Bin Ma

114 papers A* 6A 2B 19C 2Misc 5Journal 62Unranked 12
YearRankTypeTitle / Venue / Authors
2025 J jnl
Anti-Cancer Peptides Identification and Activity Type Classification With Protein Sequence Pre-Training.
IEEE J. Biomed. Health Informatics
Shaokai Wang, Bin Ma
2025 J jnl
NeoMS: Mass Spectrometry-Based Method for Uncovering Mutated MHC-I Neoantigens.
IEEE Trans. Comput. Biol. Bioinform.
Shaokai Wang, Ming Zhu, Bin Ma
2024 — conf
Novel Fine-Tuning Strategy on Pre-trained Protein Model Enhances ACP Functional Type Classification.
ISBRA (1)
Shaokai Wang, Bin Ma
2023 — conf
Deep learning boosted amyloidosis diagnosis.
BIBM
Shaokai Wang, Bin Ma
2023 — conf
NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry.
ISBRA
Shaokai Wang, Ming Zhu, Bin Ma
2022 J jnl
SPEQ: quality assessment of peptide tandem mass spectra with deep learning.
Bioinform.
Soroosh Gholamizoj, Bin Ma
2019 J jnl
Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tiancong Wang, Bin Ma
2019 J jnl
An Improved Approach for N-Linked Glycan Structure Identification from HCD MS/MS Spectra.
IEEE ACM Trans. Comput. Biol. Bioinform.
Weiping Sun, Yi Liu, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang
2019 J jnl
Designing and implementing algorithms for the closest string problem.
Theor. Comput. Sci.
Shota Yuasa, Zhi-Zhong Chen, Bin Ma, Lusheng Wang
2017 J jnl
An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yi Liu, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie
2017 Misc conf
Designing and Implementing Algorithms for the Closest String Problem.
FAW
Shota Yuasa, Zhi-Zhong Chen, Bin Ma, Lusheng Wang
2016 — ch.
Chapter 2. De novo Peptide Sequencing.
Proteome Informatics
Bin Ma
2016 — ch.
Closest String and Substring Problems.
Encyclopedia of Algorithms
Lusheng Wang, Ming Li, Bin Ma
2016 — ch.
Peptide De Novo Sequencing with MS/MS.
Encyclopedia of Algorithms
Bin Ma
2016 J jnl
Randomized Fixed-Parameter Algorithms for the Closest String Problem.
Algorithmica
Zhi-Zhong Chen, Bin Ma, Lusheng Wang
2015 — ed.
2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, DC, USA, November 9-12, 2015
BIBM
Jun Huan, Satoru Miyano, Amarda Shehu, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Vijay K. Gombar, Matthieu-P. Schapranow, Illhoi Yoo, Jiayu Zhou, Brian Chen, Vinay Pai, Brian G. Pierce
2015 — conf
A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry.
ISBRA
Weiping Sun, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang
2015 — conf
An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database.
ISBRA
Yi Liu, Weiping Sun, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang
2014 — conf
An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra.
ISBRA
Yi Liu, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie
2014 J jnl
Estimating feature ratings through an effective review selection approach.
Knowl. Inf. Syst.
Chong Long, Jie Zhang, Minlie Huang, Xiaoyan Zhu, Ming Li, Bin Ma
2014 J jnl
Optimizing Spaced $k$-mer Neighbors for Efficient Filtration in Protein Similarity Search.
IEEE ACM Trans. Comput. Biol. Bioinform.
Weiming Li, Bin Ma, Kaizhong Zhang
2014 B conf
Randomized and Parameterized Algorithms for the Closest String Problem.
CPM
Zhi-Zhong Chen, Bin Ma, Lusheng Wang
2013 J jnl
A combinatorial approach to the peptide feature matching problem for label-free quantification.
Bioinform.
Hao Lin, Lin He, Bin Ma
2013 — conf
Peptide Identification from Mass Spectrometry.
ISBRA
Bin Ma
2012 J jnl
A three-string approach to the closest string problem.
J. Comput. Syst. Sci.
Zhi-Zhong Chen, Bin Ma, Lusheng Wang
2012 — conf
Efficient filtration for similarity search with spaced k-mer neighbors.
BIBM
Weiming Li, Bin Ma, Kaizhong Zhang
2011 J jnl
Closest string with outliers.
BMC Bioinform.
Christina Boucher, Bin Ma
2011 J jnl
Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction.
J. Comb. Optim.
Bin Ma, Louxin Zhang
2010 Misc conf
A Three-String Approach to the Closest String Problem.
COCOON
Zhi-Zhong Chen, Bin Ma, Lusheng Wang
2010 J jnl
Adepts: Advanced peptide
J. Bioinform. Comput. Biol.
Lin He, Bin Ma
2010 J jnl
Ancient Chinese zither (guqin) music recovery with support vector machine.
ACM Journal on Computing and Cultural Heritage
Qing Sun, Deyun Zhang, Yifeng Fan, Kaizhong Zhang, Bin Ma
2010 J jnl
Better score function for peptide identification with ETD MS/MS spectra.
BMC Bioinform.
Xiaowen Liu, Baozhen Shan, Lei Xin, Bin Ma
2010 — ch.
De Novo Sequencing Methods in Proteomics.
Proteome Bioinformatics
Christopher Hughes, Bin Ma, Gilles A. Lajoie
2010 J jnl
On the Longest Common Rigid Subsequence Problem.
Algorithmica
Nikhil Bansal, Moshe Lewenstein, Bin Ma, Kaizhong Zhang
2010 J jnl
ZOOM Lite: next-generation sequencing data mapping and visualization software.
Nucleic Acids Res.
Zefeng Zhang, Hao Lin, Bin Ma
2009 — conf
Amino Acid Classification and Hash Seeds for Homology Search.
BICoB
Weiming Li, Bin Ma, Kaizhong Zhang
2009 J jnl
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.
Bioinform.
Xiaowen Liu, Yonghua Han, Denis Yuen, Bin Ma
2009 J jnl
Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics.
J. Comput. Sci. Technol.
Bin Ma
2009 J jnl
More Efficient Algorithms for Closest String and Substring Problems.
SIAM J. Comput.
Bin Ma, Xiaoming Sun
2009 J jnl
On the similarity metric and the distance metric.
Theor. Comput. Sci.
Shihyen Chen, Bin Ma, Kaizhong Zhang
2009 J jnl
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design.
Inf. Process. Lett.
Bin Ma, Hongyi Yao
2009 — conf
Specialized Review Selection for Feature Rating Estimation.
Web Intelligence
Chong Long, Jie Zhang, Minlie Huang, Xiaoyan Zhu, Ming Li, Bin Ma
2009 J jnl
Why greed works for shortest common superstring problem.
Theor. Comput. Sci.
Bin Ma
2008 J jnl
A new quartet approach for reconstructing phylogenetic trees: quartet joining method.
J. Comb. Optim.
Bin Ma, Lei Xin, Kaizhong Zhang
2008 J jnl
Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol.
Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie
2008 A conf
Information shared by many objects.
CIKM
Chong Long, Xiaoyan Zhu, Ming Li, Bin Ma
2008 B conf
More Efficient Algorithms for Closest String and Substring Problems.
RECOMB
Bin Ma, Xiaoming Sun
2008 A conf
PAS: Predicate-Based Authentication Services Against Powerful Passive Adversaries.
ACSAC
Xiaole Bai, Wenjun Gu, Sriram Chellappan, Xun Wang, Dong Xuan, Bin Ma
2008 — ch.
Peptide De Novo Sequencing with MS/MS.
Encyclopedia of Algorithms
Bin Ma
2008 J jnl
Rainbow Network Flow of Multiple Description Codes.
IEEE Trans. Inf. Theory
Xiaolin Wu, Bin Ma, Nima Sarshar
2008 B conf
Seed Optimization Is No Easier than Optimal Golomb Ruler Design.
APBC
Bin Ma, Hongyi Yao
2008 B conf
Why Greed Works for Shortest Common Superstring Problem.
CPM
Bin Ma
2008 J jnl
ZOOM! Zillions of oligos mapped.
Bioinform.
Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li
2007 Misc conf
A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method.
COCOON
Lei Xin, Bin Ma, Kaizhong Zhang
2007 B ed.
Combinatorial Pattern Matching, 18th Annual Symposium, CPM 2007, London, Canada, July 9-11, 2007, Proceedings
CPM
Bin Ma, Kaizhong Zhang
2007 B conf
Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry.
APBC
Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles A. Lajoie
2007 J jnl
Deploying Wireless Sensor Networks under Limited Mobility Constraints.
IEEE Trans. Mob. Comput.
Sriram Chellappan, Wenjun Gu, Xiaole Bai, Dong Xuan, Bin Ma, Kaizhong Zhang
2007 J jnl
Mobility Limited Flip-Based Sensor Networks Deployment.
IEEE Trans. Parallel Distributed Syst.
Sriram Chellappan, Xiaole Bai, Bin Ma, Dong Xuan, Changqing Xu
2007 J jnl
Near optimal multiple alignment within a band in polynomial time.
J. Comput. Syst. Sci.
Bin Ma, Lusheng Wang, Ming Li
2007 J jnl
On the complexity of the spaced seeds.
J. Comput. Syst. Sci.
Bin Ma, Ming Li
2007 J jnl
Rapid Homology Search with Neighbor Seeds.
Algorithmica
Miklós Csürös, Bin Ma
2007 — conf
The Normalized Similarity Metric and Its Applications.
BIBM
Shihyen Chen, Bin Ma, Kaizhong Zhang
2006 J jnl
Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures.
J. Bioinform. Comput. Biol.
Bin Ma, Lieyu Wu, Kaizhong Zhang
2006 J jnl
Optimizing Multiple Spaced Seeds for Homology Search.
J. Comput. Biol.
Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma
2006 J jnl
Prima: Peptide Robust Identification from Ms/ms Spectra.
J. Bioinform. Comput. Biol.
Jian Liu, Bin Ma, Ming Li
2006 A* conf
Superiority and complexity of the spaced seeds.
SODA
Ming Li, Bin Ma, Louxin Zhang
2005 J jnl
An automata approach to match gapped sequence tags against protein database.
Int. J. Found. Comput. Sci.
Yonghua Han, Bin Ma, Kaizhong Zhang
2005 J jnl
An effective algorithm for peptide de novo sequencing from MS/MS spectra.
J. Comput. Syst. Sci.
Bin Ma, Kaizhong Zhang, Chengzhi Liang
2005 Misc conf
Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures.
International Conference on Computational Science (2)
Bin Ma, Lieyu Wu, Kaizhong Zhang
2005 B conf
On the Longest Common Rigid Subsequence Problem.
CPM
Bin Ma, Kaizhong Zhang
2005 B conf
PRIME: Peptide robust identification from MS/MS spectra.
APBC
Jian Liu, Bin Ma, Ming Li
2005 B conf
Rainbow network problems and multiple description coding.
ISIT
Xiaolin Wu, Bin Ma, Nima Sarshar
2005 Misc conf
Rapid Homology Search with Two-Stage Extension and Daughter Seeds.
COCOON
Miklós Csürös, Bin Ma
2005 B conf
Sensor networks deployment using flip-based sensors.
MASS
Sriram Chellappan, Xiaole Bai, Bin Ma, Dong Xuan
2005 J jnl
Spider: Software for Protein Identification from Sequence Tags with
J. Bioinform. Comput. Biol.
Yonghua Han, Bin Ma, Kaizhong Zhang
2005 J jnl
tPatternHunter: gapped, fast and sensitive translated homology search .
Bioinform.
Derek Kisman, Ming Li, Bin Ma, Li Wang
2004 J jnl
A Tutorial of Recent Developments in the Seeding of Local Alignment.
J. Bioinform. Comput. Biol.
Daniel G. Brown, Ming Li, Bin Ma
2004 C conf
An Automata Approach to Match Gapped Sequence Tags Against Protein Database.
CIAA
Yonghua Han, Bin Ma, Kaizhong Zhang
2004 J jnl
On spaced seeds for similarity search.
Discret. Appl. Math.
Uri Keich, Ming Li, Bin Ma, John Tromp
2004 B conf
Optimizing Multiple Spaced Seeds for Homology Search.
CPM
Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma
2004 J jnl
Patternhunter Ii: Highly Sensitive and Fast Homology Search.
J. Bioinform. Comput. Biol.
Ming Li, Bin Ma, Derek Kisman, John Tromp
2004 — conf
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error.
CSB
Yonghua Han, Bin Ma, Kaizhong Zhang
2004 J jnl
The longest common subsequence problem for arc-annotated sequences.
J. Discrete Algorithms
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
2004 J jnl
The similarity metric.
IEEE Trans. Inf. Theory
Ming Li, Xin Chen, Xin Li, Bin Ma, Paul M. B. Vitányi
2003 B conf
Alignment between Two Multiple Alignments.
CPM
Bin Ma, Zhuozhi Wang, Kaizhong Zhang
2003 B conf
An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.
CPM
Bin Ma, Kaizhong Zhang, Chengzhi Liang
2003 J jnl
Distinguishing string selection problems.
Inf. Comput.
J. Kevin Lanctôt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang
2003 J jnl
Genetic Design of Drugs Without Side-Effects.
SIAM J. Comput.
Xiaotie Deng, Guojun Li, Zimao Li, Bin Ma, Lusheng Wang
2003 J jnl
Greedy method for inferring tandem duplication history.
Bioinform.
Louxin Zhang, Bin Ma, Lusheng Wang, Ying Xu
2003 A* conf
The similarity metric.
SODA
Ming Li, Xin Chen, Xin Li, Bin Ma, Paul M. B. Vitányi
2002 J jnl
A General Edit Distance between RNA Structures.
J. Comput. Biol.
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
2002 A* conf
A PTAS for Distinguishing (Sub)string Selection.
ICALP
Xiaotie Deng, Guojun Li, Zimao Li, Bin Ma, Lusheng Wang
2002 J jnl
Computing similarity between RNA structures.
Theor. Comput. Sci.
Bin Ma, Lusheng Wang, Kaizhong Zhang
2002 J jnl
DNACompress: fast and effective DNA sequence compression.
Bioinform.
Xin Chen, Ming Li, Bin Ma, John Tromp
2002 C conf
Efficient Methods for Inferring Tandem Duplication History.
WABI
Louxin Zhang, Bin Ma, Lusheng Wang
2002 J jnl
Finding Similar Regions in Many Sequences.
J. Comput. Syst. Sci.
Ming Li, Bin Ma, Lusheng Wang
2002 J jnl
Methods for reconstructing the history of tandem repeats and their application to the human genome.
J. Comput. Syst. Sci.
Deep Jaitly, Paul E. Kearney, Guo-Hui Lin, Bin Ma
2002 J jnl
On the closest string and substring problems.
J. ACM
Ming Li, Bin Ma, Lusheng Wang
2002 J jnl
PatternHunter: faster and more sensitive homology search.
Bioinform.
Bin Ma, John Tromp, Ming Li
2001 B conf
Edit distance between two RNA structures.
RECOMB
Guohui Lin, Bin Ma, Kaizhong Zhang
2001 J jnl
The similarity metric
CoRR
Ming Li, Xin Chen, Xin Li, Bin Ma, Paul M. B. Vitányi
2000 B conf
A Polynominal Time Approximation Scheme for the Closest Substring Problem.
CPM
Bin Ma
2000 J jnl
Fixed topology alignment with recombination.
Discret. Appl. Math.
Lusheng Wang, Bin Ma, Ming Li
2000 J jnl
From Gene Trees to Species Trees.
SIAM J. Comput.
Bin Ma, Ming Li, Louxin Zhang
2000 A* conf
Near optimal multiple alignment within a band in polynomial time.
STOC
Ming Li, Bin Ma, Lusheng Wang
2000 J jnl
On The Closest String and Substring Problems
CoRR
Ming Li, Bin Ma, Lusheng Wang
2000 J jnl
On the Inapproximability of Disjoint Paths and Minimum Steiner Forest with Bandwidth Constraints.
J. Comput. Syst. Sci.
Bin Ma, Lusheng Wang
2000 B conf
The Longest Common Subsequence Problem for Arc-Annotated Sequences.
CPM
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
1999 B conf
Computing Similarity between RNA Structures.
CPM
Kaizhong Zhang, Lusheng Wang, Bin Ma
1999 A* conf
Distinguishing String Selection Problems.
SODA
J. Kevin Lanctôt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang
1999 A* conf
Finding Similar Regions in Many Strings.
STOC
Ming Li, Bin Ma, Lusheng Wang
1999 J jnl
Fitting Distances by Tree Metrics with Increment Error.
J. Comb. Optim.
Bin Ma, Lusheng Wang, Louxin Zhang
1998 B conf
Fixed Topology Alignment with Recombination.
CPM
Bin Ma, Lusheng Wang, Ming Li
1998 B conf
On reconstructing species trees from gene trees in term of duplications and losses.
RECOMB
Bin Ma, Ming Li, Louxin Zhang