- Outstanding Young Computer Science Researcher prize, Canadian Association for Computer Science, 2010.
- Premier's Catalyst Award for Best Young Innovator, Ontario, 2009.
- Premier's Research Excellence Award, Ontario, 2003.
- CS882: Advanced Topics in Bioinformatics, Fall 2014.
- CS466: Design and Analysis of Algorithms, Fall 2014.
PEAKS was best-known as the peptide de novo sequencing software from mass spectrometry data. Now it includes many other functions such as protein/peptide identification with a database and protein quantification. Software was initially written by me and now being developed at Bioinformatics Solutions Inc.
- GlycoMaster DB:
GlycoMaster DB identifies glycopeptides with their mass spectral data. Software was written by my former Ph.D. student Lin He.
CHAMPS software sequences a protein's amino acid sequence from its tandem mass spectrometry data and a homologous protein. Software was written by my former postdoc Xiaowen Liu.
- Z. Chen, B. Ma, and L. Wang. Randomized Fixed-Parameter Algorithms for the Closest String Problem. Algorithmica. Accepted, Oct. 2014.
- L. He, L. Xin, B. Shan, G. Lajoie, and B. Ma. GlycoMaster DB: Software to Assist the Automated Identification of N-Linked Glycopeptides by Tandem Mass Spectrometry. Journal of Proteome Research. Accepted, Aug 2014.
- W. Li, B. Ma, and K. Zhang. Optimizing Spaced k-mer Neighbors for Efficient Filtration in Protein Similarity Search. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11(2): 398-406. 2014.
- C. Long, J. Zhang, M. Huang, X. Zhu, M. Li, and B. Ma. Estimating feature ratings through an effective review selection approach. Knowledge and Information Systems. 38(2): 419-446. 2014.
- H. Lin, L. He, and B. Ma. A Combinatorial Approach to the Peptide Feature Matching Problem for Label-Free Quantification. Bioinformatics. 29 (14): 1768-1775. 2013.
- A. Alhaider, A. Abdelgader, A. Turjoman, K. Newell, S. Hunsucker, B. Shan, B. Ma, D. Gibson, and M. Duncan. Through the Eye of an Electrospray Needle: Mass Spectrometric Identification of the Major Peptides & Proteins in the Milk of the One Humped Camel (Camelus dromedarius). Journal of Mass Spectrometry. 48 (7), 779-794. 2013.
- L. He, X. Han, and B. Ma. De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide. Journal of Bioinformatics and Computational Biology 11(4), 2013.
- A. Ibrahima, L. Yang, C. Johnstonc, X. Liu, B. Ma, and N.A. Magarvey. Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery. PNAS 109:19196-19201. 2012.
- S. Sun, F. Yang, Q. Yang, H. Zhang, Y. Wang, D. Bu, and B. Ma. MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions. Journal of Proteome Research. DOI: 10.1021/pr300235v. 2012.
- Z. Chen, B. Ma and L. Wang. A Three-String Approach to the Closest String Problem. Journal of Computer and System Sciences 78(1): 164-178. 2012.
- J. Zhang, L. Xin, B. Shan, W. Chen, M. Xie, D. Yuen, W. Zhang, Z. Zhang, G. Lajoie, and B. Ma. PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Molecular & Cellular Proteomics 11. DOI, 10.1074/mcp.M111.010587. 2012.
- B. Ma and R. Johnson. De Novo Sequencing and Homology Searching. Molecular & Cellular Proteomics 11. DOI 10.1074/mcp.O111.014902. 2012.
- X. Han, L. He, L. Xin, B. Shan, B. Ma.
PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications.
Journal of Proteomics Research 10(7): 2930-2936. 2011. (Also appeared in RECOMB-CP'2011)
- C. Boucher and B. Ma.
Closest String with Outliers.
BMC Bioinformatics 12 (Suppl 1): S55. 2011.
- L. Zhang and B. Ma.
Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Ancestral State Reconstruction.
Journal of Combinatorial Optimization. 21(4):409-422. 2011.
(Also appeared in APBC'09)
- L. He and B. Ma.
ADEPTS: Advanced Peptide De Novo Sequencing with a Pair of Tandem Mass Spectra.
Journal of Bioinformatics and Computational Biology 8(6): 981-994. 2010.
- Q. Sun, D. Zhang, Y. Fan, K. Zhang, and B. Ma.
Ancient Chinese Zither (Guqin) Music Recovery with Support Vector Machine.
Journal on Computing and Cultural Heritage 3(2). Doi 10.1145/1841317.1841320. 2010
- Z. Zhang, H. Lin, and B. Ma.
ZOOM Lite: Next-generation Sequencing Data Mapping and Visualization Software.
Nucleic Acids Research. 38(suppl 2):W743-W748. 2010.
- X. Liu, L. Xin, B. Shan, and B. Ma.
Better Score Function for Peptide Identification with ETD MS/MS Spectra.
BMC Bioinformatics 11(Suppl 1):S4. 2010.
- Nikhil Bansal, Moshe Lewenstein, Bin Ma, and Kaizhong Zhang.
On the Longest Common Rigid Subsequence Problem.
Algorithmica 56(2): 270-280. 2010.
(Some material appeared in CPM'05)
- B. Ma.
Why Greed Works for Shortest Common Superstring Problem.
Theoretical Computer Science 410(51):5374-5381. 2009.
(Also appeared in CPM'08)
- B. Ma.
Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics.
Journal of Computer Science and Technology 25(1): 107-123. Invited paper. 2009.
- B. Ma and X. Sun.
More Efficient Algorithm for Closest String and Substring Problems.
SIAM J. Computing 39(4): 1432-1443. 2009.
(Also appeared in RECOMB'08)
- B. Ma and H. Yao.
Seed Optimization for I.I.D. Similarities Is No Easier than Optimal Golomb Ruler Design.
Information Processing Letter 109(19): 1120-1124. 2009.
(Also appeared in APBC'08)
- X. Liu, Y. Han, D. Yuen, and B. Ma.
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.
Bioinformatics 25(17):2174-2180. 2009.
- S. Chen, B. Ma, and K. Zhang.
On the similarity metric and the distance metric.
Theoretical Computer Science 410(24-25):2365-2376. 2009.
(Some material appeared in ICBB'07.)
- H. Lin, Z. Zhang, M. Zhang, B. Ma, and M. Li.
ZOOM! Zillions of Oligos Mapped.
Bioinformatics 24(21): 2431-2437. 2008.
- X. Wu, B. Ma, and N. Sarshar. Rainbow Network Problems and Multiple Description Coding.
IEEE Transactions on Information Theory 54(10):4565-4574. 2008.
(Some material appeared in NetCod'05)
- B. Ma, L. Xin, and K. Zhang.
A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method.
Journal of Combinatorial Optimization 16(3):293-306. 2008.
(Also appeared in COCOON'07)
- B. Shan, K. Zhang, B. Ma, C. Zhang, G. Lajoie.
An Algorithm for Determining Glycan Structures from MS/MS Spectra.
Journal of Bioinformatics and Computational Biology 6(1):77-91. 2008.
(Some material appeared in ICBA'04 and APBC'06.)
- B. Ma and M. Li.
On the Complexity of Spaced Seeds.
Journal of Computer Science and System Sciences 73(7):1024-1034. 2007.
(Some material appeared in SODA'06)
- B. Ma, L. Wang and M. Li.
Near Optimal Multiple Alignment within a Band in Polynomial Time.
Journal of Computer Science and System Sciences 73(6):997-1011. 2007.
(Also appeared in STOC'2000, pp. 425--434, Portland, Oregon, 2000.)
- S. Chellappan, W. Gu, X. Bai, D. Xuan, B. Ma, and K. Zhang.
Deploying Wireless Sensor Networks under Limited Mobility Constraints.
IEEE Transactions on Mobile Computing 10:1142-1157. 2007.
(Some material appeared in "The Second IEEE International Conference on Mobile Ad-Hoc and Sensor Systems 2005)
- M. Csuros and B. Ma. Rapid homology search with neighbour seeds. Algorithmica 48(2):187-202.
(Some material appeared in "Rapid homology search with two-stage extension and daughter seeds"
- S. Chellappan, X. Bai, B. Ma, D. Xuan and C. Xu.
Mobility Limited Flip-based Sensor Network Deployment.
IEEE Transactions on Parallel and Distributed Systems. 18(2):199-211. 2007.
(Some material appeared in "Sensor Network Deployment using Flip-based Sensors", MASS'05).
- J. Xu, D. Brown, M. Li, and B. Ma.
Optimizing Multiple Spaced Seeds for Homology Search.
Journal of Computational Biology 13(7): 1355-1368.
(Also appeared in CPM'04, 47-58.)
- B. Ma, L. Wu, and K. Zhang.
Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures.
Journal of Bioinformatics and Computationa Biology 4(3):709-720. 2006.
(Preliminary version appeared in IWBRA'05, 960-967, 2005.)
- C. Xu, and B. Ma.
Software for Computational Peptide Identification from MS/MS.
Drug Discovery Today.
11(13/14):595-600. 2006. (Review article.)
- J. Liu, B. Ma, M. Li: PRIMA: Peptide robust identification from MS/MS spectra.
Journal of Bioinformatics and Computationa Biology 5(1):125-138. 2006.
(Also appeared in APBC'05, 181-190, 2005.)
- Y. Han, B. Ma, and K. Zhang.
SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error.
Journal of Bioinformatics and Computational Biology 3(3):697-716. 2005.
(Also appeared in CSB'04, 206-215.)(Received the Best Paper Award of CSB'04)
- Y. Han, B. Ma, and K. Zhang.
An Automata Approach to Match Gapped Sequence Tags.
Int. J. Found. Comput. Sci. . 16(3): 487-497. 2005.
(Also appeared in CIAA'04 167-177).
- Derek Kisman, Ming Li, Bin Ma, and Li Wang.
TPatternHunter: Gapped, Fast and Sensitive Translated Homology Search.
Bioinformatics 21(4): 542-544. 2005.
- Bin Ma, Kaizhong Zhang, and Chengzhi Liang.
An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.
Journal of Computer and System Sciences 70: 418-430. 2005. (Also appeared in CPM'03, 266-278.)
- M. Li, X. Chen, X. Li, B. Ma, and P. Vitanyi.
The Similarity Metric. IEEE Transaction Information Thoery.
50: 3250-3264. 2004.
(Also appeared in SODA'03, 863-872.)
- Dan Brown, Ming Li, and Bin Ma. A tutorial of recent developments in the seeding of local alignment.
Journal of Bioinformatics and Computational Biology 2(4): 819-842. 2004.
- M. Li, B. Ma, D. Kisman, and B. Ma.
PatternHunter II: Highly Sensitive and Fast Homology Search.
Journal of Bioinformatics and Computational Biology 2(3): 417-440. 2004. (Also appeared in GIW'03. GIW'03 version).
- U. Keich, M. Li, B. Ma, and J. Tromp.
Computing Optimally Spaced Seeds.
Discrete Applied Mathematics 138(3): 253-263. 2004.
- T. Jiang, G. Lin, B. Ma, and K. Zhang.
The Longest Common Subsequence Problem for Arc-annotated Sequences.
Invited paper, Journal of Discrete Algorithms 2(2): 257-270. 2004.
(also appeared in CPM'00. CPM'00 version).
- Rat Genome Sequencing Project Consortium (B. Ma is a coauthor).
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature 428: 493-521. 2004.
- L. Zhang, B. Ma, L. Wang, and Y. Xu.
Greedy Method for Inferring Tandem Duplication History.
Bioinformatics. 19(12): 1497-1504. 2004. (Also appeared in WABI'02)
- B. Ma, K. Zhang, C. Hendrie, C. Liang, M. Li, A. Doherty-Kirby, and G. Lajoie.
PEAKS: Powerful Software for Peptide De Novo Sequencing by Tandem Mass Spectrometry.
Rapid Communication in Mass Spectrometry 17(20): 2337-2342. 2003. (Also presented in 50th ASMS Conference (2002))
- X. Deng, G. Li, Z. Li, B. Ma, and L. Wang.
Genetic Design of Drug without Side Effects.
SIAM Journal on Computing 32(4): 1073-1090. 2003.
(also appeared in ICALP'02)
- JK. Lanctot, M. Li, B. Ma, S. Wang, and L. Zhang.
Distinguishing String Search Problems.
Information and Computation 185: 41-55. 2003.
(Also appeared in SODA'99. SODA'99 version)
- C.H. Bennett, M. Li, and B. Ma.
Chain Letters and Evolutionary Histories.
Scientific American, June 2003, 76-79.
- Mouse Genome Consortium (B. Ma is a coauthor.).
Initial Sequencing and Comparative Analysis of the Mouse Genome.
Nature 420: 520 - 562. 2002.
- X. Chen, M. Li, B. Ma, and J. Tromp.
DNACompress: Fast and Effective DNA Sequence Compression.
Bioinformatics 18: 1696-1698. 2002.
- D. Jaitly, P. Kearney, G. Lin, and B. Ma.
Methods for Reconstructing the History of Tandem Repeats and Their Application to the Human Genome. Invited paper,
Journal of Computer and System Sciences 65(3): 494-507. 2002.
- M. Li, B. Ma, and L. Wang.
Finding Similar Regions in Many Sequences.
Invited paper, Journal of Computer and System Sciences (Special Issue for STOC'99) 65: 73-96. 2002.
(Also appeared as part of a paper in STOC'99)
- B. Ma, L. Wang, and K. Zhang.
Computing Similarity Between RNA Structures.
Theoretical Computer Sciences 276(1-2): 111-132. 2002.
(Also appeared in CPM'99)
- T. Jiang, G. Lin, B. Ma, and K. Zhang.
A General Edit Distance between Two RNA Structures.
Journal of Computational Biology 9(2): 371-388. 2002.
(also appeared in RECOMB'01)
- B. Ma, J. Tromp, and M. Li.
PatternHunter: Faster and More Sensitive Homology Search.
Bioinformatics 18: 440-445. 2002.
- M. Li, B. Ma, and L. Wang.
On the Closest String and Substring Problems.
Journal of the ACM 49(2): 157-171. 2002. (parts of the paper appeared in STOC'99 and CPM'00)
- B. Ma, M. Li, and L. Zhang.
From Gene Trees to Species Trees.
SIAM Journal on Computing 30: 729-752. 2000.
(Also appeared in RECOMB'98)
- L. Wang, B. Ma, and M. Li.
Fixed Topology Alignment with Recombination.
Discrete Applied Mathematics, special issue on computational molecular biology, 104: 281-300. 2000.
(Also appeared in CPM'98)
- B. Ma and L. Wang.
On the Inapproximability of Disjoint Paths and Minimum Steiner Forest with Bandwidth Constraints.
Journal of Computer and System Sciences 60: 1-12. 2000.
- B. Ma, L. Wang and L. Zhang.
Fitting Distances by Tree Metrics with Incremental Errors.
Journal of Combinatorial Optimization(special issue on computational biology) 3: 213-225. 1999.
- L. Qi, W. Mao and B. Ma,
An algorithm for Ranking Football Teams,
Mathematics in Theory and Practice,1994(2), (in Chinese).
Some conference papers without journal versions
- W. Li, B. Ma, K. Zhang. Amino Acid Classification and Hash Seeds for Homology Search.
- X. Liu, B. Ma, and L. Wang.
Voting Algorithms for the Motif Finding Problem.
- Z. Wu, G. Lajoie, and B. Ma.
MSDash: Mass Spectrometry Database and Search.
- B. Ma, Z. Wang, and K. Zhang.
Alignment between Two Multiple Alignments.