sci., 2012)

Peptide Identification from Mass Spectrometry. - Bin Ma 002 (ISBRA, 2013)

A combinatorial approach to the peptide feature matching problem for label-free quantification. - Hao Lin; Lin He 002; Bin Ma 002 (Bioinform., 2013)

De novo sequencing with Limited Number of Post-Translational Modifications per peptide. - Lin He 002; Xi Han; Bin Ma 002 (J. Bioinform. Comput. Biol., 2013)

Randomized and Parameterized Algorithms for the Closest String Problem. - Zhi-Zhong Chen; Bin Ma 002; Lusheng Wang 001 (CPM, 2014)

An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra. - Yi Liu 039; Bin Ma 002; Kaizhong Zhang; Gilles A. Lajoie (ISBRA, 2014)

Estimating feature ratings through an effective review selection approach. - Chong Long; Jie Zhang 002; Minlie Huang; Xiaoyan Zhu 001; Ming Li 001; Bin Ma 002 (Knowl. Inf. Syst., 2014)

Optimizing Spaced $k$-mer Neighbors for Efficient Filtration in Protein Similarity Search. - Weiming Li; Bin Ma 002; Kaizhong Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database. - Yi Liu 039; Weiping Sun; Gilles A. Lajoie; Bin Ma 002; Kaizhong Zhang (ISBRA, 2015)

A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry. - Weiping Sun; Gilles A. Lajoie; Bin Ma 002; Kaizhong Zhang (ISBRA, 2015)

Chapter 2. De novo Peptide Sequencing. - Bin Ma 002 (Proteome Informatics, 2016)

Randomized Fixed-Parameter Algorithms for the Closest String Problem. - Zhi-Zhong Chen; Bin Ma 002; Lusheng Wang 001 (Algorithmica, 2016)

Peptide De Novo Sequencing with MS/MS. - Bin Ma 002 (Encyclopedia of Algorithms, 2016)

Closest String and Substring Problems. - Lusheng Wang 001; Ming Li 001; Bin Ma 002 (Encyclopedia of Algorithms, 2016)

An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra. - Yi Liu 039; Bin Ma 002; Kaizhong Zhang; Gilles A. Lajoie (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

An Improved Approach for N-Linked Glycan Structure Identification from HCD MS/MS Spectra. - Weiping Sun; Yi Liu 039; Gilles A. Lajoie; Bin Ma 002; Kaizhong Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing. - Tiancong Wang; Bin Ma 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Designing and implementing algorithms for the closest string problem. - Shota Yuasa; Zhi-Zhong Chen; Bin Ma 002; Lusheng Wang 001 (Theor. Comput. Sci., 2019)

SPEQ: quality assessment of peptide tandem mass spectra with deep learning. - Soroosh Gholamizoj; Bin Ma 002 (Bioinform., 2022)

Deep learning boosted amyloidosis diagnosis. - Shaokai Wang; Bin Ma 002 (BIBM, 2023)

NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry. - Shaokai Wang; Ming Zhu; Bin Ma 002 (ISBRA, 2023)

Novel Fine-Tuning Strategy on Pre-trained Protein Model Enhances ACP Functional Type Classification. - Shaokai Wang; Bin Ma 002 (ISBRA (1), 2024)