Information for


Bin MaResearch interests

Professor Bin Ma's research interests are in bioinformatics algorithms and software. He studies the mathematical problems that are abstracted from molecular biology, and develops algorithms and computer software for biologists to use. In particular, his work in recent years is focused on two areas: homology search and mass spectrometry data analysis. Homology search finds similarities in DNA and protein sequence database. This is a basic task that modern biologists need to perform regularly. The large size of the database raised the requirement for extremely efficient searching algorithm. Together with Professor Ming Li and other coworkers, he has developed the PatternHunter program for homology search.

Mass spectrometry is a wet-lab experimental method to identify and quantify proteins in given biological samples. However, the data obtained from the experiments are complicated and contain errors and noises. The analysis of the data requires the right mathematical model, efficient algorithm, and user friendly software. Together with his coworkers, he developed the PEAKS software package, which is now one of the industrial standard packages for such analysis.

Degrees and awards

BSc, PhD (Peking)

Outstanding Young Computer Science Researcher Prize, Canadian Association of Computer Science (2010); Premier’s Catalyst Award for Best Young Innovator, Ontario (2009); University Research Chair (2008-2015); Canada Research Chair II in Bioinformatics (2004-2008); Premier's Research Excellence Awards (2003-2006)

Industrial and sabbatical experience

Professor Bin Ma was a postdoc at University of Waterloo in 1999-2000. During 2000-2008 he had been an assistant professor and later an associate professor and a Canada Research Chair at University of Western Ontario. He was a visiting professor at Tsinghua University in 2006-2007.

Representative publications

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.

C.H. Bennett, M. Li, and B. Ma. Chain Letters and Evolutionary Histories. Scientific American, pp. 76-79, June 2003.

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.

M. Li, B. Ma, and L. Wang. On the Closest String and Substring Problems. Journal of the ACM, 49(2):157-171, 2002.

B. Ma, J. Tromp, and M. Li. PatternHunter: Faster and More Sensitive Homology Search. Bioinformatics, 18:440-445, 2002.

University of Waterloo
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