Bin Ma

Summary

Affiliation: University of Western Ontario
Country: Canada

Publications

  1. ncbi request reprint Improving the sensitivity and specificity of protein homology search by incorporating predicted secondary structures
    Bin Ma
    Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada
    J Bioinform Comput Biol 4:709-20. 2006
  2. ncbi request reprint PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
    Bin Ma
    Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada
    Rapid Commun Mass Spectrom 17:2337-42. 2003
  3. ncbi request reprint tPatternHunter: gapped, fast and sensitive translated homology search
    Derek Kisman
    Bioinformatics Solutions Inc 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2
    Bioinformatics 21:542-4. 2005
  4. ncbi request reprint A tutorial of recent developments in the seeding of local alignment
    Daniel G Brown
    Department of Computer Science, University of Waterloo, Waterloo, ON, Canada, N2L 3G1, Canada
    J Bioinform Comput Biol 2:819-42. 2004
  5. pmc PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification
    Jing Zhang
    Bioinformatics Solutions Inc, Waterloo, Ontario N2L 6J2, Canada
    Mol Cell Proteomics 11:M111.010587. 2012
  6. ncbi request reprint MSDash: mass spectrometry database and search
    Zhan Wu
    Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B8, Canada
    Comput Syst Bioinformatics Conf 7:63-71. 2008
  7. doi request reprint De novo interpretation of tandem mass spectra
    Bin Ma
    University of Waterloo, Waterloo, Ontario, Canada
    Curr Protoc Bioinformatics . 2009
  8. ncbi request reprint SPIDER: software for protein identification from sequence tags with de novo sequencing error
    Yonghua Han
    Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada
    J Bioinform Comput Biol 3:697-716. 2005
  9. ncbi request reprint Patternhunter II: highly sensitive and fast homology search
    Ming Li
    Department of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G
    J Bioinform Comput Biol 2:417-39. 2004
  10. doi request reprint PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications
    Xi Han
    David R Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
    J Proteome Res 10:2930-6. 2011

Detail Information

Publications31

  1. ncbi request reprint Improving the sensitivity and specificity of protein homology search by incorporating predicted secondary structures
    Bin Ma
    Computer Science Department, University of Western Ontario, London, ON N6A 5B7, Canada
    J Bioinform Comput Biol 4:709-20. 2006
    ..We solved this problem by taking into account the confidence scores output by the prediction programs...
  2. ncbi request reprint PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
    Bin Ma
    Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada
    Rapid Commun Mass Spectrom 17:2337-42. 2003
    ..The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins...
  3. ncbi request reprint tPatternHunter: gapped, fast and sensitive translated homology search
    Derek Kisman
    Bioinformatics Solutions Inc 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2
    Bioinformatics 21:542-4. 2005
    ..The new software compares favorably with tBLASTx. AVAILABILITY: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/ CONTACT: bma@csd.uwo.ca...
  4. ncbi request reprint A tutorial of recent developments in the seeding of local alignment
    Daniel G Brown
    Department of Computer Science, University of Waterloo, Waterloo, ON, Canada, N2L 3G1, Canada
    J Bioinform Comput Biol 2:819-42. 2004
    ..We show that these techniques give a vast improvement in both sensitivity and specificity over previous methods, and can achieve sensitivity at the level of classical algorithms while requiring orders of magnitude less runtime...
  5. pmc PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification
    Jing Zhang
    Bioinformatics Solutions Inc, Waterloo, Ontario N2L 6J2, Canada
    Mol Cell Proteomics 11:M111.010587. 2012
    ..Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of overconfidence that exists in the conventional target decoy method for certain types of peptide identification software...
  6. ncbi request reprint MSDash: mass spectrometry database and search
    Zhan Wu
    Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B8, Canada
    Comput Syst Bioinformatics Conf 7:63-71. 2008
    ..The searching method can also be used alone to cluster the similar spectra in a mass spectrometry dataset together, in order to to improve the speed and accuracy of the protein identification or quantification...
  7. doi request reprint De novo interpretation of tandem mass spectra
    Bin Ma
    University of Waterloo, Waterloo, Ontario, Canada
    Curr Protoc Bioinformatics . 2009
    ..A protocol for using the PEAKS online software for automated de novo sequencing is described. Finally, we show how to use the PEAKS scores to validate the de novo sequencing results...
  8. ncbi request reprint SPIDER: software for protein identification from sequence tags with de novo sequencing error
    Yonghua Han
    Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada
    J Bioinform Comput Biol 3:697-716. 2005
    ..A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software...
  9. ncbi request reprint Patternhunter II: highly sensitive and fast homology search
    Ming Li
    Department of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G
    J Bioinform Comput Biol 2:417-39. 2004
    ..At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search methodology research back to a full circle...
  10. doi request reprint PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications
    Xi Han
    David R Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
    J Proteome Res 10:2930-6. 2011
    ..Finally, a software tool, PeaksPTM, has been developed and already achieved a stronger performance than competitive tools for unrestricted identification of post-translational modifications...
  11. doi request reprint De novo sequencing methods in proteomics
    Christopher Hughes
    Department of Biochemistry, University of Western Ontario, London, ON, Canada
    Methods Mol Biol 604:105-21. 2010
    ..Another advantage of de novo methods is that the partial sequence can be used to search for posttranslation modifications or for the identification of mutations by homology based software...
  12. doi request reprint Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
    Xiaowen Liu
    David R Cheriton School of Computer Science, University of Waterloo, Waterloo, Canada
    Bioinformatics 25:2174-80. 2009
    ..De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem...
  13. ncbi request reprint ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectra
    Lin He
    David R Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
    J Bioinform Comput Biol 8:981-94. 2010
    ..We propose a general framework to combine the two different types of MS/MS data. Experiments demonstrate that our method significantly improves the de novo sequencing of existing software...
  14. ncbi request reprint Optimizing multiple spaced seeds for homology search
    Jinbo Xu
    School of Computer Science, University of Waterloo, Waterloo, ON, Canada
    J Comput Biol 13:1355-68. 2006
    ..In practice, our algorithm generates a solution which is at least 90% of the optimal. Our method not only achieves performance better than or comparable to that of a greedy algorithm, but also gives this area a mathematical foundation...
  15. ncbi request reprint Complexities and algorithms for glycan sequencing using tandem mass spectrometry
    Baozhen Shan
    Department of Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada
    J Bioinform Comput Biol 6:77-91. 2008
    ..Experiments on real MS/MS data of glycopeptides demonstrate that our heuristic algorithm gives satisfactory results on practical data...
  16. ncbi request reprint PatternHunter: faster and more sensitive homology search
    Bin Ma
    Computer Science Department, University of Western Ontario, London N6A 5B8, Canada Bioinformatics Solutions Inc, 145 Columbia Street West, Waterloo, Ont N2L 3L2, Canada
    Bioinformatics 18:440-5. 2002
    ..The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation...
  17. ncbi request reprint Software for computational peptide identification from MS-MS data
    Changjiang Xu
    Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B7, Canada
    Drug Discov Today 11:595-600. 2006
    ..The most recognized peptide identification software packages can be classified into four categories: database searching, de novo sequencing, sequence tagging and consensus of multiple engines...
  18. ncbi request reprint An algorithm for searching RNA motifs in genomic sequences
    Jingping Liu
    Department of Computer Science, University of Western Ontario, London, Ontario, Canada
    Biomol Eng 24:343-50. 2007
    ..Our new bottom-up approach searches all potential stem-loops similar to ones of the given RNA secondary structure first, and then based on located stem-loops, detects potential homologous structural RNAs in genomic sequences...
  19. pmc ZOOM Lite: next-generation sequencing data mapping and visualization software
    Zefeng Zhang
    Bioinformatics Solutions Inc, Waterloo, ON N2L 6J2, Canada
    Nucleic Acids Res 38:W743-8. 2010
    ..Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/...
  20. doi request reprint De novo sequencing with limited number of post-translational modifications per peptide
    Lin He
    David R Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1, Canada
    J Bioinform Comput Biol 11:1350007. 2013
    ..In this paper, we present an efficient de novo sequencing algorithm, DeNovoPTM, for such a purpose. The implemented software is downloadable from http://www.cs.uwaterloo.ca/~l22he/denovo_ptm . ..
  21. doi request reprint A combinatorial approach to the peptide feature matching problem for label-free quantification
    Hao Lin
    David R Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
    Bioinformatics 29:1768-75. 2013
    ..Although ad hoc software tools exist for the feature matching, the definition of a combinatorial model for this problem is still not available...
  22. ncbi request reprint Voting algorithms for the motif finding problem
    Xiaowen Liu
    Department of Computer Science, University of Western Ontario, London, ON, Canada
    Comput Syst Bioinformatics Conf 7:37-47. 2008
    ..Our experimental results show that Selecting k Voting algorithm with progressive filtering performs very well in practice and it outperforms some best known algorithms...
  23. ncbi request reprint A general edit distance between RNA structures
    Tao Jiang
    Department of Computer Science, University of California, Riverside, CA 92521, USA
    J Comput Biol 9:371-88. 2002
    ..Preliminary experimental tests confirm that our definition of edit distance and the computation model are among the most reasonable ones ever studied in the literature...
  24. ncbi request reprint Greedy method for inferring tandem duplication history
    Louxin Zhang
    Department of Mathematics, National University of Singapore, Singapore
    Bioinformatics 19:1497-504. 2003
    ..With more and more genomic sequences available, reconstructing duplication history has received extensive attention recently...
  25. ncbi request reprint PatternHunter II: highly sensitive and fast homology search
    Ming Li
    Dept Computer Science, Univ of Waterloo, Waterloo, ON, Canada N2L 3G1
    Genome Inform 14:164-75. 2003
    ..At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle...
  26. ncbi request reprint PRIMA: peptide robust identification from MS/MS spectra
    Jian Liu
    Department of Biomedical Engineering, McGill University, Montreal, QC H3A 2B2, Canada
    J Bioinform Comput Biol 4:125-38. 2006
    ..A prototype, PRIMA, was implemented. When tested with large benchmarks of varying qualities, PRIMA consistently has higher accuracy than commonly used software MASCOT, SEQUEST and X! Tandem...
  27. pmc ZOOM! Zillions of oligos mapped
    Hao Lin
    Institute for Computing Technology, Chinese Academy of Sciences, Beijing, China
    Bioinformatics 24:2431-7. 2008
    ..Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts...
  28. ncbi request reprint Chain letters & evolutionary histories
    Charles H Bennett
    University of Waterloo, Ontario
    Sci Am 288:76-81. 2003
  29. ncbi request reprint DNACompress: fast and effective DNA sequence compression
    Xin Chen
    Computer Science Department, University of California, Santa Barbara, CA 99106, USA
    Bioinformatics 18:1696-8. 2002
    ..While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs...
  30. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  31. ncbi request reprint Use of Autostitch for automatic stitching of microscope images
    Bin Ma
    Division of Molecular Biotechnology, German Research Centre of Biotechnology, Mascheroder Weg 1, D 38124 Braunschweig, Germany
    Micron 38:492-9. 2007
    ..Thus, the automatic stitching program described here may find applications in convenient image stitching and virtual microscopy in the biomedical research...