Affiliation: University of Western Ontario
- Improving the sensitivity and specificity of protein homology search by incorporating predicted secondary structuresBin 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...
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometryBin 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...
- tPatternHunter: gapped, fast and sensitive translated homology searchDerek 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: firstname.lastname@example.org...
- A tutorial of recent developments in the seeding of local alignmentDaniel 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...
- PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identificationJing 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...
- MSDash: mass spectrometry database and searchZhan 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...
- De novo interpretation of tandem mass spectraBin 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...
- SPIDER: software for protein identification from sequence tags with de novo sequencing errorYonghua 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...
- Patternhunter II: highly sensitive and fast homology searchMing 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...
- PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modificationsXi 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...
- De novo sequencing methods in proteomicsChristopher 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...
- Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracyXiaowen 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...
- ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectraLin 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...
- Optimizing multiple spaced seeds for homology searchJinbo 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...
- Complexities and algorithms for glycan sequencing using tandem mass spectrometryBaozhen 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...
- PatternHunter: faster and more sensitive homology searchBin 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...
- Software for computational peptide identification from MS-MS dataChangjiang 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...
- An algorithm for searching RNA motifs in genomic sequencesJingping 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...
- ZOOM Lite: next-generation sequencing data mapping and visualization softwareZefeng 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/...
- De novo sequencing with limited number of post-translational modifications per peptideLin 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 . ..
- A combinatorial approach to the peptide feature matching problem for label-free quantificationHao 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...
- Voting algorithms for the motif finding problemXiaowen 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...
- A general edit distance between RNA structuresTao 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...
- Greedy method for inferring tandem duplication historyLouxin 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...
- PatternHunter II: highly sensitive and fast homology searchMing 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...
- PRIMA: peptide robust identification from MS/MS spectraJian 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...
- ZOOM! Zillions of oligos mappedHao 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...
- Chain letters & evolutionary historiesCharles H Bennett
University of Waterloo, Ontario
Sci Am 288:76-81. 2003
- DNACompress: fast and effective DNA sequence compressionXin 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...
- Initial sequencing and comparative analysis of the mouse genomeRobert 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....
- Use of Autostitch for automatic stitching of microscope imagesBin 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...